SRS10548871 SAMN22246961 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-02-20 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3049 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 9.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.136719 host_height 111.5210772 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-02-20T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 43832 FinalReads_ASVpipeline 13491 sampling_induced_expectorated expectorated barcode BYE136T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 16020.34 templateDNA_16SqPCR_Cq 24.0649065 templateDNA_16SqPCR 0.0114 well E03 plate_number P3 barcode_806R 806rcbc221 index_sequence TGGAGCACGTTG DOB 2009-04-30T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-08-02T00:00:00 datehiv 2015-05-15T00:00:00 ageyart 7.26 duryart 1.17 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z 0.922853683 weight 24.8 f24mrcscore 3 FEV1_baseline 1.57 FEVpcpred 111.5210772 FVC 1.660624981 FVCZ 0.322933286 FVCpcpred 104.0801806 FEV1FVC 0.945427216 FEV1FVCZ 1.153972026 cd4 NA vload NA zwauk -1.4992467 zhauk -1.5419675 zbmiuk -0.76237047 vllog NA endtreatdate ['NA', '2018-09-05T00:00:00'] sp05time 09:50:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-20T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-20T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548872 SAMN22246898 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-10-04 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3051 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.928448 host_height 79.41232953 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-09-30T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 31356 FinalReads_ASVpipeline 10198 sampling_induced_expectorated expectorated barcode BYC11ET3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 100456.57 templateDNA_16SqPCR_Cq 21.42354275 templateDNA_16SqPCR 0.071254245 well E03 plate_number P1 barcode_806R 806rcbc28 index_sequence GACTTTCCCTCG DOB 2001-09-10T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2006-06-15T00:00:00 datehiv 2006-06-15T00:00:00 ageyart 4.76 duryart 11.3 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.5311676 weight 50.6 f24mrcscore 4 FEV1_baseline 2.44 FEVpcpred 79.41232953 FVC 2.787499905 FVCZ -1.637743164 FVCpcpred 79.6937741 FEV1FVC 0.875336373 FEV1FVCZ -0.074871183 cd4 726 vload 0 zwauk -1.1801847 zhauk -1.3336345 zbmiuk -0.48097697 vllog 0 endtreatdate ['2018-09-05T00:00:00', '2018-09-05T00:00:00'] sp05time 09:40:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2019-02-20T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-20T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548873 SAMN22246962 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-02-20 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3051 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 20.95717 host_height 79.06523637 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-02-20T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 19558 FinalReads_ASVpipeline 4906 sampling_induced_expectorated expectorated barcode BYE138T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 289276.95 templateDNA_16SqPCR_Cq 19.88918276 templateDNA_16SqPCR 0.205185296 well E05 plate_number P1 barcode_806R 806rcbc44 index_sequence CGATCCGTATTA DOB 2001-09-10T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2006-06-15T00:00:00 datehiv 2006-06-15T00:00:00 ageyart 4.76 duryart 11.3 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.586631927 weight 55 f24mrcscore 2 FEV1_baseline 2.47 FEVpcpred 79.06523637 FVC 2.917500019 FVCZ -1.439611014 FVCpcpred 82.11101807 FEV1FVC 0.846615257 FEV1FVCZ -0.551070321 cd4 NA vload NA zwauk -1.2974368 zhauk -2.0594926 zbmiuk 0.079907447 vllog NA endtreatdate ['NA', '2018-09-05T00:00:00'] sp05time 11:20:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2019-02-20T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-20T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548874 SAMN22246900 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-10-17 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3054 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 10.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.120095 host_height 82.15276893 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-10-10T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 42671 FinalReads_ASVpipeline 13941 sampling_induced_expectorated expectorated barcode BYC11MT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 309.85 templateDNA_16SqPCR_Cq 29.96138694 templateDNA_16SqPCR 0.000219776 well A04 plate_number P3 barcode_806R 806rcbc225 index_sequence ATGTACGGCGAC DOB 2007-08-07T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-11-10T00:00:00 datehiv 2016-11-10T00:00:00 ageyart 9.26 duryart 0.93 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.4189442 weight 19 f24mrcscore 2 FEV1_baseline 0.95 FEVpcpred 82.15276893 FVC 1.009374976 FVCZ -1.731517718 FVCpcpred 78.39218126 FEV1FVC 0.941176481 FEV1FVCZ 0.821246761 cd4 896 vload 39 zwauk -4.2459869 zhauk -3.7336235 zbmiuk -1.6529472 vllog 1.5910646 endtreatdate ['2018-09-19T00:00:00', '2018-09-19T00:00:00'] sp05time 08:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-03-06T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-03-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548875 SAMN22246931 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-09-19 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3054 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.049718 host_height 69.18921583 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-09-19T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 47726 FinalReads_ASVpipeline 21961 sampling_induced_expectorated expectorated barcode BYD11GT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 8984.43 templateDNA_16SqPCR_Cq 24.92925726 templateDNA_16SqPCR 0.006372691 well A05 plate_number P3 barcode_806R 806rcbc233 index_sequence GCTAATTACGCT DOB 2007-08-07T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-11-10T00:00:00 datehiv 2016-11-10T00:00:00 ageyart 9.26 duryart 0.93 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.419207555 weight 22.4 f24mrcscore 2 FEV1_baseline 0.9 FEVpcpred 69.18921583 FVC 1.012500048 FVCZ -2.475806582 FVCpcpred 69.45756958 FEV1FVC 0.888888823 FEV1FVCZ -0.024893534 cd4 926 vload 39 zwauk -3.2756727 zhauk -3.2698135 zbmiuk -1.1793109 vllog 1.5910646 endtreatdate ['NA', '2018-09-19T00:00:00'] sp05time 10:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-03-06T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-03-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548876 SAMN22246963 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-03-06 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3054 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.5 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.310966 host_height 82.50645621 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-03-06T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 45860 FinalReads_ASVpipeline 14418 sampling_induced_expectorated expectorated barcode BYE13BT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 545.31 templateDNA_16SqPCR_Cq 29.11659098 templateDNA_16SqPCR 0.000386794 well A07 plate_number P3 barcode_806R 806rcbc249 index_sequence ACACAAAGGGAG DOB 2007-08-07T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-11-10T00:00:00 datehiv 2016-11-10T00:00:00 ageyart 9.26 duryart 0.93 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.37098869 weight 24 f24mrcscore 3 FEV1_baseline 1.15 FEVpcpred 82.50645621 FVC 1.272500038 FVCZ -1.515679805 FVCpcpred 81.2723853 FEV1FVC 0.903732764 FEV1FVCZ 0.267284582 cd4 NA vload NA zwauk -2.9476986 zhauk -3.0136588 zbmiuk -1.1340629 vllog NA endtreatdate ['NA', '2018-09-19T00:00:00'] sp05time 11:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-03-06T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-03-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548877 SAMN22246901 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-10-18 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3055 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.925167 host_height 80.27352043 samp_size ['5', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-10-12T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 41928 FinalReads_ASVpipeline 13370 sampling_induced_expectorated expectorated barcode BYC11NT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 23699.29 templateDNA_16SqPCR_Cq 23.58 templateDNA_16SqPCR 0.01681 well A01 plate_number P4 barcode_806R 806rcbc297 index_sequence TCCCAACTTCGC DOB 2002-08-22T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2007-06-15T00:00:00 datehiv 2007-06-15T00:00:00 ageyart 4.81 duryart 10.34 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -1.4576075 weight 27 f24mrcscore 2 FEV1_baseline 1.54 FEVpcpred 80.27352043 FVC 1.948125005 FVCZ -0.620045062 FVCpcpred 92.29509151 FEV1FVC 0.790503668 FEV1FVCZ -1.645901174 cd4 1086 vload 39 zwauk -4.5780368 zhauk -4.3805285 zbmiuk -2.8037903 vllog 1.5910646 endtreatdate ['2018-09-19T00:00:00', '2018-09-19T00:00:00'] sp05time 10:00:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2018-09-19T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2018-09-19T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548878 SAMN22246930 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-09-19 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3055 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.516596 host_height 75.85509624 samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-09-19T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 44312 FinalReads_ASVpipeline 18292 sampling_induced_expectorated expectorated barcode BYD11FT3 sequencing_controls no sequencing_control_details NA WRrepeats AAL WRrepeats_WP AAL WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 294796.03 templateDNA_16SqPCR_Cq 19.85 templateDNA_16SqPCR 0.2091 well A02 plate_number P4 barcode_806R 806rcbc305 index_sequence AGTTAGTGCGTC DOB 2002-08-22T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2007-06-15T00:00:00 datehiv 2007-06-15T00:00:00 ageyart 4.81 duryart 10.34 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -1.791603333 weight 31 f24mrcscore 2 FEV1_baseline 1.57 FEVpcpred 75.85509624 FVC 1.975625038 FVCZ -1.062116733 FVCpcpred 86.80304676 FEV1FVC 0.794685237 FEV1FVCZ -1.581615333 cd4 810 vload 39 zwauk -4.7300706 zhauk -4.8393173 zbmiuk -1.9002268 vllog 1.5910646 endtreatdate ['NA', '2018-09-19T00:00:00'] sp05time 09:30:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2018-09-19T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2018-09-19T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548879 SAMN22246902 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-12-04 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3061 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.621063 host_height 85.96727916 samp_size ['5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-11-22T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 36858 FinalReads_ASVpipeline 6622 sampling_induced_expectorated expectorated barcode BYC11VT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 25207.81 templateDNA_16SqPCR_Cq 23.48 templateDNA_16SqPCR 0.01788 well A01 plate_number P3 barcode_806R 806rcbc201 index_sequence CGTTTAGAGTCG DOB 2008-11-17T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-12 attendschool yes rs15antibty NA rs14antib no dateart 2016-06-15T00:00:00 datehiv 2016-06-15T00:00:00 ageyart 7.58 duryart 1.47 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.0858105 weight 24.8 f24mrcscore 2 FEV1_baseline 1.15 FEVpcpred 85.96727916 FVC 2.043750048 FVCZ 2.741896192 FVCpcpred 135.4281593 FEV1FVC 0.562691107 FEV1FVCZ -3.722767735 cd4 845 vload 960 zwauk -0.9702031 zhauk -1.2929018 zbmiuk -0.26863945 vllog 2.9822712 endtreatdate ['2018-11-05T00:00:00', '2018-11-05T00:00:00'] sp05time 10:15:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2019-04-24T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-04-24T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548880 SAMN22246949 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-06-11 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3007 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.2 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.361475 host_height 53.2791748 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-06-11T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 37879 FinalReads_ASVpipeline 14387 sampling_induced_expectorated expectorated barcode BYE10FT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 46575.03 templateDNA_16SqPCR_Cq 22.4699998 templateDNA_16SqPCR 0.033035853 well B07 plate_number P3 barcode_806R 806rcbc250 index_sequence TTAGGTGCAGCT DOB 2002-02-28T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2016-12 attendschool yes rs15antibty NA rs14antib no dateart 2011-06-07T00:00:00 datehiv 2010-10-20T00:00:00 ageyart 9.27 duryart 5.56 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.411977424 weight 34.4 f24mrcscore 2 FEV1_baseline 1.26 FEVpcpred 53.2791748 FVC 1.680624962 FVCZ -2.922674147 FVCpcpred 63.93562999 FEV1FVC 0.749721097 FEV1FVCZ -2.050706295 cd4 NA vload NA zwauk -4.1639953 zhauk -3.9160349 zbmiuk -2.0803192 vllog NA endtreatdate ['NA', '2017-11-15T00:00:00'] sp05time 09:00:00 all_3 no visit012 no visit1218 yes visit018 no only2visits yes one_visit no endfollowup 2018-06-11T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-11T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548881 SAMN22246951 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-04-24 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3061 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 10.