ERS14338737 SAMEA112227834 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428081 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227834 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428081_bin.25_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 99.43 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307577 sample name SRR13428081_bin.25_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338739 SAMEA112227836 167968 uncultured Desulfovibrio sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428082 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227836 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428082_bin.17_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 96.75 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307576 sample name SRR13428082_bin.17_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__ taxonomic identity marker multi-marker approach ERS14338741 SAMEA112227838 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428082 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227838 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428082_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.13 completeness software CheckM contamination score 2.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307576 sample name SRR13428082_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338744 SAMEA112227841 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227841 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428083_bin.10_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 97.44 completeness software CheckM contamination score 1.72 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.10_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338746 SAMEA112227843 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227843 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428083_bin.37_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 97.18 completeness software CheckM contamination score 0.08 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.37_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338747 SAMEA112227844 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227844 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428083_bin.40_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.36 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.40_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338748 SAMEA112227845 194843 uncultured Bacteroidales bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227845 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428083_bin.43_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.51 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.43_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338753 SAMEA112227850 1729681 uncultured Faecalibaculum sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428084 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227850 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428084_bin.30_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.11 completeness software CheckM contamination score 1.35 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307574 sample name SRR13428084_bin.30_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum;s__ taxonomic identity marker multi-marker approach ERS14338755 SAMEA112227852 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428085 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227852 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428085_bin.2_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 97.99 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307573 sample name SRR13428085_bin.2_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338759 SAMEA112227856 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227856 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428087_bin.10_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 92.31 completeness software CheckM contamination score 1.14 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.10_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338760 SAMEA112227857 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227857 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428087_bin.13_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 52.28 completeness software CheckM contamination score 0.81 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.13_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338762 SAMEA112227859 876416 uncultured Odoribacter sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227859 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428087_bin.31_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 100 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.31_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Odoribacter;s__ taxonomic identity marker multi-marker approach ERS14338764 SAMEA112227861 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227861 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428087_bin.37_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 96.86 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.37_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338765 SAMEA112227862 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227862 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428087_bin.47_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 50.77 completeness software CheckM contamination score 0.82 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.47_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338770 SAMEA112227867 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428088 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227867 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428088_bin.22_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 88.89 completeness software CheckM contamination score 0.85 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307570 sample name SRR13428088_bin.22_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338772 SAMEA112227869 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227869 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428089_bin.11_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 87.16 completeness software CheckM contamination score 1.53 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.11_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338773 SAMEA112227870 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227870 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428089_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 90.64 completeness software CheckM contamination score 3.51 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338777 SAMEA112227874 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227874 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428089_bin.2_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 99.43 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.2_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338781 SAMEA112227878 1353 Enterococcus gallinarum This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428090 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227878 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428090_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 99.25 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307582 sample name SRR13428090_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__Enterococcus gallinarum taxonomic identity marker multi-marker approach ERS14338782 SAMEA112227879 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428090 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227879 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428090_bin.4_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 91.08 completeness software CheckM contamination score 1.75 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307582 sample name SRR13428090_bin.4_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338784 SAMEA112227881 512314 uncultured Roseburia sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428090 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227881 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428090_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.1 completeness software CheckM contamination score 1.06 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307582 sample name SRR13428090_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ taxonomic identity marker multi-marker approach ERS14338788 SAMEA112227885 1351 Enterococcus faecalis This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227885 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.10_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 99.06 completeness software CheckM contamination score 0.43 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.10_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__Enterococcus faecalis taxonomic identity marker multi-marker approach ERS14338791 SAMEA112227888 286138 uncultured Dorea sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227888 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.14_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 87.44 completeness software CheckM contamination score 0.49 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.14_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Dorea;s__ taxonomic identity marker multi-marker approach ERS14338792 SAMEA112227889 905011 uncultured Anaerotruncus sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227889 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.99 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus;s__ taxonomic identity marker multi-marker approach ERS14338795 SAMEA112227892 1193534 uncultured Flavonifractor sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227892 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.21_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 95.03 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.21_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Flavonifractor;s__ taxonomic identity marker multi-marker approach ERS14338799 SAMEA112227896 297316 uncultured Turicibacter sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227896 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 90.5 completeness software CheckM contamination score 2.03 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Turicibacter;s__ taxonomic identity marker multi-marker approach ERS14338800 SAMEA112227897 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227897 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 83.45 completeness software CheckM contamination score 1.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338802 SAMEA112227899 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227899 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428092_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.7 completeness software CheckM contamination score 1.32 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338806 SAMEA112227903 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428094 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227903 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428094_bin.27_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 64.51 completeness software CheckM contamination score 1.2 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307578 sample name SRR13428094_bin.27_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338807 SAMEA112227904 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428094 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227904 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428094_bin.32_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 95.11 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307578 sample name SRR13428094_bin.32_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338809 SAMEA112227906 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428094 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227906 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR13428094_bin.5_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 95.12 completeness software CheckM contamination score 1.15 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307578 sample name SRR13428094_bin.5_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338812 SAMEA112227909 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428096 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227909 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428096_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 74.79 completeness software CheckM contamination score 0.73 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307568 sample name SRR13428096_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338813 SAMEA112227910 1796652 Turicimonas muris This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428096 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227910 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428096_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.75 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307568 sample name SRR13428096_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Sutterellaceae;g__Turicimonas;s__Turicimonas muris taxonomic identity marker multi-marker approach ERS14338815 SAMEA112227912 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428096 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227912 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR13428096_bin.19_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.81 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307568 sample name SRR13428096_bin.19_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338818 SAMEA112227915 1796646 Muribaculum intestinale This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257128 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227915 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257128_bin.31_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 98.68 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154420 sample name SRR17257128_bin.31_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__Muribaculum intestinale taxonomic identity marker multi-marker approach ERS14338820 SAMEA112227917 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257131 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227917 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257131_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 60.36 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154417 sample name SRR17257131_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338823 SAMEA112227920 1193532 uncultured Butyricicoccus sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227920 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257134_bin.14_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 56.8 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.14_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Butyricicoccus;s__ taxonomic identity marker multi-marker approach ERS14338825 SAMEA112227922 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227922 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257134_bin.17_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 50.0 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.17_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338826 SAMEA112227923 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227923 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257134_bin.18_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 92.74 completeness software CheckM contamination score 0.03 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.18_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338828 SAMEA112227925 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227925 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257134_bin.21_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 97.47 completeness software CheckM contamination score 0.16 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.21_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338831 SAMEA112227928 153152 uncultured Lactobacillus sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227928 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257134_bin.4_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 99.48 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.4_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus murinus taxonomic identity marker multi-marker approach ERS14338833 SAMEA112227930 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257135 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227930 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257135_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.92 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154456 sample name SRR17257135_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338836 SAMEA112227933 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257135 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227933 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257135_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 95.01 completeness software CheckM contamination score 0.84 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154456 sample name SRR17257135_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338837 SAMEA112227934 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257135 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227934 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257135_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 99.43 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154456 sample name SRR17257135_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338838 SAMEA112227935 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257136 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227935 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257136_bin.23_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 98.68 completeness software CheckM contamination score 0.57 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154455 sample name SRR17257136_bin.23_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338841 SAMEA112227938 1935179 uncultured Angelakisella sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257137 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227938 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257137_bin.26_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 52.43 completeness software CheckM contamination score 0.89 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154454 sample name SRR17257137_bin.26_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Angelakisella;s__ taxonomic identity marker multi-marker approach ERS14338843 SAMEA112227940 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257138 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227940 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257138_bin.23_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 94.35 completeness software CheckM contamination score 0.03 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154453 sample name SRR17257138_bin.23_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338844 SAMEA112227941 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257139 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227941 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257139_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 71.07 completeness software CheckM contamination score 1.32 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154452 sample name SRR17257139_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338848 SAMEA112227945 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257140 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227945 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257140_bin.27_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 69.28 completeness software CheckM contamination score 0.29 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154451 sample name SRR17257140_bin.27_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338849 SAMEA112227946 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227946 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257141_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 99.52 completeness software CheckM contamination score 0.48 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338850 SAMEA112227947 1671927 uncultured Acetatifactor sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227947 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257141_bin.11_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 50.95 completeness software CheckM contamination score 0.29 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.11_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Acetatifactor;s__ taxonomic identity marker multi-marker approach ERS14338852 SAMEA112227949 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227949 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257141_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 97.7 completeness software CheckM contamination score 