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.233241 host_height 88.43915412 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-04-24T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 36845 FinalReads_ASVpipeline 12553 sampling_induced_expectorated expectorated barcode BYE11HT3 sequencing_controls no sequencing_control_details NA WRrepeats AAS WRrepeats_WP AAS WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 19846.51 templateDNA_16SqPCR_Cq 23.74483688 templateDNA_16SqPCR 0.014077211 well A03 plate_number P3 barcode_806R 806rcbc217 index_sequence GTCGTCCTAAAT DOB 2008-11-17T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-12 attendschool yes rs15antibty NA rs14antib no dateart 2016-06-15T00:00:00 datehiv 2016-06-15T00:00:00 ageyart 7.58 duryart 1.47 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -0.922677643 weight 24.8 f24mrcscore 2 FEV1_baseline 1.35 FEVpcpred 88.43915412 FVC 1.461249948 FVCZ -1.286835049 FVCpcpred 83.96314807 FEV1FVC 0.923866602 FEV1FVCZ 0.845393433 cd4 NA vload NA zwauk -1.9423912 zhauk -1.3501118 zbmiuk -1.6204423 vllog NA endtreatdate ['NA', '2018-11-05T00:00:00'] sp05time 12:30:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2019-04-24T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-04-24T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548882 SAMN22246934 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-11-07 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3063 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.979189 host_height 54.74471137 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-11-07T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 61309 FinalReads_ASVpipeline 10990 sampling_induced_expectorated expectorated barcode BYD13VT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 6987.62 templateDNA_16SqPCR_Cq 25.41837723 templateDNA_16SqPCR 0.004956345 well B04 plate_number P2 barcode_806R 806rcbc129 index_sequence CGTGACAATGTC DOB 2002-05-24T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-12 attendschool yes rs15antibty NA rs14antib no dateart 2010-07-15T00:00:00 datehiv 2010-07-15T00:00:00 ageyart 8.14 duryart 7.39 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.316421013 weight 48 f24mrcscore 2 FEV1_baseline 1.51 FEVpcpred 54.74471137 FVC 1.946249962 FVCZ -3.025916832 FVCpcpred 62.6703373 FEV1FVC 0.775851006 FEV1FVCZ -1.624602454 cd4 244 vload 2900 zwauk -1.7977084 zhauk -2.6689067 zbmiuk -0.098764002 vllog 3.4623981 endtreatdate ['NA', '2018-11-07T00:00:00'] sp05time 10:15:00 all_3 no visit012 no visit1218 yes visit018 no only2visits yes one_visit no endfollowup 2019-04-25T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-04-25T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548883 SAMN22246952 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-04-25 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3063 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 20.594965 host_height 62.66748184 samp_size ['3', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-04-25T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 47141 FinalReads_ASVpipeline 18519 sampling_induced_expectorated expectorated barcode BYE11IT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 3884.18 templateDNA_16SqPCR_Cq 26.29956273 templateDNA_16SqPCR 0.002755061 well B05 plate_number P2 barcode_806R 806rcbc137 index_sequence GACACATTTCTG DOB 2002-05-24T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-12 attendschool yes rs15antibty NA rs14antib no dateart 2010-07-15T00:00:00 datehiv 2010-07-15T00:00:00 ageyart 8.14 duryart 7.39 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.771868127 weight 48.4 f24mrcscore 2 FEV1_baseline 1.71 FEVpcpred 62.66748184 FVC 2.233750105 FVCZ -2.19337607 FVCpcpred 72.83524282 FEV1FVC 0.7655288 FEV1FVCZ -1.767001003 cd4 NA vload NA zwauk -2.0290151 zhauk -3.1085215 zbmiuk 0.050338544 vllog NA endtreatdate ['NA', '2018-11-07T00:00:00'] sp05time 08:40:00 all_3 no visit012 no visit1218 yes visit018 no only2visits yes one_visit no endfollowup 2019-04-25T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-04-25T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548884 SAMN22246903 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-01-24 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3065 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 23.558792 host_height 71.59970429 samp_size ['1', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-01-20T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 36436 FinalReads_ASVpipeline 14824 sampling_induced_expectorated expectorated barcode BYC11ZT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 677194.51 templateDNA_16SqPCR_Cq 18.65524381 templateDNA_16SqPCR 0.480336762 well D11 plate_number P1 barcode_806R 806rcbc91 index_sequence ATCGGCGTTACA DOB 1999-12-22T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-01 attendschool yes rs15antibty NA rs14antib no dateart NA datehiv NA ageyart NA duryart NA artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.1501684 weight 56.6 f24mrcscore 5 FEV1_baseline 1.86 FEVpcpred 71.59970429 FVC 3.256249905 FVCZ 0.920476724 FVCpcpred 112.4010625 FEV1FVC 0.571209234 FEV1FVCZ -3.530188453 cd4 480 vload 326000 zwauk -0.12285809 zhauk -1.4197149 zbmiuk 0.77892709 vllog 5.5132174 endtreatdate ['2019-01-03T00:00:00', '2019-01-03T00:00:00'] sp05time 10:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-03-28T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-03-28T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548885 SAMN22246935 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-01-03 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3065 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 22.060354 host_height 77.08871006 samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-01-03T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 36910 FinalReads_ASVpipeline 15298 sampling_induced_expectorated expectorated barcode BYD13ZT3 sequencing_controls no sequencing_control_details NA WRrepeats AAO WRrepeats_WP AAO WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 438166.12 templateDNA_16SqPCR_Cq 19.28682697 templateDNA_16SqPCR 0.310792971 well D12 plate_number P1 barcode_806R 806rcbc99 index_sequence ATTGGGCTAGGC DOB 1999-12-22T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-01 attendschool yes rs15antibty NA rs14antib no dateart NA datehiv NA ageyart NA duryart NA artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.741923684 weight 53 f24mrcscore 2 FEV1_baseline 2 FEVpcpred 77.08871006 FVC 2.742500067 FVCZ -0.416919134 FVCpcpred 94.44935101 FEV1FVC 0.729261605 FEV1FVCZ -2.288147112 cd4 551 vload 12700 zwauk -0.64601707 zhauk -1.4289073 zbmiuk 0.20477222 vllog 4.1038036 endtreatdate ['NA', '2019-01-03T00:00:00'] sp05time 10:45:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-03-28T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-03-28T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548886 SAMN22246953 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-06-20 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3065 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index NA host_height NA samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-06-20T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 51713 FinalReads_ASVpipeline 20761 sampling_induced_expectorated expectorated barcode BYE11PT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 389536.8 templateDNA_16SqPCR_Cq 19.44 templateDNA_16SqPCR 0.2763 well E01 plate_number P1 barcode_806R 806rcbc12 index_sequence CCAGTGTATGCA DOB 1999-12-22T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-01 attendschool yes rs15antibty NA rs14antib no dateart NA datehiv NA ageyart NA duryart NA artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z NA weight NA f24mrcscore NA FEV1_baseline NA FEVpcpred NA FVC NA FVCZ NA FVCpcpred NA FEV1FVC NA FEV1FVCZ NA cd4 NA vload NA zwauk NA zhauk NA zbmiuk NA vllog NA endtreatdate ['NA', '2019-01-03T00:00:00'] sp05time 10:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-03-28T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-03-28T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548887 SAMN22246905 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-02-07 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3072 host_sex missing host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18.3 ethnicity black host_occupation missing host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 23.042248 host_height 87.1886026 samp_size ['1', ''] study_complt_stat missing isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-01-27T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 46563 FinalReads_ASVpipeline 19135 sampling_induced_expectorated expectorated barcode BYC12AT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 49551.65 templateDNA_16SqPCR_Cq 22.44877629 templateDNA_16SqPCR 0.035147181 well D09 plate_number P1 barcode_806R 806rcbc75 index_sequence CCTGAACTAGTT DOB 1999-09-17T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth missing attendschool missing rs15antibty NA rs14antib no dateart missing datehiv missing ageyart missing duryart missing artdrug1stline missing artdrug2ndline missing artreg missing fev1z -0.9832902 weight 51.5 f24mrcscore 3 FEV1_baseline 2.1 FEVpcpred 87.1886026 FVC 2.460624933 FVCZ -0.605498936 FVCpcpred 91.97718769 FEV1FVC 0.853441691 FEV1FVCZ -0.806509974 cd4 569 vload 0 zwauk -0.83275968 zhauk -2.3353236 zbmiuk 0.59184235 vllog 0 endtreatdate ['2019-01-09T00:00:00', 'missing'] sp05time 10:25:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup missing dow missing dod missing lastvisit missing visittotno missing lastvisitdate missing treatstopreason missing cough_enrl missing cotrimoxazole missing adm missing nadm missing tbtreat missing acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548888 SAMN22246936 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-01-09 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3072 host_sex missing host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.3 ethnicity black host_occupation missing host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 22.30718 host_height 74.83118634 samp_size ['2', ''] study_complt_stat missing isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-01-09T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 37750 FinalReads_ASVpipeline 13799 sampling_induced_expectorated expectorated barcode BYD146T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 95147.36 templateDNA_16SqPCR_Cq 21.50231446 templateDNA_16SqPCR 0.067488404 well D10 plate_number P1 barcode_806R 806rcbc83 index_sequence CGAGAAGAGAAC DOB 1999-09-17T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth missing attendschool missing rs15antibty NA rs14antib no dateart missing datehiv missing ageyart missing duryart missing artdrug1stline missing artdrug2ndline missing artreg missing fev1z -1.909008356 weight 51.2 f24mrcscore 3 FEV1_baseline 1.85 FEVpcpred 74.83118634 FVC 2.168124914 FVCZ -1.636745802 FVCpcpred 78.52477453 FEV1FVC 0.853271881 FEV1FVCZ -0.737678476 cd4 485 vload 0 zwauk -0.91574156 zhauk -2.0084174 zbmiuk 0.26419145 vllog 0 endtreatdate ['NA', 'missing'] sp05time 08:50:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup missing dow missing dod missing lastvisit missing visittotno missing lastvisitdate missing treatstopreason missing cough_enrl missing cotrimoxazole missing adm missing nadm missing tbtreat missing acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548889 SAMN22246904 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-02-12 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3076 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.813732 host_height 83.92483544 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-02-03T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 40885 FinalReads_ASVpipeline 18110 sampling_induced_expectorated expectorated barcode BYC128T3 sequencing_controls no sequencing_control_details NA WRrepeats AAG WRrepeats_WP NA WRrepeats_BP AAG BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 69455.65 templateDNA_16SqPCR_Cq 21.87277375 templateDNA_16SqPCR 0.049265172 well F12 plate_number P3 barcode_806R 806rcbc294 index_sequence GTTTCTAGAGCT DOB 2002-03-02T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2018-02 attendschool yes rs15antibty NA rs14antib no dateart 2012-06-15T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 10.29 duryart 5.66 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.231395 weight 43.4 f24mrcscore 2 FEV1_baseline 1.92 FEVpcpred 83.92483544 FVC 2.154999971 FVCZ -1.102017046 FVCpcpred 85.64514871 FEV1FVC 0.890951268 FEV1FVCZ -0.334301257 cd4 918 vload 0 zwauk -1.7939779 zhauk -2.4932714 zbmiuk -0.23905379 vllog 0 endtreatdate ['2019-01-14T00:00:00', '2019-01-14T00:00:00'] sp05time 09:17:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-07-01T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-07-01T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548890 SAMN22246937 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-01-14 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3076 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 21.280119 host_height 77.86719108 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-01-14T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 34842 FinalReads_ASVpipeline 12096 sampling_induced_expectorated expectorated barcode BYD148T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 236710.92 templateDNA_16SqPCR_Cq 20.17 templateDNA_16SqPCR 0.1679 well G01 plate_number P3 barcode_806R 806rcbc207 index_sequence GAGGCCATCAGT DOB 2002-03-02T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2018-02 attendschool yes rs15antibty NA rs14antib no dateart 2012-06-15T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 10.29 duryart 5.66 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.686324831 weight 48.2 f24mrcscore 2 FEV1_baseline 1.88 FEVpcpred 77.86719108 FVC 2.188750029 FVCZ -1.379659545 FVCpcpred 82.0106965 FEV1FVC 0.858937736 FEV1FVCZ -0.787746406 cd4 763 vload 0 zwauk -1.1900569 zhauk -2.1460397 zbmiuk 0.17803033 vllog 0 endtreatdate ['NA', '2019-01-14T00:00:00'] sp05time 08:15:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-07-01T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-07-01T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548891 SAMN22246886 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2016-01-04 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3008 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.84034 host_height 70.55986413 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2016-12-28T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 49334 FinalReads_ASVpipeline 21204 sampling_induced_expectorated expectorated barcode BYC108T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 270969.86 templateDNA_16SqPCR_Cq 19.97 templateDNA_16SqPCR 0.1922 well F02 plate_number P3 barcode_806R 806rcbc214 index_sequence TGACCGGTCAAT DOB 1998-10-30T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-01 attendschool yes rs15antibty NA rs14antib no dateart 2004-11-08T00:00:00 datehiv NA ageyart 6.03 duryart 12.16 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.2380841 weight 47.4 f24mrcscore 2 FEV1_baseline 2.28 FEVpcpred 70.55986413 FVC 3.291874886 FVCZ -0.866632306 FVCpcpred 89.20301502 FEV1FVC 0.692614407 FEV1FVCZ -2.496772546 cd4 594 vload 0 zwauk -2.8424356 zhauk -2.0269241 zbmiuk -1.660494 vllog 0 endtreatdate ['2018-12-06T00:00:00', '2018-12-06T00:00:00'] sp05time 10:00:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-05-23T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-05-23T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548892 SAMN22246954 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-07-01 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3076 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 21.583099 host_height 88.62768124 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-07-01T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 42041 FinalReads_ASVpipeline 3677 sampling_induced_expectorated expectorated barcode BYE11ST3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 692791.83 templateDNA_16SqPCR_Cq 18.59 templateDNA_16SqPCR 0.4914 well G02 plate_number P3 barcode_806R 806rcbc215 index_sequence TGTGATGGAGAA DOB 2002-03-02T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2018-02 attendschool yes rs15antibty NA rs14antib no dateart 2012-06-15T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 10.29 duryart 5.66 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -0.874447589 weight 49.8 f24mrcscore 3 FEV1_baseline 2.19 FEVpcpred 88.62768124 FVC 2.538125038 FVCZ -0.55623232 FVCpcpred 92.65689396 FEV1FVC 0.862841674 FEV1FVCZ -0.695877506 cd4 NA vload NA zwauk -1.0022801 zhauk -1.9200621 zbmiuk 0.2245658 vllog NA endtreatdate ['NA', '2019-01-14T00:00:00'] sp05time 09:58:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-07-01T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-07-01T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548893 SAMN22246907 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-02-26 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3079 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 10.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.089844 host_height 69.58609585 samp_size ['10', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-02-21T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 32760 FinalReads_ASVpipeline 11646 sampling_induced_expectorated expectorated barcode BYC12LT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 13327.73 templateDNA_16SqPCR_Cq 24.33990703 templateDNA_16SqPCR 0.009453413 well A09 plate_number P3 barcode_806R 806rcbc265 index_sequence TCCAGGCTTAAT DOB 2007-08-29T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-02 attendschool yes rs15antibty NA rs14antib no dateart 2016-09-21T00:00:00 datehiv 2016-09-21T00:00:00 ageyart 9.07 duryart 1.43 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.2989199 weight 28 f24mrcscore 2 FEV1_baseline 0.98 FEVpcpred 69.58609585 FVC 0.984375 FVCZ -3.00159732 FVCpcpred 62.98171682 FEV1FVC 0.995555575 FEV1FVCZ 2.066387232 cd4 1468 vload 0 zwauk -1.1367714 zhauk -1.9969755 zbmiuk -0.040333707 vllog 0 endtreatdate ['2019-01-28T00:00:00', '2019-01-28T00:00:00'] sp05time 11:20:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-04-24T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-04-24T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548894 SAMN22246938 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-01-28 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3079 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.930273 host_height 81.29814391 samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-01-28T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 41494 FinalReads_ASVpipeline 13077 sampling_induced_expectorated expectorated barcode BYD14DT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 11579.89 templateDNA_16SqPCR_Cq 24.54999549 templateDNA_16SqPCR 0.00821366 well A10 plate_number P3 barcode_806R 806rcbc273 index_sequence TGAGTTCGCTAT DOB 2007-08-29T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-02 attendschool yes rs15antibty NA rs14antib no dateart 2016-09-21T00:00:00 datehiv 2016-09-21T00:00:00 ageyart 9.07 duryart 1.43 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.429914796 weight 30.4 f24mrcscore 2 FEV1_baseline 1.31 FEVpcpred 81.29814391 FVC 1.328750014 FVCZ -2.055712684 FVCpcpred 74.27221394 FEV1FVC 0.98588894 FEV1FVCZ 1.815291548 cd4 1321 vload 0 zwauk -1.1967001 zhauk -1.770249 zbmiuk -0.37447691 vllog 0 endtreatdate ['NA', '2019-01-28T00:00:00'] sp05time 09:20:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-04-24T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-04-24T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548895 SAMN22246939 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-02-11 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3082 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.6 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.699032 host_height 84.13792645 samp_size ['1', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-02-11T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 44888 FinalReads_ASVpipeline 13831 sampling_induced_expectorated expectorated barcode BYD14FT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 6454.83 templateDNA_16SqPCR_Cq 25.42342601 templateDNA_16SqPCR 0.004578434 well C11 plate_number P3 barcode_806R 806rcbc283 index_sequence CATCCAAATGCG DOB 2007-07-07T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2018-03 attendschool yes rs15antibty NA rs14antib no dateart 2014-11-06T00:00:00 datehiv 2014-11-06T00:00:00 ageyart 7.33 duryart 3.35 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.243573354 weight 28.4 f24mrcscore 3 FEV1_baseline 1.48 FEVpcpred 84.13792645 FVC 1.813125014 FVCZ -0.812826177 FVCpcpred 89.93239519 FEV1FVC 0.816270256 FEV1FVCZ -0.960438919 cd4 279 vload 72 zwauk -1.6393372 zhauk -1.0410511 zbmiuk -1.5997473 vllog 1.8573325 endtreatdate ['NA', '2019-02-11T00:00:00'] sp05time 10:04:00 all_3 no visit012 no visit1218 no visit018 no only2visits no one_visit yes endfollowup 2019-05-06T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-05-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m yes hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548896 SAMN22246908 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-03-26 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3084 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.781919 host_height 82.22029962 samp_size ['5', ''] study_complt_stat withdrawal isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-03-17T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 37389 FinalReads_ASVpipeline 13946 sampling_induced_expectorated expectorated barcode BYC12YT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 28914.86 templateDNA_16SqPCR_Cq 23.2872256 templateDNA_16SqPCR 0.020509425 well F10 plate_number P2 barcode_806R 806rcbc181 index_sequence TCAAGCTCAAGC DOB 2003-05-27T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2018-03 attendschool yes rs15antibty NA rs14antib no dateart 2014-04-25T00:00:00 datehiv 2014-03-28T00:00:00 ageyart 10.91 duryart 3.92 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.3597343 weight 39.8 f24mrcscore 2 FEV1_baseline 2.03 FEVpcpred 82.22029962 FVC 2.240624905 FVCZ -1.399215822 FVCpcpred 81.95583082 FEV1FVC 0.905997236 FEV1FVCZ 0.012880458 cd4 510 vload 426000 zwauk -1.9816538 zhauk -1.2557911 zbmiuk -1.4621361 vllog 5.6294098 endtreatdate ['2018-06-18T00:00:00', '2018-06-18T00:00:00'] sp05time 09:30:00 all_3 no visit012 no visit1218 no visit018 no only2visits no one_visit yes endfollowup 2018-06-18T00:00:00 dow 43269 dod NA lastvisit 2 wks visittotno 1 lastvisitdate 2018-04-09T00:00:00 treatstopreason Moved away cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548897 SAMN22246909 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-04-05 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3086 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.076376 host_height 83.6598039 samp_size ['5', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-03-17T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 48575 FinalReads_ASVpipeline 22910 sampling_induced_expectorated expectorated barcode BYC130T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 322309.37 templateDNA_16SqPCR_Cq 19.64246743 templateDNA_16SqPCR 0.228615322 well G08 plate_number P4 barcode_806R 806rcbc359 index_sequence GGATAGCCACTT DOB 2004-12-01T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-04 attendschool yes rs15antibty NA rs14antib no dateart 2004-12-01T00:00:00 datehiv 2004-12-01T00:00:00 ageyart 0 duryart 13.34 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.251117 weight 36.8 f24mrcscore 2 FEV1_baseline 1.77 FEVpcpred 83.6598039 FVC 2.279999971 FVCZ -0.204568827 FVCpcpred 97.35000327 FEV1FVC 0.776315791 FEV1FVCZ -1.906759419 cd4 1658 vload 11000 zwauk -1.4961342 zhauk -1.4916365 zbmiuk -0.88121063 vllog 4.0413928 endtreatdate ['2019-03-07T00:00:00', '2019-03-07T00:00:00'] sp05time 08:40:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-05-30T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-05-30T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548898 SAMN22246941 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-03-07 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3086 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.2 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.1099 host_height 91.64567054 samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-03-07T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 42171 FinalReads_ASVpipeline 15098 sampling_induced_expectorated expectorated barcode BYD14JT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 31198.47 templateDNA_16SqPCR_Cq 23.08153597 templateDNA_16SqPCR 0.022129201 well G09 plate_number P4 barcode_806R 806rcbc367 index_sequence ACAATCGGTTGC DOB 2004-12-01T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-04 attendschool yes rs15antibty NA rs14antib no dateart 2004-12-01T00:00:00 datehiv 2004-12-01T00:00:00 ageyart 0 duryart 13.34 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -0.643951277 weight 38.6 f24mrcscore 1 FEV1_baseline 2.1 FEVpcpred 91.64567054 FVC 2.512500048 FVCZ -0.056111243 FVCpcpred 99.26700357 FEV1FVC 0.835820842 FEV1FVCZ -1.146636064 cd4 NA vload 1020 zwauk -1.8508112 zhauk -1.5908529 zbmiuk -1.1270096 vllog 3.0086002 endtreatdate ['NA', '2019-03-07T00:00:00'] sp05time 10:42:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-05-30T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-05-30T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548899 SAMN22246910 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-04-09 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3087 host_sex missing host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.4 ethnicity black host_occupation missing host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.698231 host_height 99.40323953 samp_size ['2', ''] study_complt_stat missing isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-03-31T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 50214 FinalReads_ASVpipeline 17991 sampling_induced_expectorated expectorated barcode BYC131T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 143379.99 templateDNA_16SqPCR_Cq 20.91 templateDNA_16SqPCR 0.1017 well H01 plate_number P1 barcode_806R 806rcbc15 index_sequence GACTTGGTATTC DOB 2006-11-03T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth missing attendschool missing rs15antibty NA rs14antib no dateart missing datehiv missing ageyart missing duryart missing artdrug1stline missing artdrug2ndline missing artreg missing fev1z -0.047341127 weight 22.6 f24mrcscore 2 FEV1_baseline 1.35 FEVpcpred 99.40323953 FVC 1.481250048 FVCZ -0.228174038 FVCpcpred 97.16623645 FEV1FVC 0.911392392 FEV1FVCZ 0.396600877 cd4 1496 vload 409 zwauk -3.3835964 zhauk -3.1164601 zbmiuk -1.5438963 vllog 2.6117234 endtreatdate ['2019-02-27T00:00:00', 'missing'] sp05time 09:15:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup missing dow missing dod missing lastvisit missing visittotno missing lastvisitdate missing treatstopreason missing cough_enrl missing cotrimoxazole missing adm missing nadm missing tbtreat missing acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548900 SAMN22246940 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-03-06 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3087 host_sex missing host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12.3 ethnicity black host_occupation missing host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.25203 host_height 81.39361241 samp_size ['2', ''] study_complt_stat missing isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-03-06T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 49941 FinalReads_ASVpipeline 14900 sampling_induced_expectorated expectorated barcode BYD14IT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 126983.64 templateDNA_16SqPCR_Cq 21.09 templateDNA_16SqPCR 0.09007 well H02 plate_number P1 barcode_806R 806rcbc23 index_sequence GGATGGTGTTGC DOB 2006-11-03T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth missing attendschool missing rs15antibty NA rs14antib no dateart missing datehiv missing ageyart missing duryart missing artdrug1stline missing artdrug2ndline missing artreg missing fev1z -1.429390658 weight 24.6 f24mrcscore 3 FEV1_baseline 1.2 FEVpcpred 81.39361241 FVC 1.351874948 FVCZ -1.463304558 FVCpcpred 81.94030295 FEV1FVC 0.887656103 FEV1FVCZ -0.066765941 cd4 1064 vload 0 zwauk -3.2193408 zhauk -3.150255 zbmiuk -1.4327124 vllog 0 endtreatdate ['NA', 'missing'] sp05time 10:20:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup missing dow missing dod missing lastvisit missing visittotno missing lastvisitdate missing treatstopreason missing cough_enrl missing cotrimoxazole missing adm missing nadm missing tbtreat missing acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548901 SAMN22246885 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2016-12-21 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3006 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.888708 host_height 58.54764513 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2016-12-12T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 40289 FinalReads_ASVpipeline 10019 sampling_induced_expectorated expectorated barcode BYC105T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 85889.14 templateDNA_16SqPCR_Cq 21.65082322 templateDNA_16SqPCR 0.060921509 well B11 plate_number P1 barcode_806R 806rcbc89 index_sequence GAGGAATAGCAG DOB 2004-01-09T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2016-12 attendschool yes rs15antibty NA rs14antib no dateart 2012-04-04T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 8.24 duryart 4.71 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.0988727 weight 32.4 f24mrcscore 2 FEV1_baseline 1.15625 FEVpcpred 58.54764513 FVC 1.479375005 FVCZ -2.573432005 FVCpcpred 67.73020516 FEV1FVC 0.781580057 FEV1FVCZ -1.852129921 cd4 710 vload 40 zwauk -1.9710411 zhauk -1.7597767 zbmiuk -1.4227496 vllog 1.60206 endtreatdate ['2017-11-15T00:00:00', '2017-11-15T00:00:00'] sp05time 09:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-05-07T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-05-07T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548902 SAMN22246919 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-01-11 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3010 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.459467 host_height 84.65156543 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-01-11T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 49833 FinalReads_ASVpipeline 12351 sampling_induced_expectorated expectorated barcode BYD107T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 13970.03 templateDNA_16SqPCR_Cq 24.36 templateDNA_16SqPCR 0.009909 well C02 plate_number P2 barcode_806R 806rcbc114 index_sequence AGCCTAAGCACG DOB 2000-08-04T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-02 attendschool yes rs15antibty NA rs14antib no dateart 2013-02-08T00:00:00 datehiv 2012-09-10T00:00:00 ageyart 12.51 duryart 4 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -1.167898273 weight 42.4 f24mrcscore 2 FEV1_baseline 2.59 FEVpcpred 84.65156543 FVC 2.998125076 FVCZ -1.100060712 FVCpcpred 86.31372577 FEV1FVC 0.863873204 FEV1FVCZ -0.309501451 cd4 704 vload 39 zwauk -3.4549572 zhauk -2.269012 zbmiuk -2.3838303 vllog 1.5910646 endtreatdate ['NA', '2018-01-11T00:00:00'] sp05time 09:42:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-06-28T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-28T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548903 SAMN22246922 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-06-28 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3010 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.291994 host_height 78.24388133 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-06-28T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 46313 FinalReads_ASVpipeline 13245 sampling_induced_expectorated expectorated barcode BYD10ST3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 20264.77 templateDNA_16SqPCR_Cq 23.82064004 templateDNA_16SqPCR 0.014373885 well C03 plate_number P2 barcode_806R 806rcbc122 index_sequence ACTCACGGTATG DOB 2000-08-04T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-02 attendschool yes rs15antibty NA rs14antib no dateart 2013-02-08T00:00:00 datehiv 2012-09-10T00:00:00 ageyart 12.51 duryart 4 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -1.65829674 weight 48.6 f24mrcscore 2 FEV1_baseline 2.5 