1.15 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338853 SAMEA112227950 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227950 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257141_bin.18_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 98.71 completeness software CheckM contamination score 1.9 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.18_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338856 SAMEA112227953 562 Escherichia coli This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227953 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257141_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 99.93 completeness software CheckM contamination score 0.1 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli taxonomic identity marker multi-marker approach ERS14338857 SAMEA112227954 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227954 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257141_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 78.47 completeness software CheckM contamination score 1.34 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338858 SAMEA112227955 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257142 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227955 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257142_bin.28_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 61.72 completeness software CheckM contamination score 0.32 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154450 sample name SRR17257142_bin.28_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338861 SAMEA112227958 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257142 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227958 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257142_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 79.13 completeness software CheckM contamination score 1.97 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154450 sample name SRR17257142_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338862 SAMEA112227959 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257143 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227959 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257143_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 94.35 completeness software CheckM contamination score 0.32 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154449 sample name SRR17257143_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338863 SAMEA112227960 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257143 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227960 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257143_bin.29_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 73.87 completeness software CheckM contamination score 1.45 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154449 sample name SRR17257143_bin.29_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338865 SAMEA112227962 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257144 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227962 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257144_bin.24_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 93.93 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154448 sample name SRR17257144_bin.24_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338866 SAMEA112227963 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257144 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227963 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257144_bin.37_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 71.27 completeness software CheckM contamination score 1.74 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154448 sample name SRR17257144_bin.37_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338869 SAMEA112227966 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257145 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227966 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257145_bin.17_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 99.97 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154447 sample name SRR17257145_bin.17_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338870 SAMEA112227967 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257145 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227967 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257145_bin.29_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 91.39 completeness software CheckM contamination score 0.02 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154447 sample name SRR17257145_bin.29_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338871 SAMEA112227968 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257145 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227968 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257145_bin.37_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 98.08 completeness software CheckM contamination score 1.06 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154447 sample name SRR17257145_bin.37_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338873 SAMEA112227970 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257148 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227970 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257148_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 98.03 completeness software CheckM contamination score 0.13 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154444 sample name SRR17257148_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338874 SAMEA112227971 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257149 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227971 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:53Z INSDC last update 2022-12-12T20:27:53Z INSDC status public Submitter Id SRR17257149_bin.11_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 97.92 completeness software CheckM contamination score 0.1 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154443 sample name SRR17257149_bin.11_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338879 SAMEA112227976 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257152 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227976 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257152_bin.17_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 94.68 completeness software CheckM contamination score 1.48 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154414 sample name SRR17257152_bin.17_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338880 SAMEA112227977 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257152 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-12 ENA-LAST-UPDATE 2022-12-12 External Id SAMEA112227977 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-12T20:27:54Z INSDC last update 2022-12-12T20:27:54Z INSDC status public Submitter Id SRR17257152_bin.34_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 83.88 completeness software CheckM contamination score 2.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154414 sample name SRR17257152_bin.34_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338881 SAMEA112227978 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257152 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227978 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257152_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 98.56 completeness software CheckM contamination score 0.16 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154414 sample name SRR17257152_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338882 SAMEA112227979 114712 uncultured Azospirillum sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257153 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227979 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257153_bin.13_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 95.7 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154440 sample name SRR17257153_bin.13_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Azospirillum;s__ taxonomic identity marker multi-marker approach ERS14338883 SAMEA112227980 344338 uncultured Bacillota bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257153 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227980 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257153_bin.21_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 55.26 completeness software CheckM contamination score 3.51 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154440 sample name SRR17257153_bin.21_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338884 SAMEA112227981 1694 Bifidobacterium pseudolongum This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257154 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227981 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257154_bin.5_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 93.94 completeness software CheckM contamination score 0.22 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154439 sample name SRR17257154_bin.5_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium pseudolongum taxonomic identity marker multi-marker approach ERS14338887 SAMEA112227984 512314 uncultured Roseburia sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257155 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227984 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257155_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 95.19 completeness software CheckM contamination score 0.67 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154438 sample name SRR17257155_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ taxonomic identity marker multi-marker approach ERS14338889 SAMEA112227986 85831 Bacteroides acidifaciens This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257156 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227986 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257156_bin.18_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 52.89 completeness software CheckM contamination score 4.51 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154437 sample name SRR17257156_bin.18_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides acidifaciens taxonomic identity marker multi-marker approach ERS14338890 SAMEA112227987 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257156 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227987 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257156_bin.19_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 81.7 completeness software CheckM contamination score 2.13 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154437 sample name SRR17257156_bin.19_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338891 SAMEA112227988 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257157 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227988 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257157_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 98.3 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154436 sample name SRR17257157_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338892 SAMEA112227989 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257157 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227989 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257157_bin.13_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 96.56 completeness software CheckM contamination score 0.89 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154436 sample name SRR17257157_bin.13_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338894 SAMEA112227991 162156 uncultured Bacteroides sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257157 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227991 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257157_bin.5_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 98.37 completeness software CheckM contamination score 0.19 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154436 sample name SRR17257157_bin.5_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__ taxonomic identity marker multi-marker approach ERS14338895 SAMEA112227992 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257159 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227992 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257159_bin.17_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 97.59 completeness software CheckM contamination score 2.87 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154434 sample name SRR17257159_bin.17_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338898 SAMEA112227995 512314 uncultured Roseburia sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227995 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257160_bin.36_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 78.07 completeness software CheckM contamination score 1.08 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.36_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ taxonomic identity marker multi-marker approach ERS14338900 SAMEA112227997 85831 Bacteroides acidifaciens This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227997 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257160_bin.40_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 59.48 completeness software CheckM contamination score 3.45 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.40_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides acidifaciens taxonomic identity marker multi-marker approach ERS14338901 SAMEA112227998 512314 uncultured Roseburia sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227998 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257160_bin.48_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 54.27 completeness software CheckM contamination score 1.61 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.48_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ taxonomic identity marker multi-marker approach ERS14338902 SAMEA112227999 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112227999 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257160_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 62.09 completeness software CheckM contamination score 1.04 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338903 SAMEA112228000 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228000 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257160_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 97.13 completeness software CheckM contamination score 0.02 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338906 SAMEA112228003 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257165 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228003 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257165_bin.26_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 93.85 completeness software CheckM contamination score 2.12 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154429 sample name SRR17257165_bin.26_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338908 SAMEA112228005 658143 uncultured Tenericutes bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257165 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228005 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257165_bin.33_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 91.57 completeness software CheckM contamination score 2.81 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154429 sample name SRR17257165_bin.33_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Tenericutes;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338912 SAMEA112228009 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257168 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228009 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257168_bin.19_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.32 completeness software CheckM contamination score 0.67 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154426 sample name SRR17257168_bin.19_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis;g__;s__ taxonomic identity marker multi-marker approach ERS14338914 SAMEA112228011 97253 Eubacterium plexicaudatum This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257168 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228011 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257168_bin.39_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 94.11 completeness software CheckM contamination score 1.33 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154426 sample name SRR17257168_bin.39_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium plexicaudatum taxonomic identity marker multi-marker approach ERS14338916 SAMEA112228013 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257168 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228013 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257168_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 95.86 completeness software CheckM contamination score 0.57 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154426 sample name SRR17257168_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338917 SAMEA112228014 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257170 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228014 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257170_bin.4_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 92.34 completeness software CheckM contamination score 2.78 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154424 sample name SRR17257170_bin.4_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338919 SAMEA112228016 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257174 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228016 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257174_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 92.67 completeness software CheckM contamination score 0.22 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154412 sample name SRR17257174_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__Catabacter;s__ taxonomic identity marker multi-marker approach ERS14338920 SAMEA112228017 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257174 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-13 ENA-LAST-UPDATE 2022-12-13 External Id SAMEA112228017 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-13T00:42:52Z INSDC last update 2022-12-13T00:42:52Z INSDC status public Submitter Id SRR17257174_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 92.62 completeness software CheckM contamination score 0.02 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154412 sample name SRR17257174_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338738 SAMEA112227835 512314 uncultured Roseburia sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428081 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227835 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428081_bin.28_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 53.57 completeness software CheckM contamination score 1.04 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307577 sample name SRR13428081_bin.28_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ taxonomic identity marker multi-marker approach ERS14338749 SAMEA112227846 344338 uncultured Bacillota bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227846 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428083_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 91.57 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338757 SAMEA112227854 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428086 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227854 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428086_bin.20_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 92.84 completeness software CheckM contamination score 1.62 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307572 sample name SRR13428086_bin.20_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338758 SAMEA112227855 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428086 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227855 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428086_bin.35_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.68 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307572 sample name SRR13428086_bin.35_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338766 SAMEA112227863 508451 Lactobacillus taiwanensis This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227863 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428087_bin.48_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 99.03 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.48_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus taiwanensis taxonomic identity marker multi-marker approach ERS14338769 SAMEA112227866 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428088 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227866 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428088_bin.13_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 56.52 completeness software CheckM contamination score 0.45 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307570 sample name SRR13428088_bin.13_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338779 SAMEA112227876 1796620 Acutalibacter muris This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227876 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428089_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 78.11 completeness software CheckM contamination score 1.