FEVpcpred 78.24388133 FVC 2.928124905 FVCZ -1.580339705 FVCpcpred 80.3654167 FEV1FVC 0.853788715 FEV1FVCZ -0.421070601 cd4 NA vload NA zwauk -2.501138 zhauk -1.998387 zbmiuk -1.3164092 vllog NA endtreatdate ['NA', '2018-01-11T00:00:00'] sp05time 08:45:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-06-28T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-28T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548904 SAMN22246943 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-03-13 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3088 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 26.417706 host_height NA samp_size ['NA', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-03-13T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 53370 FinalReads_ASVpipeline 21425 sampling_induced_expectorated expectorated barcode BYD14NT3 sequencing_controls no sequencing_control_details NA WRrepeats AAQ WRrepeats_WP AAQ WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 3233.75 templateDNA_16SqPCR_Cq 26.40831418 templateDNA_16SqPCR 0.002293711 well G05 plate_number P1 barcode_806R 806rcbc46 index_sequence TCCGAATTCACA DOB 1999-05-10T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2018-04 attendschool yes rs15antibty NA rs14antib no dateart 2005-12-20T00:00:00 datehiv 2005-12-20T00:00:00 ageyart 6.61 duryart 12.3 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z NA weight 54.4 f24mrcscore 4 FEV1_baseline NA FEVpcpred NA FVC NA FVCZ NA FVCpcpred NA FEV1FVC NA FEV1FVCZ NA cd4 246 vload 1170 zwauk -0.47338852 zhauk -3.3354092 zbmiuk 1.4028693 vllog 3.0681858 endtreatdate ['NA', '2018-12-10T00:00:00'] sp05time 10:29:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-06-03T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-06-03T00:00:00 treatstopreason By Physician cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m yes any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548905 SAMN22246912 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-04-09 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3089 host_sex missing host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.3 ethnicity black host_occupation missing host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.603359 host_height 91.9582773 samp_size ['2', ''] study_complt_stat missing isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-03-31T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 46188 FinalReads_ASVpipeline 9561 sampling_induced_expectorated expectorated barcode BYC133T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 39436.23 templateDNA_16SqPCR_Cq 22.73644865 templateDNA_16SqPCR 0.027972276 well F08 plate_number P4 barcode_806R 806rcbc358 index_sequence GCACTTTACCAA DOB 2000-11-20T00:00:00 trial_arm Placebo adherence Adherent enrolmonth missing attendschool missing rs15antibty NA rs14antib no dateart missing datehiv missing ageyart missing duryart missing artdrug1stline missing artdrug2ndline missing artreg missing fev1z -0.62003636 weight 40.2 f24mrcscore 2 FEV1_baseline 2.12 FEVpcpred 91.9582773 FVC 2.466875076 FVCZ -0.228820308 FVCpcpred 96.96692165 FEV1FVC 0.859386803 FEV1FVCZ -0.793701129 cd4 486 vload 78 zwauk -2.7340579 zhauk -2.7300768 zbmiuk -1.0234042 vllog 1.8920946 endtreatdate ['2019-03-11T00:00:00', 'missing'] sp05time 10:15:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup missing dow missing dod missing lastvisit missing visittotno missing lastvisitdate missing treatstopreason missing cough_enrl missing cotrimoxazole missing adm missing nadm missing tbtreat missing acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548906 SAMN22246942 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-03-11 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3089 host_sex missing host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18.3 ethnicity black host_occupation missing host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.727829 host_height 89.49073528 samp_size ['1', ''] study_complt_stat missing isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-03-11T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 45848 FinalReads_ASVpipeline 11265 sampling_induced_expectorated expectorated barcode BYD14LT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats AB EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 31467.53 templateDNA_16SqPCR_Cq 23.06888919 templateDNA_16SqPCR 0.022320048 well F09 plate_number P4 barcode_806R 806rcbc366 index_sequence ATACACGTGGCG DOB 2000-11-20T00:00:00 trial_arm Placebo adherence Adherent enrolmonth missing attendschool missing rs15antibty NA rs14antib no dateart missing datehiv missing ageyart missing duryart missing artdrug1stline missing artdrug2ndline missing artreg missing fev1z -0.808188603 weight 40.8 f24mrcscore 2 FEV1_baseline 2.09 FEVpcpred 89.49073528 FVC 2.5337500569999998 FVCZ -0.15758393 FVCpcpred 97.90117815 FEV1FVC 0.824864279 FEV1FVCZ -1.236681671 cd4 649 vload 39 zwauk -2.7082446 zhauk -2.6482215 zbmiuk -1.0953147 vllog 1.5910646 endtreatdate ['NA', 'missing'] sp05time 10:45:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup missing dow missing dod missing lastvisit missing visittotno missing lastvisitdate missing treatstopreason missing cough_enrl missing cotrimoxazole missing adm missing nadm missing tbtreat missing acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548907 SAMN22246913 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-04-12 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3093 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.770508 host_height 76.02195557 samp_size ['2.1', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-03-31T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 55265 FinalReads_ASVpipeline 19000 sampling_induced_expectorated expectorated barcode BYC138T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 25982 templateDNA_16SqPCR_Cq 23.44771558 templateDNA_16SqPCR 0.018429134 well G08 plate_number P2 barcode_806R 806rcbc166 index_sequence ACTATTGTCACG DOB 2004-04-01T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2018-04 attendschool yes rs15antibty NA rs14antib no dateart 2005-08-17T00:00:00 datehiv 2005-04-10T00:00:00 ageyart 1.38 duryart 12.65 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.774026 weight 24.2 f24mrcscore 2 FEV1_baseline 1.23 FEVpcpred 76.02195557 FVC 1.413750052 FVCZ -1.665415628 FVCpcpred 79.42502873 FEV1FVC 0.870026506 FEV1FVCZ -0.542387449 cd4 1557 vload 7790 zwauk -4.3834968 zhauk -4.1647711 zbmiuk -2.4738221 vllog 3.8915374 endtreatdate ['2019-03-14T00:00:00', '2019-03-14T00:00:00'] sp05time 09:45:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-06-06T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-06-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548908 SAMN22246944 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-03-14 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3093 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.990166 host_height 72.25285117 samp_size ['1', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-03-14T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 49171 FinalReads_ASVpipeline 16478 sampling_induced_expectorated expectorated barcode BYD14PT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 7233.52 templateDNA_16SqPCR_Cq 25.36647832 templateDNA_16SqPCR 0.005130763 well G09 plate_number P2 barcode_806R 806rcbc174 index_sequence CGGACTACAACT DOB 2004-04-01T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2018-04 attendschool yes rs15antibty NA rs14antib no dateart 2005-08-17T00:00:00 datehiv 2005-04-10T00:00:00 ageyart 1.38 duryart 12.65 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.037977331 weight 28.2 f24mrcscore 3 FEV1_baseline 1.33 FEVpcpred 72.25285117 FVC 1.524374962 FVCZ -1.991428471 FVCpcpred 75.38415278 FEV1FVC 0.872488775 FEV1FVCZ -0.513215686 cd4 914 vload 39 zwauk -4.0735297 zhauk -4.3985691 zbmiuk -1.8713146 vllog 1.5910646 endtreatdate ['NA', '2019-03-14T00:00:00'] sp05time 09:40:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-06-06T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-06-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548909 SAMN22246906 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-05-24 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3098 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.067457 host_height 86.2312516 samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-05-05T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 55657 FinalReads_ASVpipeline 19867 sampling_induced_expectorated expectorated barcode BYC12CT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 7242.41 templateDNA_16SqPCR_Cq 25.23235348 templateDNA_16SqPCR 0.005137073 well E12 plate_number P4 barcode_806R 806rcbc4 index_sequence TATCGTTGACCA DOB 2004-03-24T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2018-05 attendschool yes rs15antibty NA rs14antib no dateart 2012-06-15T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 8.23 duryart 5.94 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.0565227 weight 47.6 f24mrcscore 2 FEV1_baseline 2.19 FEVpcpred 86.2312516 FVC 2.727499962 FVCZ -0.271144332 FVCpcpred 96.4703075 FEV1FVC 0.802933121 FEV1FVCZ -1.53168555 cd4 205 vload 8990 zwauk -0.401214 zhauk -0.33263987 zbmiuk -0.17351843 vllog 3.9537597 endtreatdate ['2019-04-25T00:00:00', '2019-04-25T00:00:00'] sp05time 09:20:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-04-25T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2019-04-25T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548910 SAMN22246932 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-04-25 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3098 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.40975 host_height 83.13765132 samp_size ['1', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-04-25T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 50792 FinalReads_ASVpipeline 17999 sampling_induced_expectorated expectorated barcode BYD13FT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 26631.74 templateDNA_16SqPCR_Cq 23.4 templateDNA_16SqPCR 0.01889 well F01 plate_number P4 barcode_806R 806rcbc302 index_sequence GGTGAAGATACA DOB 2004-03-24T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2018-05 attendschool yes rs15antibty NA rs14antib no dateart 2012-06-15T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 8.23 duryart 5.94 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.290666383 weight 50 f24mrcscore 1 FEV1_baseline 2.24 FEVpcpred 83.13765132 FVC 2.821249962 FVCZ -0.452301631 FVCpcpred 94.08856712 FEV1FVC 0.793974316 FEV1FVCZ -1.644532958 cd4 205 vload 54500 zwauk -0.47414532 zhauk -0.29355249 zbmiuk -0.23781431 vllog 4.7363963 endtreatdate ['NA', '2019-04-25T00:00:00'] sp05time 08:15:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-04-25T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2019-04-25T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548911 SAMN22246914 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-06-04 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3101 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.463055 host_height 74.38920611 samp_size ['3', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-05-26T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 54805 FinalReads_ASVpipeline 14751 sampling_induced_expectorated expectorated barcode BYC157T3 sequencing_controls no sequencing_control_details NA WRrepeats AAI WRrepeats_WP AAI WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 28075.51 templateDNA_16SqPCR_Cq 23.23686836 templateDNA_16SqPCR 0.019914073 well G05 plate_number P4 barcode_806R 806rcbc335 index_sequence ACATCCGCGAAG DOB 2001-06-20T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-06 attendschool yes rs15antibty NA rs14antib no dateart 2015-06-15T00:00:00 datehiv 2015-06-15T00:00:00 ageyart 13.98 duryart 2.97 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.9198601 weight 39.8 f24mrcscore 3 FEV1_baseline 1.74 FEVpcpred 74.38920611 FVC 2.155625105 FVCZ -1.359588278 FVCpcpred 83.10839291 FEV1FVC 0.807190455 FEV1FVCZ -1.343566242 cd4 1079 vload 39 zwauk -3.6439369 zhauk -4.5490737 zbmiuk -0.4598076 vllog 1.5910646 endtreatdate ['2019-04-30T00:00:00', '2019-04-30T00:00:00'] sp05time 08:35:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-05-06T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2019-05-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548912 SAMN22246933 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-05-06 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3101 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.277456 host_height 80.0621072 samp_size ['3', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2019-05-06T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 50047 FinalReads_ASVpipeline 22404 sampling_induced_expectorated expectorated barcode BYD13JT3 sequencing_controls no sequencing_control_details NA WRrepeats AAV WRrepeats_WP AAV WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 16090.89 templateDNA_16SqPCR_Cq 24.05666359 templateDNA_16SqPCR 0.011413331 well G07 plate_number P4 barcode_806R 806rcbc351 index_sequence GCTGGGTCATAT DOB 2001-06-20T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2018-06 attendschool yes rs15antibty NA rs14antib no dateart 2015-06-15T00:00:00 datehiv 2015-06-15T00:00:00 ageyart 13.98 duryart 2.97 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.5213634 weight 41.6 f24mrcscore 2 FEV1_baseline 2.03 FEVpcpred 80.0621072 FVC 2.352499962 FVCZ -1.365057537 FVCpcpred 83.02701855 FEV1FVC 0.862911798 FEV1FVCZ -0.497875645 cd4 949 vload 0 zwauk -3.9041758 zhauk -4.2883673 zbmiuk -0.77863425 vllog 0 endtreatdate ['NA', '2019-04-30T00:00:00'] sp05time 09:30:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-05-06T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2019-05-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548913 SAMN22246915 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-07-16 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3105 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.5 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 13.571428 host_height 76.77966982 samp_size ['5', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-06-23T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 53356 FinalReads_ASVpipeline 9148 sampling_induced_expectorated expectorated barcode BYC15FT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 10874.77 templateDNA_16SqPCR_Cq 24.63369598 templateDNA_16SqPCR 0.007713519 well C04 plate_number P4 barcode_806R 806rcbc323 index_sequence ATGAGTTGGAAG DOB 2007-01-07T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2018-07 attendschool yes rs15antibty NA rs14antib no dateart 2015-06-15T00:00:00 datehiv 2015-06-15T00:00:00 ageyart 8.44 duryart 3.09 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.7682461 weight 26.6 f24mrcscore 0 FEV1_baseline 1.36 FEVpcpred 76.77966982 FVC 1.751875043 FVCZ -0.900971672 FVCpcpred 88.55711966 FEV1FVC 0.776311084 FEV1FVCZ -1.85265246 cd4 600 vload 0 zwauk -2.0761435 zhauk -0.99697071 zbmiuk -2.537024 vllog 0 endtreatdate ['2019-04-30T00:00:00', '2019-04-30T00:00:00'] sp05time 11:15:00 all_3 no visit012 no visit1218 no visit018 no only2visits no one_visit yes endfollowup 2019-06-17T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2019-06-17T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole NA adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548914 SAMN22246948 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-05-23 