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Acutalibacter;s__Acutalibacter muris taxonomic identity marker multi-marker approach ERS14338786 SAMEA112227883 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428091 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227883 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428091_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 85.0 completeness software CheckM contamination score 1.81 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307581 sample name SRR13428091_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338787 SAMEA112227884 286138 uncultured Dorea sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428091 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227884 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428091_bin.5_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.17 completeness software CheckM contamination score 2.83 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307581 sample name SRR13428091_bin.5_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Dorea;s__ taxonomic identity marker multi-marker approach ERS14338794 SAMEA112227891 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227891 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:25Z INSDC last update 2022-12-15T16:21:25Z INSDC status public Submitter Id SRR13428092_bin.20_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 81.27 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.20_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338801 SAMEA112227898 344338 uncultured Bacillota bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227898 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428092_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 58.64 completeness software CheckM contamination score 0.67 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338808 SAMEA112227905 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428094 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227905 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428094_bin.46_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 93.78 completeness software CheckM contamination score 0.97 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307578 sample name SRR13428094_bin.46_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338810 SAMEA112227907 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428094 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227907 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428094_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 91.88 completeness software CheckM contamination score 1.15 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307578 sample name SRR13428094_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338817 SAMEA112227914 1586779 uncultured Lachnoclostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428096 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227914 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR13428096_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 96.62 completeness software CheckM contamination score 0.68 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307568 sample name SRR13428096_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__ taxonomic identity marker multi-marker approach ERS14338819 SAMEA112227916 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257128 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227916 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257128_bin.34_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 55.51 completeness software CheckM contamination score 1.14 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154420 sample name SRR17257128_bin.34_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338821 SAMEA112227918 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257131 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227918 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257131_bin.18_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.7 completeness software CheckM contamination score 0.57 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154417 sample name SRR17257131_bin.18_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338822 SAMEA112227919 165185 uncultured Eubacterium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257131 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227919 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257131_bin.26_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.01 completeness software CheckM contamination score 1.82 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154417 sample name SRR17257131_bin.26_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__ taxonomic identity marker multi-marker approach ERS14338824 SAMEA112227921 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227921 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257134_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 97.59 completeness software CheckM contamination score 0.69 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338827 SAMEA112227924 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227924 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257134_bin.20_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 97.47 completeness software CheckM contamination score 1.58 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.20_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338829 SAMEA112227926 344338 uncultured Bacillota bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227926 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257134_bin.23_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 78.82 completeness software CheckM contamination score 0.67 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.23_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338830 SAMEA112227927 876091 uncultured Oscillibacter sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227927 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257134_bin.24_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 94.97 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.24_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__ taxonomic identity marker multi-marker approach ERS14338835 SAMEA112227932 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257135 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227932 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257135_bin.25_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 68.34 completeness software CheckM contamination score 2.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154456 sample name SRR17257135_bin.25_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338842 SAMEA112227939 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257137 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227939 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257137_bin.30_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 91.85 completeness software CheckM contamination score 2.31 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154454 sample name SRR17257137_bin.30_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338845 SAMEA112227942 162156 uncultured Bacteroides sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257139 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227942 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257139_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 94.61 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154452 sample name SRR17257139_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__ taxonomic identity marker multi-marker approach ERS14338846 SAMEA112227943 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257139 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227943 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257139_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 96.75 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154452 sample name SRR17257139_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338851 SAMEA112227948 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227948 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257141_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 93.69 completeness software CheckM contamination score 1.58 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338854 SAMEA112227951 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227951 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:25Z INSDC last update 2022-12-15T16:21:25Z INSDC status public Submitter Id SRR17257141_bin.2_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 95.57 completeness software CheckM contamination score 0.63 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.2_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338859 SAMEA112227956 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257142 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227956 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:25Z INSDC last update 2022-12-15T16:21:25Z INSDC status public Submitter Id SRR17257142_bin.29_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.36 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154450 sample name SRR17257142_bin.29_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338860 SAMEA112227957 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257142 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227957 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257142_bin.32_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 64.71 completeness software CheckM contamination score 1.24 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154450 sample name SRR17257142_bin.32_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338864 SAMEA112227961 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257143 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227961 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257143_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 97.7 completeness software CheckM contamination score 1.81 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154449 sample name