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3008 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.5 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 20.811655 host_height 71.31002208 samp_size ['3', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-05-23T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 40099 FinalReads_ASVpipeline 16655 sampling_induced_expectorated expectorated barcode BYE10ET3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 107710.94 templateDNA_16SqPCR_Cq 21.21705611 templateDNA_16SqPCR 0.076399796 well F04 plate_number P3 barcode_806R 806rcbc230 index_sequence CCTAATGGAACC DOB 1998-10-30T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-01 attendschool yes rs15antibty NA rs14antib no dateart 2004-11-08T00:00:00 datehiv NA ageyart 6.03 duryart 12.16 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.213587108 weight 50 f24mrcscore 1 FEV1_baseline 2.08 FEVpcpred 71.31002208 FVC 2.983750105 FVCZ -0.796049348 FVCpcpred 90.07016746 FEV1FVC 0.697109292 FEV1FVCZ -2.466132661 cd4 NA vload NA zwauk -2.7542248 zhauk -3.1977599 zbmiuk -0.41262236 vllog NA endtreatdate ['NA', '2018-12-06T00:00:00'] sp05time 09:00:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-05-23T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-05-23T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548915 SAMN22246964 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-06-28 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id C301 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12.4 ethnicity black host_occupation student host_disease No HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.368498 host_height 101.6032173 samp_size ['10', ''] study_complt_stat not applicable isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group comparison group visit Week 0 visit_date 2017-06-28T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 45261 FinalReads_ASVpipeline 14614 sampling_induced_expectorated expectorated barcode BYF100T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 225629.28 templateDNA_16SqPCR_Cq 20.16767545 templateDNA_16SqPCR 0.160039748 well A03 plate_number P4 barcode_806R 806rcbc313 index_sequence CGATAACATGCC DOB 2005-01-25T00:00:00 trial_arm not applicable adherence not applicable enrolmonth NA attendschool yes rs15antibty NA rs14antib no dateart 2007-04-17T00:00:00 datehiv 2007-04-17T00:00:00 ageyart 2.22 duryart 10.2 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z 0.12457924 weight 43 f24mrcscore NA FEV1_baseline 2.14 FEVpcpred 101.6032173 FVC 2.388750076 FVCZ 0.117714164 FVCpcpred 101.5214022 FEV1FVC 0.895866054 FEV1FVCZ -0.039538214 cd4 1389 vload 39 zwauk 0.079170138 zhauk -0.44555041 zbmiuk 0.38664582 vllog NA endtreatdate ['NA', 'not applicable'] sp05time 11:55:00 all_3 not applicable visit012 not applicable visit1218 not applicable visit018 not applicable only2visits not applicable one_visit yes endfollowup not applicable dow not applicable dod not applicable lastvisit not applicable visittotno not applicable lastvisitdate not applicable treatstopreason not applicable cough_enrl not applicable cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m not applicable hospitalised12m not applicable reason_hospi not applicable antibiotic12m not applicable any3_reasons not applicable BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548916 SAMN22246965 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-07-12 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id C303 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12 ethnicity black host_occupation student host_disease No HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 20.342798 host_height 124.2389294 samp_size ['5', ''] study_complt_stat not applicable isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group comparison group visit Week 0 visit_date 2017-07-12T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 51498 FinalReads_ASVpipeline 12205 sampling_induced_expectorated expectorated barcode BYF102T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 13026.85 templateDNA_16SqPCR_Cq 24.46 templateDNA_16SqPCR 0.00924 well G02 plate_number P1 barcode_806R 806rcbc22 index_sequence AGCTGTTGTTTG DOB 2005-07-01T00:00:00 trial_arm not applicable adherence not applicable enrolmonth NA attendschool yes rs15antibty NA rs14antib no dateart 2013-09-09T00:00:00 datehiv 2013-08-10T00:00:00 ageyart 8.19 duryart 3.84 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z 1.9167622 weight 47 f24mrcscore 3 FEV1_baseline 2.7 FEVpcpred 124.2389294 FVC 3.008749962 FVCZ 1.53449675 FVCpcpred 119.1275103 FEV1FVC 0.897382661 FEV1FVCZ 0.611596475 cd4 614 vload 41 zwauk 1.068199 zhauk 0.48130941 zbmiuk 1.1662415 vllog NA endtreatdate ['NA', 'not applicable'] sp05time 10:25:00 all_3 not applicable visit012 not applicable visit1218 not applicable visit018 not applicable only2visits not applicable one_visit yes endfollowup not applicable dow not applicable dod not applicable lastvisit not applicable visittotno not applicable lastvisitdate not applicable treatstopreason not applicable cough_enrl not applicable cotrimoxazole NA adm no nadm NA tbtreat NA acut_exac12m not applicable hospitalised12m not applicable reason_hospi not applicable antibiotic12m not applicable any3_reasons not applicable BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548917 SAMN22246966 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-02-19 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id C318 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 17.3 ethnicity black host_occupation student host_disease No HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.82711 host_height 111.2655288 samp_size ['5', ''] study_complt_stat not applicable isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group comparison group visit Week 0 visit_date 2018-02-17T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 32757 FinalReads_ASVpipeline 8161 sampling_induced_expectorated expectorated barcode BYF10IT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 904758.25 templateDNA_16SqPCR_Cq 18.03650001 templateDNA_16SqPCR 0.641748625 well C07 plate_number P3 barcode_806R 806rcbc251 index_sequence CATCGGTCAAGG DOB 2000-09-27T00:00:00 trial_arm not applicable adherence not applicable enrolmonth NA attendschool yes rs15antibty NA rs14antib no dateart 2013-06-15T00:00:00 datehiv NA ageyart 12.69 duryart 4.7 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z 0.88148147 weight 47 f24mrcscore 1 FEV1_baseline 2.99 FEVpcpred 111.2655288 FVC 3.420000076 FVCZ 1.050956922 FVCpcpred 114.1376683 FEV1FVC 0.874268989 FEV1FVCZ -0.454126162 cd4 388 vload 59 zwauk -1.4547364 zhauk -0.91216838 zbmiuk -0.91549796 vllog NA endtreatdate ['NA', 'not applicable'] sp05time 08:15:00 all_3 not applicable visit012 not applicable visit1218 not applicable visit018 not applicable only2visits not applicable one_visit yes endfollowup not applicable dow not applicable dod not applicable lastvisit not applicable visittotno not applicable lastvisitdate not applicable treatstopreason not applicable cough_enrl not applicable cotrimoxazole NA adm no nadm NA tbtreat no acut_exac12m not applicable hospitalised12m not applicable reason_hospi not applicable antibiotic12m not applicable any3_reasons not applicable BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548918 SAMN22246967 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-05-28 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id C321 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12.3 ethnicity black host_occupation student host_disease No HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 22.910118 host_height 103.4813855 samp_size ['2', ''] study_complt_stat not applicable isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group comparison group visit Week 0 visit_date 2018-05-26T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 52299 FinalReads_ASVpipeline 20789 sampling_induced_expectorated expectorated barcode BYF10LT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 31266.56 templateDNA_16SqPCR_Cq 23.11678101 templateDNA_16SqPCR 0.022177494 well C10 plate_number P1 barcode_806R 806rcbc82 index_sequence ACTGACAGCCAT DOB 2006-01-11T00:00:00 trial_arm not applicable adherence not applicable enrolmonth NA attendschool yes rs15antibty NA rs14antib no dateart 2008-06-15T00:00:00 datehiv 2008-06-15T00:00:00 ageyart 2.43 duryart 10.01 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z 0.27091503 weight 43 f24mrcscore 2 FEV1_baseline 1.82 FEVpcpred 103.4813855 FVC 2.094374895 FVCZ 0.602397576 FVCpcpred 107.8250835 FEV1FVC 0.868994399 FEV1FVCZ -0.640426686 cd4 1287 vload 0 zwauk 0.06860476 zhauk -2.1536031 zbmiuk 1.4765602 vllog NA endtreatdate ['NA', 'not applicable'] sp05time 11:15:00 all_3 not applicable visit012 not applicable visit1218 not applicable visit018 not applicable only2visits not applicable one_visit yes endfollowup not applicable dow not applicable dod not applicable lastvisit not applicable visittotno not applicable lastvisitdate not applicable treatstopreason not applicable cough_enrl not applicable cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m not applicable hospitalised12m not applicable reason_hospi not applicable antibiotic12m not applicable any3_reasons not applicable BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548919 SAMN22246887 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-02-09 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3010 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.5 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.087444 host_height 77.18131869 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-02-02T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 48669 FinalReads_ASVpipeline 5545 sampling_induced_expectorated expectorated barcode BYC10AT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 6633.26 templateDNA_16SqPCR_Cq 25.46 templateDNA_16SqPCR 0.004705 well C01 plate_number P2 barcode_806R 806rcbc106 index_sequence TGACCTCCAAGA DOB 2000-08-04T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-02 attendschool yes rs15antibty NA rs14antib no dateart 2013-02-08T00:00:00 datehiv 2012-09-10T00:00:00 ageyart 12.51 duryart 4 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -1.7037843 weight 40 f24mrcscore 1 FEV1_baseline 2.086250067 FEVpcpred 77.18131869 FVC 2.663125038 FVCZ -0.991410469 FVCpcpred 87.67211797 FEV1FVC 0.783384196 FEV1FVCZ -1.542445662 cd4 672 vload 39 zwauk -3.2162957 zhauk -2.9697497 zbmiuk -1.6593581 vllog 1.5910646 endtreatdate ['2018-01-11T00:00:00', '2018-01-11T00:00:00'] sp05time 08:55:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-06-28T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-28T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548920 SAMN22246888 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-02-09 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3011 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 10.6 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.648438 host_height 65.03623162 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-01-31T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 48981 FinalReads_ASVpipeline 14668 sampling_induced_expectorated expectorated barcode BYC10BT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 54754.79 templateDNA_16SqPCR_Cq 22.25312359 templateDNA_16SqPCR 0.038837789 well B08 plate_number P4 barcode_806R 806rcbc354 index_sequence TCCGTACCATAA DOB 2006-07-05T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-02 attendschool yes rs15antibty NA rs14antib no dateart 2014-06-04T00:00:00 datehiv 2014-05-15T00:00:00 ageyart 7.92 duryart 2.69 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.7560456 weight 24 f24mrcscore 3 FEV1_baseline 0.93 FEVpcpred 65.03623162 FVC 1.184375048 FVCZ -2.169116485 FVCpcpred 73.09724623 FEV1FVC 0.785224249 FEV1FVCZ -1.532919922 cd4 795 vload 1200 zwauk -2.3312023 zhauk -2.0840068 zbmiuk -1.3305693 vllog 3.0791812 endtreatdate ['NA', 'NA'] sp05time 09:48:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2018-06-27T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-27T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548921 SAMN22246950 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-06-27 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3011 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.363512 host_height 62.37412819 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-06-27T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 50757 FinalReads_ASVpipeline 22638 sampling_induced_expectorated induced barcode BYE10HT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 931.49 templateDNA_16SqPCR_Cq 28.25284168 templateDNA_16SqPCR 0.000660709 well B09 plate_number P4 barcode_806R 806rcbc362 index_sequence GTCCAGTAATGC DOB 2006-07-05T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-02 attendschool yes rs15antibty NA rs14antib no dateart 2014-06-04T00:00:00 datehiv 2014-05-15T00:00:00 ageyart 7.92 duryart 2.69 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.884918325 weight 28 f24mrcscore 2 FEV1_baseline 1.04 FEVpcpred 62.37412819 FVC 1.413750052 FVCZ -2.060258338 FVCpcpred 74.62088519 FEV1FVC 0.73563213 FEV1FVCZ -2.172730895 cd4 NA vload NA zwauk -1.9806019 zhauk -1.8442178 zbmiuk -1.2278066 vllog NA endtreatdate ['NA', 'NA'] sp05time 10:15:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2018-06-27T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-27T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548922 SAMN22246889 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-02-27 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3018 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 23.586456 host_height 67.53724162 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-02-18T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 49917 FinalReads_ASVpipeline 19298 sampling_induced_expectorated expectorated barcode BYC10IT3 sequencing_controls no sequencing_control_details NA WRrepeats AAD WRrepeats_WP AAD WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 26025.51 templateDNA_16SqPCR_Cq 23.44 templateDNA_16SqPCR 0.01846 well A02 plate_number P2 barcode_806R 806rcbc112 index_sequence TCTGTTGCTCTC DOB 1999-02-17T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-03 attendschool yes rs15antibty NA rs14antib no dateart 2007-02-06T00:00:00 datehiv 2007-01-10T00:00:00 ageyart 7.97 duryart 10.06 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.4482775 weight 57.4 f24mrcscore 2 FEV1_baseline 1.76 FEVpcpred 67.53724162 FVC 2.303124905 FVCZ -1.587509873 FVCpcpred 79.25662863 FEV1FVC 0.764179132 FEV1FVCZ -1.953900133 cd4 571 vload 3520 zwauk -0.019790869 zhauk -1.2530532 zbmiuk 0.7928282 vllog 3.5465426 endtreatdate ['NA', 'NA'] sp05time 10:09:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-11-12T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-11-12T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548923 SAMN22246921 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-01-31 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3018 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 21.148893 host_height 69.77729784 samp_size ['NA', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-01-31T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 50758 FinalReads_ASVpipeline 17024 sampling_induced_expectorated expectorated barcode BYD10IT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 14299.56 templateDNA_16SqPCR_Cq 24.34382626 templateDNA_16SqPCR 0.010142735 well A03 plate_number P2 barcode_806R 806rcbc120 index_sequence TCTTCCGCTACT DOB 1999-02-17T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-03 attendschool yes rs15antibty NA rs14antib no dateart 2007-02-06T00:00:00 datehiv 2007-01-10T00:00:00 ageyart 7.97 duryart 10.06 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.282374637 weight 51.6 f24mrcscore 2 FEV1_baseline 1.84 FEVpcpred 69.77729784 FVC 2.4712500569999998 FVCZ -1.239661893 FVCpcpred 83.66960731 FEV1FVC 0.744562465 FEV1FVCZ -2.12418981 cd4 337 vload 33400 zwauk -0.8442257 zhauk -1.2302181 zbmiuk -0.12060468 vllog 4.5237465 endtreatdate ['NA', 'NA'] sp05time 11:44:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-11-12T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-11-12T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548924 SAMN22246946 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-11-12 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3018 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.7 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 21.786493 host_height 64.56481497 samp_size ['3', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-11-12T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 36496 FinalReads_ASVpipeline 11362 sampling_induced_expectorated expectorated barcode BYE108T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 57923.52 templateDNA_16SqPCR_Cq 22.24466901 templateDNA_16SqPCR 0.04108538 well A04 plate_number P2 barcode_806R 806rcbc128 index_sequence ACGGCATGGCAT DOB 1999-02-17T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-03 attendschool yes rs15antibty NA rs14antib no dateart 2007-02-06T00:00:00 datehiv 2007-01-10T00:00:00 ageyart 7.97 duryart 10.06 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.659866343 weight 51 f24mrcscore 2 FEV1_baseline 1.63 FEVpcpred 64.56481497 FVC 2.079375029 FVCZ -2.026180896 FVCpcpred 73.52034719 FEV1FVC 0.783889377 FEV1FVCZ -1.649506004 cd4 NA vload NA zwauk -0.95606798 zhauk -1.7604622 zbmiuk 0.042602941 vllog NA endtreatdate ['NA', 'NA'] sp05time 13:20:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-11-12T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-11-12T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548925 SAMN22246890 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-04-19 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3021 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 11.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.190933 host_height 70.94808658 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-03-24T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 48789 FinalReads_ASVpipeline 23641 sampling_induced_expectorated expectorated barcode BYC10LT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 153861.46 templateDNA_16SqPCR_Cq 20.77870601 templateDNA_16SqPCR 0.109134543 well C08 plate_number P2 barcode_806R 806rcbc162 index_sequence CTAGATTTGCCA DOB 2005-05-22T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-04 attendschool yes rs15antibty NA rs14antib no dateart 2012-11-02T00:00:00 datehiv 2012-08-04T00:00:00 ageyart 7.45 duryart 4.46 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.2000895 weight 35.4 f24mrcscore 2 FEV1_baseline 1.34 FEVpcpred 70.94808658 FVC 1.678125024 FVCZ -1.620401755 FVCpcpred 79.56276641 FEV1FVC 0.798510251 FEV1FVCZ -1.573280099 cd4 639 vload 0 zwauk -0.64912182 zhauk -0.80605441 zbmiuk -0.39380503 vllog 0 endtreatdate ['NA', 'NA'] sp05time 11:48:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-10-29T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 6 lastvisitdate 2018-10-29T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m yes hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548926 SAMN22246920 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-05-02 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3021 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.973576 host_height 70.30645359 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-05-02T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 44950 FinalReads_ASVpipeline 16326 sampling_induced_expectorated expectorated barcode BYD10FT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 2689477.33 templateDNA_16SqPCR_Cq 16.48546427 templateDNA_16SqPCR 1.907656979 well C09 plate_number P2 barcode_806R 806rcbc170 index_sequence TACTAATCTGCG DOB 2005-05-22T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-04 attendschool yes rs15antibty NA rs14antib no dateart 2012-11-02T00:00:00 datehiv 2012-08-04T00:00:00 ageyart 7.45 duryart 4.46 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.246299161 weight 41 f24mrcscore 3 FEV1_baseline 1.47 FEVpcpred 70.30645359 FVC 1.835625052 FVCZ -1.646541965 FVCpcpred 79.09295981 FEV1FVC 0.800817153 FEV1FVCZ -1.586286382 cd4 899 vload 0 zwauk -0.54491341 zhauk -1.1506522 zbmiuk 0.096785188 vllog 0 endtreatdate ['NA', 'NA'] sp05time 10:15:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-10-29T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 6 lastvisitdate 2018-10-29T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m yes hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548927 SAMN22246945 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-10-29 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3021 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.905041 host_height 63.85479146 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-10-29T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 40379 FinalReads_ASVpipeline 16626 sampling_induced_expectorated expectorated barcode BYE105T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 283387.1 templateDNA_16SqPCR_Cq 19.86220818 templateDNA_16SqPCR 0.201007601 well C10 plate_number P2 barcode_806R 806rcbc178 index_sequence AGCAAACACCCG DOB 2005-05-22T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-04 attendschool yes rs15antibty NA rs14antib no dateart 2012-11-02T00:00:00 datehiv 2012-08-04T00:00:00 ageyart 7.45 duryart 4.46 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.716828649 weight 43.6 f24mrcscore 3 FEV1_baseline 1.38 FEVpcpred 63.85479146 FVC 1.856874943 FVCZ -1.759764819 FVCpcpred 77.6127202 FEV1FVC 0.743184133 FEV1FVCZ -2.270180563 cd4 NA vload NA zwauk -0.51918542 zhauk -1.385057 zbmiuk 0.33053911 vllog NA endtreatdate ['NA', 'NA'] sp05time 09:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-10-29T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 6 lastvisitdate 2018-10-29T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m yes hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548928 SAMN22246917 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-11-15 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3006 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.75493 host_height 54.73657529 samp_size ['5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2017-11-15T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 45965 FinalReads_ASVpipeline 13613 sampling_induced_expectorated expectorated barcode BYD104T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 102365.17 templateDNA_16SqPCR_Cq 21.39623878 templateDNA_16SqPCR 0.072608026 well B12 plate_number P1 barcode_806R 806rcbc97 index_sequence TGTTATCGCACA DOB 2004-01-09T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2016-12 attendschool yes rs15antibty NA rs14antib no dateart 2012-04-04T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 8.24 duryart 4.71 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.3694653 weight 36.7 f24mrcscore 2 FEV1_baseline 1.2 FEVpcpred 54.73657529 FVC 1.993749976 FVCZ -1.376620406 FVCpcpred 82.35080128 FEV1FVC 0.601880909 FEV1FVCZ -3.379101543 cd4 591 vload 39 zwauk -1.9009607 zhauk -1.6776509 zbmiuk -1.203795 vllog 1.5910646 endtreatdate ['NA', '2017-11-15T00:00:00'] sp05time 14:15:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-05-07T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-05-07T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548929 SAMN22246923 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-06-01 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3026 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.6 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.804968 host_height 82.90296815 samp_size ['1', ''] study_complt_stat LTFU isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-06-01T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 42214 FinalReads_ASVpipeline 8366 sampling_induced_expectorated expectorated barcode BYD10TT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 34284.35 templateDNA_16SqPCR_Cq 22.94262711 templateDNA_16SqPCR 0.024318023 well C09 plate_number P4 barcode_806R 806rcbc363 index_sequence TATGTGGCCCAA DOB 2003-10-15T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-06 attendschool yes rs15antibty NA rs14antib no dateart 2005-01-08T00:00:00 datehiv 2004-10-10T00:00:00 ageyart 1.23 duryart 12.47 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.308262631 weight 39 f24mrcscore 2 FEV1_baseline 1.86 FEVpcpred 82.90296815 FVC 2.204375029 FVCZ -0.829480832 FVCpcpred 89.23826908 FEV1FVC 0.843776576 FEV1FVCZ -1.06057201 cd4 647 vload NA zwauk -2.0118842 zhauk -2.1223762 zbmiuk -0.86365491 vllog NA endtreatdate ['NA', '2018-06-01T00:00:00'] sp05time 14:20:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2018-06-01T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2018-06-01T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548930 SAMN22246891 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-06-29 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3026 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.7 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.653061 host_height 82.96886085 samp_size ['10', ''] study_complt_stat LTFU isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-06-22T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 45599 FinalReads_ASVpipeline 18505 sampling_induced_expectorated expectorated barcode BYC10RT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 58942.09 templateDNA_16SqPCR_Cq 22.14459621 templateDNA_16SqPCR 0.041807857 well C08 plate_number P4 barcode_806R 806rcbc355 index_sequence TCCATAACTAGC DOB 2003-10-15T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-06 attendschool yes rs15antibty NA rs14antib no dateart 2005-01-08T00:00:00 datehiv 2004-10-10T00:00:00 ageyart 1.23 duryart 12.47 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.303201 weight 34.6 f24mrcscore 2 FEV1_baseline 1.62 FEVpcpred 82.96886085 FVC 1.872499943 FVCZ -0.978511695 FVCpcpred 87.40633944 FEV1FVC 0.865153567 FEV1FVCZ -0.772430927 cd4 1062 vload 42700 zwauk -2.1791914 zhauk -2.7797129 zbmiuk -0.69500828 vllog 4.6304278 endtreatdate ['2018-06-01T00:00:00', '2018-06-01T00:00:00'] sp05time 10:15:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2018-06-01T00:00:00 dow NA dod NA lastvisit 12 mths visittotno 5 lastvisitdate 2018-06-01T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548931 SAMN22246892 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-07-24 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3028 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage SHI host_hiv_stat yes host_body_mass_index 19.357195 host_height 66.10838055 samp_size ['5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-07-15T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 34565 FinalReads_ASVpipeline 16368 sampling_induced_expectorated expectorated barcode BYC10VT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 1023949 templateDNA_16SqPCR_Cq 17.93454728 templateDNA_16SqPCR 0.726291101 well B11 plate_number P2 barcode_806R 806rcbc185 index_sequence ATGGACCGAACC DOB 2000-08-14T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-07 attendschool yes rs15antibty SHI rs14antib no dateart 2009-12-15T00:00:00 datehiv 2009-12-01T00:00:00 ageyart 9.34 duryart 7.61 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -2.5536878 weight 42.4 f24mrcscore 3 FEV1_baseline 1.53 FEVpcpred 66.10838055 FVC 1.882500052 FVCZ -2.027592347 FVCpcpred 73.78345772 FEV1FVC 0.812748966 FEV1FVCZ -1.461731749 cd4 136 vload 45 zwauk -2.2163587 zhauk -2.5608392 zbmiuk -0.60213381 vllog 1.6532125 endtreatdate ['2018-06-25T00:00:00', '2018-06-25T00:00:00'] sp05time 09:00:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2018-12-12T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-12-12T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548932 SAMN22246955 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-12-12 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3028 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.900658 host_height 67.26161899 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-12-12T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 42123 FinalReads_ASVpipeline 17595 sampling_induced_expectorated expectorated barcode BYE12MT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 2287669.02 templateDNA_16SqPCR_Cq 16.72827878 templateDNA_16SqPCR 1.622652743 well B12 plate_number P2 barcode_806R 806rcbc193 index_sequence TAACTCTGATGC DOB 2000-08-14T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-07 attendschool yes rs15antibty NA rs14antib no dateart 2009-12-15T00:00:00 datehiv 2009-12-01T00:00:00 ageyart 9.34 duryart 7.61 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -2.467781596 weight 41.4 f24mrcscore 3 FEV1_baseline 1.58 FEVpcpred 67.26161899 FVC 1.874374986 FVCZ -2.159160131 FVCpcpred 71.96957238 FEV1FVC 0.842947679 FEV1FVCZ -0.978363269 cd4 NA vload NA zwauk -2.5847681 zhauk -2.5820153 zbmiuk -1.0143524 vllog NA endtreatdate ['NA', '2018-06-25T00:00:00'] sp05time 09:30:00 all_3 no visit012 no visit1218 no visit018 yes only2visits yes one_visit no endfollowup 2018-12-12T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-12-12T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548933 SAMN22246893 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-08-14 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3036 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.168846 host_height 58.26562946 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-06-22T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 66922 FinalReads_ASVpipeline 18354 sampling_induced_expectorated expectorated barcode BYC114T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 5952.31 templateDNA_16SqPCR_Cq 25.62 templateDNA_16SqPCR 0.004222 well B02 plate_number P1 barcode_806R 806rcbc17 index_sequence GCACACACGTTA DOB 2003-08-01T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-08 attendschool yes rs15antibty NA rs14antib no dateart 2012-03-15T00:00:00 datehiv 2012-03-15T00:00:00 ageyart 8.62 duryart 5.42 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.1187022 weight 38.2 f24mrcscore 2 FEV1_baseline 1.24 FEVpcpred 58.26562946 FVC 1.731874943 FVCZ -2.056564763 FVCpcpred 73.85904909 FEV1FVC 0.715987037 FEV1FVCZ -2.558605842 cd4 591 vload 70100 zwauk -1.7678136 zhauk -2.2567873 zbmiuk -0.53815979 vllog 4.8457179 endtreatdate ['2018-07-16T00:00:00', '2018-07-16T00:00:00'] sp05time 11:14:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-01-10T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-01-10T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548934 SAMN22246924 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-07-16 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3036 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.173727 host_height 64.69745065 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-07-16T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 48503 FinalReads_ASVpipeline 16645 sampling_induced_expectorated