SRR17257143_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338872 SAMEA112227969 162156 uncultured Bacteroides sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257146 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227969 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257146_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 81.03 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154446 sample name SRR17257146_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__ taxonomic identity marker multi-marker approach ERS14338875 SAMEA112227972 331632 uncultured Coriobacteriaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257149 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227972 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257149_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 100 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154443 sample name SRR17257149_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338877 SAMEA112227974 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257150 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227974 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257150_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software not provided binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 76.61 completeness software CheckM contamination score 1.22 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154442 sample name SRR17257150_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338885 SAMEA112227982 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257155 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227982 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257155_bin.2_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 84.7 completeness software CheckM contamination score 1.12 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154438 sample name SRR17257155_bin.2_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338888 SAMEA112227985 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257156 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227985 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257156_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 55.4 completeness software CheckM contamination score 3.02 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154437 sample name SRR17257156_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338897 SAMEA112227994 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227994 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257160_bin.31_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 90.18 completeness software CheckM contamination score 0.75 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.31_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338899 SAMEA112227996 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112227996 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257160_bin.39_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 96.62 completeness software CheckM contamination score 0.47 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.39_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338904 SAMEA112228001 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228001 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257160_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 90.09 completeness software CheckM contamination score 2.22 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338905 SAMEA112228002 220137 uncultured Mollicutes bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257165 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228002 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257165_bin.22_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.33 completeness software CheckM contamination score 1.44 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154429 sample name SRR17257165_bin.22_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Tenericutes;c__Mollicutes;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338907 SAMEA112228004 159272 uncultured Prevotella sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257165 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228004 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257165_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 97.65 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154429 sample name SRR17257165_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__ taxonomic identity marker multi-marker approach ERS14338909 SAMEA112228006 85831 Bacteroides acidifaciens This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257167 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228006 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257167_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 98.51 completeness software CheckM contamination score 0.09 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154427 sample name SRR17257167_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides acidifaciens taxonomic identity marker multi-marker approach ERS14338913 SAMEA112228010 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257168 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228010 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257168_bin.31_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 98.93 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154426 sample name SRR17257168_bin.31_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338915 SAMEA112228012 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257168 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228012 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:26Z INSDC last update 2022-12-15T16:21:26Z INSDC status public Submitter Id SRR17257168_bin.4_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 57.34 completeness software CheckM contamination score 0.68 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154426 sample name SRR17257168_bin.4_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338918 SAMEA112228015 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257174 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228015 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:25Z INSDC last update 2022-12-15T16:21:25Z INSDC status public Submitter Id SRR17257174_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 98.85 completeness software CheckM contamination score 1.05 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154412 sample name SRR17257174_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338921 SAMEA112228018 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257175 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-15 ENA-LAST-UPDATE 2022-12-15 External Id SAMEA112228018 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-15T16:21:25Z INSDC last update 2022-12-15T16:21:25Z INSDC status public Submitter Id SRR17257175_bin.27_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 98.64 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154411 sample name SRR17257175_bin.27_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338736 SAMEA112227833 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428081 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227833 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428081_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.13 completeness software CheckM contamination score 1.32 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307577 sample name SRR13428081_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338740 SAMEA112227837 1751881 uncultured Hungatella sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428082 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227837 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428082_bin.21_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 98.1 completeness software CheckM contamination score 1.42 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307576 sample name SRR13428082_bin.21_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hungatella;s__ taxonomic identity marker multi-marker approach ERS14338742 SAMEA112227839 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428082 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227839 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428082_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 94.18 completeness software CheckM contamination score 2.35 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307576 sample name SRR13428082_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338745 SAMEA112227842 159272 uncultured Prevotella sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227842 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428083_bin.2_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 99.44 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.2_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__ taxonomic identity marker multi-marker approach ERS14338750 SAMEA112227847 59620 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428084 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227847 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428084_bin.10_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 80.86 completeness software CheckM contamination score 3.91 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307574 sample name SRR13428084_bin.10_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__ taxonomic identity marker multi-marker approach ERS14338754 SAMEA112227851 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428085 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227851 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428085_bin.12_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 97.61 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307573 sample name SRR13428085_bin.12_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338756 SAMEA112227853 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428085 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227853 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428085_bin.26_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 92.79 completeness software CheckM contamination score 1.31 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307573 sample name SRR13428085_bin.26_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338771 SAMEA112227868 153152 uncultured Lactobacillus sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227868 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428089_bin.10_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 99.46 