expectorated barcode BYD10YT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 61125.63 templateDNA_16SqPCR_Cq 22.14424885 templateDNA_16SqPCR 0.043356649 well B03 plate_number P1 barcode_806R 806rcbc25 index_sequence TAGGATTGCTCG DOB 2003-08-01T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-08 attendschool yes rs15antibty NA rs14antib no dateart 2012-03-15T00:00:00 datehiv 2012-03-15T00:00:00 ageyart 8.62 duryart 5.42 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.656049558 weight 41 f24mrcscore 2 FEV1_baseline 1.51 FEVpcpred 64.69745065 FVC 2.22874999 FVCZ -1.032845707 FVCpcpred 86.60659607 FEV1FVC 0.677509814 FEV1FVCZ -2.879801112 cd4 458 vload 0 zwauk -1.8297726 zhauk -1.9070736 zbmiuk -0.76300764 vllog 0 endtreatdate ['NA', '2018-07-16T00:00:00'] sp05time 09:20:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-01-10T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-01-10T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548935 SAMN22246956 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-01-10 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3036 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.27841 host_height 59.52540441 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-01-10T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 44185 FinalReads_ASVpipeline 14253 sampling_induced_expectorated expectorated barcode BYE12VT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 386726.55 templateDNA_16SqPCR_Cq 19.46799239 templateDNA_16SqPCR 0.274306682 well B04 plate_number P1 barcode_806R 806rcbc33 index_sequence TCACGGGAGTTG DOB 2003-08-01T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-08 attendschool yes rs15antibty NA rs14antib no dateart 2012-03-15T00:00:00 datehiv 2012-03-15T00:00:00 ageyart 8.62 duryart 5.42 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.029246322 weight 42.8 f24mrcscore 2 FEV1_baseline 1.38 FEVpcpred 59.52540441 FVC 2.418124914 FVCZ -0.401838672 FVCpcpred 94.73409712 FEV1FVC 0.570690119 FEV1FVCZ -3.561324822 cd4 NA vload NA zwauk -1.7260072 zhauk -2.2419808 zbmiuk -0.36719221 vllog NA endtreatdate ['NA', '2018-07-16T00:00:00'] sp05time 10:20:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-01-10T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-01-10T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548936 SAMN22246925 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-08-08 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3039 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 20.728409 host_height 73.809285 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-08-08T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 39398 FinalReads_ASVpipeline 9056 sampling_induced_expectorated expectorated barcode BYD113T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 1731274.65 templateDNA_16SqPCR_Cq 17.23 templateDNA_16SqPCR 1.228 well E02 plate_number P4 barcode_806R 806rcbc309 index_sequence ATGCGTAGTGCG DOB 2004-06-16T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-08 attendschool yes rs15antibty NA rs14antib no dateart 2017-01-03T00:00:00 datehiv 2017-01-03T00:00:00 ageyart 12.55 duryart 0.65 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.932116769 weight 49.8 f24mrcscore 2 FEV1_baseline 1.84 FEVpcpred 73.809285 FVC 2.075000048 FVCZ -2.188097751 FVCpcpred 73.01393003 FEV1FVC 0.886746984 FEV1FVCZ 0.14928217 cd4 484 vload 0 zwauk -0.030220361 zhauk -1.0118594 zbmiuk 0.78105879 vllog 0 endtreatdate ['NA', '2017-11-20T00:00:00'] sp05time 09:40:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-01-14T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-01-14T00:00:00 treatstopreason By Physician cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548937 SAMN22246894 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-08-28 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3039 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.760773 host_height 80.55857637 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-08-24T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 46512 FinalReads_ASVpipeline 15985 sampling_induced_expectorated expectorated barcode BYC117T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 1106090.92 templateDNA_16SqPCR_Cq 17.82646229 templateDNA_16SqPCR 0.784554694 well H04 plate_number P4 barcode_806R 806rcbc328 index_sequence GCAAAGCAAAGT DOB 2004-06-16T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-08 attendschool yes rs15antibty NA rs14antib NA dateart 2017-01-03T00:00:00 datehiv 2017-01-03T00:00:00 ageyart 12.55 duryart 0.65 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.4618492 weight 37.6 f24mrcscore 2 FEV1_baseline 1.67 FEVpcpred 80.55857637 FVC 1.903749943 FVCZ -1.566535097 FVCpcpred 80.66473312 FEV1FVC 0.877216025 FEV1FVCZ -0.031464431 cd4 549 vload 0 zwauk -0.91539347 zhauk -1.3482053 zbmiuk -0.19559047 vllog 0 endtreatdate ['2017-11-20T00:00:00', '2017-11-20T00:00:00'] sp05time 09:55:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-01-14T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-01-14T00:00:00 treatstopreason By Physician cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548938 SAMN22246957 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-01-14 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3039 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.5 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index not applicable host_height not applicable samp_size ['not applicable', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date not applicable run_processing_batch R1 sample_type SP RawReads_ASVpipeline 28323 FinalReads_ASVpipeline 11922 sampling_induced_expectorated expectorated barcode BYE12WT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 4.08 templateDNA_16SqPCR_Cq 36.25061138 templateDNA_16SqPCR 2.89e-06 well E03 plate_number P4 barcode_806R 806rcbc317 index_sequence CGTGGTTAGCAT DOB 2004-06-16T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2017-08 attendschool yes rs15antibty NA rs14antib no dateart 2017-01-03T00:00:00 datehiv 2017-01-03T00:00:00 ageyart 12.55 duryart 0.65 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z not applicable weight not applicable f24mrcscore not applicable FEV1_baseline not applicable FEVpcpred not applicable FVC not applicable FVCZ not applicable FVCpcpred not applicable FEV1FVC not applicable FEV1FVCZ not applicable cd4 not applicable vload not applicable zwauk not applicable zhauk not applicable zbmiuk not applicable vllog not applicable endtreatdate ['not applicable', '2017-11-20T00:00:00'] sp05time not applicable all_3 not applicable visit012 not applicable visit1218 not applicable visit018 not applicable only2visits not applicable one_visit not applicable endfollowup 2019-01-14T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-01-14T00:00:00 treatstopreason By Physician cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m not applicable hospitalised12m not applicable reason_hospi not applicable antibiotic12m not applicable any3_reasons not applicable BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548939 SAMN22246947 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-05-07 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3006 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 18.632677 host_height 62.74458778 samp_size ['3', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2018-05-07T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 56552 FinalReads_ASVpipeline 19161 sampling_induced_expectorated expectorated barcode BYE10DT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 33384.84 templateDNA_16SqPCR_Cq 23.07 templateDNA_16SqPCR 0.02368 well C01 plate_number P1 barcode_806R 806rcbc10 index_sequence GTACATACCGGT DOB 2004-01-09T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2016-12 attendschool yes rs15antibty NA rs14antib no dateart 2012-04-04T00:00:00 datehiv 2012-06-15T00:00:00 ageyart 8.24 duryart 4.71 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.7971566 weight 41.2 f24mrcscore 2 FEV1_baseline 1.41 FEVpcpred 62.74458778 FVC 1.778749943 FVCZ -2.218912055 FVCpcpred 71.77783774 FEV1FVC 0.792691504 FEV1FVCZ -1.733281813 cd4 NA vload NA zwauk -1.4439087 zhauk -1.8591859 zbmiuk -0.39943728 vllog NA endtreatdate ['NA', '2017-11-15T00:00:00'] sp05time 13:55:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-05-07T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-05-07T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548940 SAMN22246895 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-09-18 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3041 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.116107 host_height 75.35406193 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-09-14T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 41421 FinalReads_ASVpipeline 15221 sampling_induced_expectorated expectorated barcode BYC119T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 240940.42 templateDNA_16SqPCR_Cq 20.15 templateDNA_16SqPCR 0.1709 well G02 plate_number P2 barcode_806R 806rcbc118 index_sequence GCAGGATAGATA DOB 2005-09-08T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-09 attendschool yes rs15antibty NA rs14antib no dateart 2013-06-15T00:00:00 datehiv 2013-06-15T00:00:00 ageyart 7.77 duryart 4.26 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.9030006 weight 23.6 f24mrcscore 2 FEV1_baseline 1.15 FEVpcpred 75.35406193 FVC 1.476250052 FVCZ -1.146535789 FVCpcpred 85.82972166 FEV1FVC 0.779000803 FEV1FVCZ -1.666977808 cd4 613 vload 0 zwauk -3.365123 zhauk -2.6649523 zbmiuk -2.2447364 vllog 0 endtreatdate ['2019-08-20T00:00:00', '2019-08-20T00:00:00'] sp05time 10:46:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-04T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-04T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548941 SAMN22246926 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-08-20 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3041 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 12.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.257072 host_height 78.11104648 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-08-20T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 37872 FinalReads_ASVpipeline 12651 sampling_induced_expectorated expectorated barcode BYD114T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 58412.95 templateDNA_16SqPCR_Cq 22.2320428 templateDNA_16SqPCR 0.041432539 well G03 plate_number P2 barcode_806R 806rcbc126 index_sequence TCTACGGAGAGC DOB 2005-09-08T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-09 attendschool yes rs15antibty NA rs14antib no dateart 2013-06-15T00:00:00 datehiv 2013-06-15T00:00:00 ageyart 7.77 duryart 4.26 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.652337018 weight 25.6 f24mrcscore 3 FEV1_baseline 1.33 FEVpcpred 78.11104648 FVC 1.634374976 FVCZ -1.177133589 FVCpcpred 85.45448951 FEV1FVC 0.813766769 FEV1FVCZ -1.189995686 cd4 620 vload 0 zwauk -3.3069029 zhauk -2.6105163 zbmiuk -2.4799061 vllog 0 endtreatdate ['NA', '2019-08-20T00:00:00'] sp05time 09:50:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-04T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-04T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548942 SAMN22246958 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-02-04 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3041 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 14.922145 host_height 70.64548635 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-02-04T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 47769 FinalReads_ASVpipeline 11566 sampling_induced_expectorated expectorated barcode BYE12ZT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 12933.05 templateDNA_16SqPCR_Cq 24.49454943 templateDNA_16SqPCR 0.00917346 well G04 plate_number P2 barcode_806R 806rcbc134 index_sequence AATCTTGCTGCA DOB 2005-09-08T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2017-09 attendschool yes rs15antibty NA rs14antib no dateart 2013-06-15T00:00:00 datehiv 2013-06-15T00:00:00 ageyart 7.77 duryart 4.26 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.183741544 weight 27.6 f24mrcscore 3 FEV1_baseline 1.27 FEVpcpred 70.64548635 FVC 1.580000043 FVCZ -1.747704117 FVCpcpred 78.43645747 FEV1FVC 0.803797434 FEV1FVCZ -1.347175984 cd4 NA vload NA zwauk -3.070452 zhauk -2.7008457 zbmiuk -2.0931709 vllog NA endtreatdate ['NA', '2019-08-20T00:00:00'] sp05time 11:07:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-04T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-04T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548943 SAMN22246896 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-09-20 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3042 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 13.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.352589 host_height 72.53364037 samp_size ['0.1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-09-16T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 41850 FinalReads_ASVpipeline 18225 sampling_induced_expectorated expectorated barcode BYC11AT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 151003.44 templateDNA_16SqPCR_Cq 20.83226527 templateDNA_16SqPCR 0.107107338 well D05 plate_number P1 barcode_806R 806rcbc43 index_sequence AAGGAGCGCCTT DOB 2003-10-10T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-09 attendschool yes rs15antibty NA rs14antib no dateart 2009-06-15T00:00:00 datehiv 2009-06-15T00:00:00 ageyart 5.68 duryart 8.27 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -2.0820103 weight 40 f24mrcscore 2 FEV1_baseline 1.8 FEVpcpred 72.53364037 FVC 2.414375067 FVCZ -0.975376149 FVCpcpred 87.42489297 FEV1FVC 0.745534518 FEV1FVCZ -2.213044917 cd4 571 vload 49 zwauk -1.3995142 zhauk -0.45978156 zbmiuk -1.4614246 vllog 1.690196 endtreatdate ['2018-08-22T00:00:00', '2018-08-22T00:00:00'] sp05time 09:12:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-06T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548944 SAMN22246899 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-10-02 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3047 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.845949 host_height 69.10276983 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-09-23T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 40140 FinalReads_ASVpipeline 15297 sampling_induced_expectorated expectorated barcode BYC11I3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 180176.63 templateDNA_16SqPCR_Cq 20.58 templateDNA_16SqPCR 0.1278 well B02 plate_number P3 barcode_806R 806rcbc210 index_sequence CTCCTGAAAGTT DOB 2002-11-04T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-05-04T00:00:00 datehiv 2016-05-03T00:00:00 ageyart 13.5 duryart 1.41 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.3346956 weight 35 f24mrcscore 2 FEV1_baseline 1.24 FEVpcpred 69.10276983 FVC 1.444375038 FVCZ -2.009330659 FVCpcpred 74.28228166 FEV1FVC 0.858502797 FEV1FVCZ -0.995376132 cd4 248 vload 49000 zwauk -2.9950669 zhauk -4.6729279 zbmiuk -0.024155859 vllog 4.690196 endtreatdate ['2019-09-03T00:00:00', '2019-09-03T00:00:00'] sp05time 08:40:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-18T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 8 lastvisitdate 2019-02-18T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548945 SAMN22246928 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-09-03 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3047 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 19.733854 host_height 70.00734204 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-09-03T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 45478 FinalReads_ASVpipeline 19340 sampling_induced_expectorated expectorated barcode BYD11AT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 98482.84 templateDNA_16SqPCR_Cq 21.35091396 templateDNA_16SqPCR 0.069854273 well B03 plate_number P3 barcode_806R 806rcbc218 index_sequence CCTTGGCTATCC DOB 2002-11-04T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-05-04T00:00:00 datehiv 2016-05-03T00:00:00 ageyart 13.5 duryart 1.41 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.268645457 weight 39.4 f24mrcscore 2 FEV1_baseline 1.46 FEVpcpred 70.00734204 FVC 1.669999957 FVCZ -2.080166549 FVCpcpred 73.26185221 FEV1FVC 0.874251542 FEV1FVCZ -0.670615026 cd4 248 vload 0 zwauk -2.5169561 zhauk -3.5733135 zbmiuk -0.25008607 vllog 0 endtreatdate ['NA', '2019-09-03T00:00:00'] sp05time 10:49:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-18T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 8 lastvisitdate 2019-02-18T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548946 SAMN22246960 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-02-18 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3047 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 16.2 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 21.829887 host_height 75.13237928 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-02-18T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 44936 FinalReads_ASVpipeline 16369 sampling_induced_expectorated expectorated barcode BYE135T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 108052.25 templateDNA_16SqPCR_Cq 21.21232796 templateDNA_16SqPCR 0.07664189 well B04 plate_number P3 barcode_806R 806rcbc226 index_sequence TAATCGGATTCC DOB 2002-11-04T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-05-04T00:00:00 datehiv 2016-05-03T00:00:00 ageyart 13.5 duryart 1.41 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -1.890110411 weight 43.4 f24mrcscore 3 FEV1_baseline 1.57 FEVpcpred 75.13237928 FVC 1.925624967 FVCZ -1.207033604 FVCpcpred 84.26953308 FEV1FVC 0.815319743 FEV1FVCZ -1.499698215 cd4 NA vload NA zwauk -1.8886598 zhauk -3.6806846 zbmiuk 0.45230114 vllog NA endtreatdate ['NA', '2019-09-03T00:00:00'] sp05time 10:15:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-18T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 8 lastvisitdate 2019-02-18T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548947 SAMN22246916 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-11-15 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3007 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15.7 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.159665 host_height 57.03082752 samp_size ['NA', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2017-11-15T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 39050 FinalReads_ASVpipeline 8958 sampling_induced_expectorated expectorated barcode BYD103T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 32629.03 templateDNA_16SqPCR_Cq 23.00182528 templateDNA_16SqPCR 0.023143899 well B05 plate_number P3 barcode_806R 806rcbc234 index_sequence GTCATTCACGAG DOB 2002-02-28T00:00:00 trial_arm Azithromycin adherence Adherent enrolmonth 2016-12 attendschool yes rs15antibty NA rs14antib NA dateart 2011-06-07T00:00:00 datehiv 2010-10-20T00:00:00 ageyart 9.27 duryart 5.56 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -3.130210341 weight 31 f24mrcscore 2 FEV1_baseline 1.28 FEVpcpred 57.03082752 FVC 1.673125029 FVCZ -2.659921312 FVCpcpred 67.16701864 FEV1FVC 0.765035457 FEV1FVCZ -1.885622262 cd4 385 vload 1510000 zwauk -4.2567172 zhauk -3.7792814 zbmiuk -2.8207591 vllog 6.178977 endtreatdate ['NA', '2017-11-15T00:00:00'] sp05time NA all_3 no visit012 no visit1218 yes visit018 no only2visits yes one_visit no endfollowup 2018-06-11T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-06-11T00:00:00 treatstopreason Completed cough_enrl yes cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548948 SAMN22246897 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-10-04 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3049 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 8.4 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 15.990325 host_height 71.38061769 samp_size ['1', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2017-09-30T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 43337 FinalReads_ASVpipeline 18217 sampling_induced_expectorated expectorated barcode BYC11CT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 557165.91 templateDNA_16SqPCR_Cq 18.91 templateDNA_16SqPCR 0.3952 well E01 plate_number P3 barcode_806R 806rcbc205 index_sequence TCGCATGAAGTC DOB 2009-04-30T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-08-02T00:00:00 datehiv 2015-05-15T00:00:00 ageyart 7.26 duryart 1.17 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.1460261 weight 23.8 f24mrcscore 3 FEV1_baseline 0.88 FEVpcpred 71.38061769 FVC 1.261250019 FVCZ -0.662888368 FVCpcpred 91.40420276 FEV1FVC 0.697720501 FEV1FVCZ -2.62395791 cd4 743 vload 0 zwauk -0.84518182 zhauk -1.4719398 zbmiuk 0.081678689 vllog 0 endtreatdate ['2018-09-05T00:00:00', '2018-09-05T00:00:00'] sp05time 08:56:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-20T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-20T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10548949 SAMN22246929 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-09-05 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3049 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 9.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.244032 host_height 103.6074761 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-09-05T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 58054 FinalReads_ASVpipeline 25307 sampling_induced_expectorated expectorated barcode BYD11BT3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 254.47 templateDNA_16SqPCR_Cq 30.27 templateDNA_16SqPCR 0.0001805 well E02 plate_number P3 barcode_806R 806rcbc213 index_sequence GATAGCTGTCTT DOB 2009-04-30T00:00:00 trial_arm Azithromycin adherence Not Adherent enrolmonth 2017-10 attendschool yes rs15antibty NA rs14antib no dateart 2016-08-02T00:00:00 datehiv 2015-05-15T00:00:00 ageyart 7.26 duryart 1.17 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z 0.284556523 weight 26.2 f24mrcscore 3 FEV1_baseline 1.42 FEVpcpred 103.6074761 FVC 1.597499967 FVCZ 0.241484961 FVCpcpred 103.0755005 FEV1FVC 0.888888881 FEV1FVCZ 0.038445876 cd4 1714 vload 39 zwauk -0.7736972 zhauk -1.3631442 zbmiuk 0.048038106 vllog 1.5910646 endtreatdate ['NA', '2018-09-05T00:00:00'] sp05time 10:15:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-20T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-20T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10549158 SAMN22246911 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-04-09 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3088 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 18.9 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 21.821068 host_height 68.24164801 samp_size ['2', ''] study_complt_stat study ended isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2018-03-31T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 46980 FinalReads_ASVpipeline 17148 sampling_induced_expectorated expectorated barcode BYC132T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 69445.36 templateDNA_16SqPCR_Cq 21.95912461 templateDNA_16SqPCR 0.049257872 well G04 plate_number P1 barcode_806R 806rcbc38 index_sequence CGGAGCTATGGT DOB 1999-05-10T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2018-04 attendschool yes rs15antibty NA rs14antib no dateart 2005-12-20T00:00:00 datehiv 2005-12-20T00:00:00 ageyart 6.61 duryart 12.3 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.3949366 weight 44 f24mrcscore 3 FEV1_baseline 1.47 FEVpcpred 68.24164801 FVC 1.730625033 FVCZ -2.094730131 FVCpcpred 72.72544224 FEV1FVC 0.849404117 FEV1FVCZ -0.907983547 cd4 257 vload 31700 zwauk -2.1075337 zhauk -3.581378 zbmiuk 0.13179554 vllog 4.5010591 endtreatdate ['2018-12-10T00:00:00', '2018-12-10T00:00:00'] sp05time 09:38:00 all_3 no visit012 yes visit1218 no visit018 no only2visits yes one_visit no endfollowup 2019-06-03T00:00:00 dow NA dod NA lastvisit 15 mths visittotno 6 lastvisitdate 2019-06-03T00:00:00 treatstopreason By Physician cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m yes any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10549159 SAMN22246918 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2017-12-07 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3008 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.1 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.777779 host_height 66.51893427 samp_size ['0.5', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2017-12-07T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 30511 FinalReads_ASVpipeline 9366 sampling_induced_expectorated expectorated barcode BYD105T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 325436.49 templateDNA_16SqPCR_Cq 19.56459633 templateDNA_16SqPCR 0.230833399 well F03 plate_number P3 barcode_806R 806rcbc222 index_sequence GCGACTTGTGTA DOB 1998-10-30T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-01 attendschool yes rs15antibty NA rs14antib no dateart 2004-11-08T00:00:00 datehiv NA ageyart 6.03 duryart 12.16 artdrug1stline yes artdrug2ndline no artreg EFV/NVP fev1z -2.563006059 weight 48.4 f24mrcscore 2 FEV1_baseline 2.22 FEVpcpred 66.51893427 FVC 3.28125 FVCZ -1.152066152 FVCpcpred 85.6521068 FEV1FVC 0.676571437 FEV1FVCZ -2.627288547 cd4 741 vload 0 zwauk -2.9554086 zhauk -1.7618465 zbmiuk -1.9320426 vllog 0 endtreatdate ['NA', '2018-12-06T00:00:00'] sp05time 09:10:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2018-05-23T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2018-05-23T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm 0 tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10549160 SAMN22246884 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2016-11-17 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3005 host_sex male host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 19.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 16.833599 host_height 74.44555014 samp_size ['5', ''] study_complt_stat death isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 0 visit_date 2016-11-10T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 47218 FinalReads_ASVpipeline 20072 sampling_induced_expectorated expectorated barcode BYC104T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 11457.34 templateDNA_16SqPCR_Cq 24.67635236 templateDNA_16SqPCR 0.008126739 well F05 plate_number P2 barcode_806R 806rcbc141 index_sequence GTATTACGATCC DOB 1997-07-11T00:00:00 trial_arm Placebo adherence Not Adherent enrolmonth 2016-11 attendschool yes rs15antibty NA rs14antib no dateart 2005-03-25T00:00:00 datehiv NA ageyart 7.7 duryart 11.65 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -1.9734808 weight 45 f24mrcscore 5 FEV1_baseline 2.44 FEVpcpred 74.44555014 FVC 3.053750038 FVCZ -1.507125366 FVCpcpred 81.25122652 FEV1FVC 0.79901761 FEV1FVCZ -1.151572127 cd4 487 vload 130000 zwauk -3.7389657 zhauk -1.9785727 zbmiuk -2.6425681 vllog 5.1139436 endtreatdate ['NA', 'NA'] sp05time 09:31:00 all_3 no visit012 no visit1218 no visit018 no only2visits no one_visit yes endfollowup 2017-04-05T00:00:00 dow NA dod 42830 lastvisit 3 mths visittotno 2 lastvisitdate 2017-02-27T00:00:00 treatstopreason Died cough_enrl yes cotrimoxazole yes adm no nadm NA tbtreat yes acut_exac12m no hospitalised12m yes reason_hospi meningitis cause not confirmed microbiologically antibiotic12m no any3_reasons 1 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10549161 SAMN22246927 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2018-08-22 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3042 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 14.8 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.623438 host_height 51.6546244 samp_size ['2', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 48 visit_date 2018-08-22T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 48669 FinalReads_ASVpipeline 23250 sampling_induced_expectorated expectorated barcode BYD116T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 262233.79 templateDNA_16SqPCR_Cq 20.03156755 templateDNA_16SqPCR 0.186003469 well D07 plate_number P1 barcode_806R 806rcbc59 index_sequence GGTGTCTATTGT DOB 2003-10-10T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-09 attendschool yes rs15antibty NA rs14antib no dateart 2009-06-15T00:00:00 datehiv 2009-06-15T00:00:00 ageyart 5.68 duryart 8.27 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -3.58685026 weight 47.4 f24mrcscore 2 FEV1_baseline 1.45 FEVpcpred 51.6546244 FVC 1.659374952 FVCZ -3.772553228 FVCpcpred 52.93967125 FEV1FVC 0.873823029 FEV1FVCZ -0.448434326 cd4 580 vload 34600 zwauk -0.75781792 zhauk 0.32872301 zbmiuk -1.0147096 vllog 4.5390763 endtreatdate ['NA', '2018-08-22T00:00:00'] sp05time 10:20:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-06T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated SRS10549162 SAMN22246959 2517771 human sputum metagenome bioproject 769290 PRJNA769290 collection_date 2019-02-06 env_broad_scale human env_local_scale respiratory tract env_medium sputum geo_loc_name Malawi: Blantyre host Homo sapiens lat_lon 15.77 S 35.02 E host_subject_id B3042 host_sex female host_tissue_sampled ['human respiratory', 'human respiratory'] host_age 15.3 ethnicity black host_occupation student host_disease HIV-associated chronic lung disease drug_usage NA host_hiv_stat yes host_body_mass_index 17.940908 host_height 58.7451305 samp_size ['3', ''] study_complt_stat completed 18 months isolation_source sputum pulmonary_disord HIV-associated chronic lung disease samp_mat_process stored in primestore samp_store_temp -80 °C smoker no group trial visit Week 72 visit_date 2019-02-06T00:00:00 run_processing_batch R1 sample_type SP RawReads_ASVpipeline 44849 FinalReads_ASVpipeline 20470 sampling_induced_expectorated expectorated barcode BYE131T3 sequencing_controls no sequencing_control_details NA WRrepeats NA WRrepeats_WP NA WRrepeats_BP NA BRrepeats NA EXrepeats NA nontemplate NA primestore_detail NA mock NA sample_extraction_controls no zymo_DNA no templateDNA_16SqPCR_copies 77032.91 templateDNA_16SqPCR_Cq 21.80869671 templateDNA_16SqPCR 0.054639746 well D08 plate_number P1 barcode_806R 806rcbc67 index_sequence GCACGACAACAC DOB 2003-10-10T00:00:00 trial_arm Placebo adherence Adherent enrolmonth 2017-09 attendschool yes rs15antibty NA rs14antib no dateart 2009-06-15T00:00:00 datehiv 2009-06-15T00:00:00 ageyart 5.68 duryart 8.27 artdrug1stline no artdrug2ndline yes artreg ATV/LPV/PI fev1z -3.085034515 weight 49.2 f24mrcscore 2 FEV1_baseline 1.7 FEVpcpred 58.7451305 FVC 2.638750076 FVCZ -1.424281265 FVCpcpred 81.58269318 FEV1FVC 0.644244433 FEV1FVCZ -3.078189747 cd4 NA vload NA zwauk -0.66875064 zhauk 0.47779077 zbmiuk -0.96228057 vllog NA endtreatdate ['NA', '2018-08-22T00:00:00'] sp05time 13:30:00 all_3 yes visit012 yes visit1218 yes visit018 yes only2visits no one_visit no endfollowup 2019-02-06T00:00:00 dow NA dod NA lastvisit 18 mths visittotno 7 lastvisitdate 2019-02-06T00:00:00 treatstopreason Completed cough_enrl no cotrimoxazole yes adm no nadm NA tbtreat no acut_exac12m no hospitalised12m no reason_hospi no antibiotic12m no any3_reasons 0 BioSampleModel MIMARKS.survey BioSampleModel MIGS/MIMS/MIMARKS.human-associated