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.10_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus reuteri taxonomic identity marker multi-marker approach ERS14338774 SAMEA112227871 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227871 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428089_bin.13_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 96.08 completeness software CheckM contamination score 1.83 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.13_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338775 SAMEA112227872 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227872 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428089_bin.14_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 96.55 completeness software CheckM contamination score 1.15 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.14_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338783 SAMEA112227880 239935 Akkermansia muciniphila This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428090 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227880 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428090_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.96 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307582 sample name SRR13428090_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia muciniphila taxonomic identity marker multi-marker approach ERS14338793 SAMEA112227890 286138 uncultured Dorea sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227890 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428092_bin.19_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 77.76 completeness software CheckM contamination score 0.78 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.19_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Dorea;s__ taxonomic identity marker multi-marker approach ERS14338796 SAMEA112227893 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227893 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428092_bin.23_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 87.43 completeness software CheckM contamination score 0.22 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.23_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__Catabacter;s__ taxonomic identity marker multi-marker approach ERS14338797 SAMEA112227894 331630 uncultured Erysipelotrichaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227894 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428092_bin.25_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 96.23 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.25_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338811 SAMEA112227908 97253 Eubacterium plexicaudatum This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428094 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227908 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428094_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 90.15 completeness software CheckM contamination score 2.68 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307578 sample name SRR13428094_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium plexicaudatum taxonomic identity marker multi-marker approach ERS14338814 SAMEA112227911 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428096 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227911 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428096_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 95.17 completeness software CheckM contamination score 0.57 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307568 sample name SRR13428096_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338832 SAMEA112227929 1586779 uncultured Lachnoclostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227929 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257134_bin.5_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 98.73 completeness software CheckM contamination score 1.11 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154457 sample name SRR17257134_bin.5_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__ taxonomic identity marker multi-marker approach ERS14338834 SAMEA112227931 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257135 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227931 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257135_bin.15_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 87.04 completeness software CheckM contamination score 1.58 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154456 sample name SRR17257135_bin.15_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338839 SAMEA112227936 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257136 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227936 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257136_bin.25_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 97.48 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154455 sample name SRR17257136_bin.25_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338855 SAMEA112227952 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227952 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257141_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 77.06 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154415 sample name SRR17257141_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__Catabacter;s__ taxonomic identity marker multi-marker approach ERS14338867 SAMEA112227964 876091 uncultured Oscillibacter sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257144 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227964 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257144_bin.4_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 92.91 completeness software CheckM contamination score 1.34 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154448 sample name SRR17257144_bin.4_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__ taxonomic identity marker multi-marker approach ERS14338751 SAMEA112227848 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428084 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227848 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428084_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 94.64 completeness software CheckM contamination score 0.37 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307574 sample name SRR13428084_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338752 SAMEA112227849 538949 uncultured Alistipes sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428084 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227849 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428084_bin.25_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 84.6 completeness software CheckM contamination score 1.39 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307574 sample name SRR13428084_bin.25_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__ taxonomic identity marker multi-marker approach ERS14338778 SAMEA112227875 344338 uncultured Bacillota bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227875 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428089_bin.3_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 83.56 completeness software CheckM contamination score 0.67 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.3_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338780 SAMEA112227877 1586779 uncultured Lachnoclostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227877 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428089_bin.8_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 63.15 completeness software CheckM contamination score 1.35 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.8_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__ taxonomic identity marker multi-marker approach ERS14338785 SAMEA112227882 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428091 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227882 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428091_bin.11_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 95.16 completeness software CheckM contamination score 3.25 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307581 sample name SRR13428091_bin.11_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338789 SAMEA112227886 1221379 uncultured Pseudoflavonifractor sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227886 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428092_bin.11_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 92.62 completeness software CheckM contamination score 0.0 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.11_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Pseudoflavonifractor;s__ taxonomic identity marker multi-marker approach ERS14338798 SAMEA112227895 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227895 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428092_bin.28_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 97.99 completeness software CheckM contamination score 1.68 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.28_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338803 SAMEA112227900 165185 uncultured Eubacterium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428093 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227900 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428093_bin.19_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 80.47 completeness software CheckM contamination score 1.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307579 sample name SRR13428093_bin.19_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__ taxonomic identity marker multi-marker approach ERS14338805 SAMEA112227902 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428093 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227902 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR13428093_bin.7_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 96.17 completeness software CheckM contamination score 3.45 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307579 sample name SRR13428093_bin.7_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338840 SAMEA112227937 244328 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257137 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227937 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257137_bin.10_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 92.74 completeness software CheckM contamination score 0.2 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154454 sample name SRR17257137_bin.10_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338868 SAMEA112227965 248039 Mucispirillum schaedleri This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257144 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227965 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257144_bin.43_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 97.41 completeness software CheckM contamination score 2.59 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154448 sample name SRR17257144_bin.43_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Mucispirillum;s__Mucispirillum schaedleri taxonomic identity marker multi-marker approach ERS14338876 SAMEA112227973 195049 uncultured Clostridiaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257149 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227973 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257149_bin.31_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-10-02 completeness score 77.37 completeness software CheckM contamination score 3.03 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154443 sample name SRR17257149_bin.31_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338878 SAMEA112227975 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257150 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227975 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257150_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software not provided binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 63.09 completeness software CheckM contamination score 0.95 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154442 sample name SRR17257150_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338886 SAMEA112227983 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257155 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227983 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257155_bin.33_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 96.96 completeness software CheckM contamination score 0.13 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154438 sample name SRR17257155_bin.33_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338893 SAMEA112227990 194843 uncultured Bacteroidales bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257157 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227990 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257157_bin.36_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 96.43 completeness software CheckM contamination score 0.48 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154436 sample name SRR17257157_bin.36_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338896 SAMEA112227993 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257160 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112227993 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257160_bin.18_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 95.53 completeness software CheckM contamination score 1.17 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154433 sample name SRR17257160_bin.18_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338910 SAMEA112228007 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257167 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112228007 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257167_bin.6_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 58.97 completeness software CheckM contamination score 1.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154427 sample name SRR17257167_bin.6_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338911 SAMEA112228008 77133 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257168 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-17 ENA-LAST-UPDATE 2022-12-17 External Id SAMEA112228008 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-17T00:47:17Z INSDC last update 2022-12-17T00:47:17Z INSDC status public Submitter Id SRR17257168_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-05 completeness score 86.5 completeness software CheckM contamination score 1.77 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154426 sample name SRR17257168_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ taxonomic identity marker multi-marker approach ERS14338763 SAMEA112227860 348578 uncultured Porphyromonadaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227860 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428087_bin.32_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 99.03 completeness software CheckM contamination score 0.75 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.32_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338767 SAMEA112227864 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227864 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428087_bin.9_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 94.28 completeness software CheckM contamination score 2.01 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.9_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338768 SAMEA112227865 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428088 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227865 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428088_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 98.68 completeness software CheckM contamination score 0.75 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307570 sample name SRR13428088_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338776 SAMEA112227873 328812 Parabacteroides goldsteinii This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428089 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227873 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428089_bin.16_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 99.62 completeness software CheckM contamination score 1.41 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307583 sample name SRR13428089_bin.16_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides goldsteinii taxonomic identity marker multi-marker approach ERS14338790 SAMEA112227887 1527 Anaerocolumna aminovalerica This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428092 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227887 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428092_bin.13_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 98.77 completeness software CheckM contamination score 2.91 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307580 sample name SRR13428092_bin.13_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerocolumna;s__Anaerocolumna aminovalerica taxonomic identity marker multi-marker approach ERS14338804 SAMEA112227901 1671927 uncultured Acetatifactor sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428093 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227901 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428093_bin.24_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-30 completeness score 76.92 completeness software CheckM contamination score 3.33 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307579 sample name SRR13428093_bin.24_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Acetatifactor;s__ taxonomic identity marker multi-marker approach ERS14338816 SAMEA112227913 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428096 of study SRP301591. ENA-FIRST-PUBLIC 2022-12-19 ENA-LAST-UPDATE 2022-12-19 External Id SAMEA112227913 INSDC center alias EMG INSDC center name EMG INSDC first public 2022-12-19T12:21:48Z INSDC last update 2022-12-19T12:21:48Z INSDC status public Submitter Id SRR13428096_bin.39_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 96.46 completeness software CheckM contamination score 1.13 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307568 sample name SRR13428096_bin.39_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338743 SAMEA112227840 195049 uncultured Clostridiaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591. ENA-FIRST-PUBLIC 2023-01-18 ENA-LAST-UPDATE 2023-01-18 External Id SAMEA112227840 INSDC center alias EMG INSDC center name EMG INSDC first public 2023-01-18T16:18:32Z INSDC last update 2023-01-18T16:18:32Z INSDC status public Submitter Id SRR13428083_bin.1_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 78.35 completeness software CheckM contamination score 0.22 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307575 sample name SRR13428083_bin.1_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338761 SAMEA112227858 297314 uncultured Lachnospiraceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591. ENA-FIRST-PUBLIC 2023-01-18 ENA-LAST-UPDATE 2023-01-18 External Id SAMEA112227858 INSDC center alias EMG INSDC center name EMG INSDC first public 2023-01-18T16:18:32Z INSDC last update 2023-01-18T16:18:32Z INSDC status public Submitter Id SRR13428087_bin.27_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2019-09-09 completeness score 59.54 completeness software CheckM contamination score 0.86 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN17307571 sample name SRR13428087_bin.27_metawrap_v1.3_MAG sequencing method NextSeq 500 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__ taxonomic identity marker multi-marker approach ERS14338847 SAMEA112227944 2301481 uncultured Muribaculaceae bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257140 of study SRP301591. ENA-FIRST-PUBLIC 2023-01-18 ENA-LAST-UPDATE 2023-01-18 External Id SAMEA112227944 INSDC center alias EMG INSDC center name EMG INSDC first public 2023-01-18T16:18:32Z INSDC last update 2023-01-18T16:18:32Z INSDC status public Submitter Id SRR17257140_bin.25_metawrap_v1.3_MAG assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics assembly software metaSPAdes v3.15.3 binning parameters MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. binning software metawrap v1.3 broad-scale environmental context mouse digestive system broker name EMG broker account, EMBL-EBI collection date 2020-09-12 completeness score 99.06 completeness software CheckM contamination score 0.38 environmental medium feces geographic location (country and/or sea) Luxembourg geographic location (latitude) not provided geographic location (longitude) not provided investigation type metagenome-assembled genome isolation_source mouse gut metagenome local environmental context digestive tube metagenomic source mouse gut metagenome project name The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale. sample derived from SAMN24154451 sample name SRR17257140_bin.25_metawrap_v1.3_MAG sequencing method NextSeq 550 taxonomic classification The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ taxonomic identity marker multi-marker approach