Gut microbiome dynamics during TB antibiotic treatment in Haiti
367 longitudinal gut microbiome samples from adults undergoing multidrug-resistant and drug-sensitive tuberculosis treatment, mostly from Haiti, tracking microbiome recovery and antimicrobial resistance evolution during antibiotic therapy. machine-written summary
263 samples · 367 runs · HT · Adult · 2024 · 0.66 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,841 sample values (country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 263 sample values (location locality) · PMC11017772 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
55 of 55 people sampled more than once (263 samples; median 5, up to 6 per person). Schedule stated by the source: “Gut microbiome sampled repeatedly over 20 months of MDR-TB treatment and 6 months of drug-sensitive TB treatment” (time origin: intervention_start); stated follow-up 20 mo.
Genera, mean relative abundance over 339 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 263 | 100% | ||||
| country | 263 | 100% | 263 | |||
| health_condition | 263 | 100% | 263 | |||
| subject_id | 263 | 100% | 263 | |||
| detailed_location | 263 | 100% | ||||
| health_condition_detail | 263 | 100% | 263 | |||
| latitude | 263 | 100% | 263 | |||
| location_locality | 263 | 100% | 263 | |||
| location_region | 263 | 100% | 263 | |||
| longitude | 263 | 100% | 263 |
- Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption. 2024 PMID 38232140 PMC11017772 own_data
Archive description
Despite their therapeutic benefits, antibiotics exert collateral damage on the microbiome and promote antimicrobial resistance. However, the mechanisms governing microbiome recovery from antibiotics are poorly understood. Treatment of Mycobacterium tuberculosis, the world's most common infection, represents the longest antimicrobial exposure in humans. Here, we investigate microbiome dynamics over 20 months of multi-drug-resistant tuberculosis and 6 months of drug-sensitive TB treatment in humans. We find that microbiome dynamics and TB clearance are shared predictive cofactors of the resolution of TB-driven inflammation. The initial severe taxonomic and functional microbiome disruption, pathobiont domination, and enhancement of antibiotic resistance that initially accompanies long-term antibiotics is countered by surprising later recovery of commensals. This resilience is driven by the competing evolution of antimicrobial resistance mutations in pathobionts and commensals, with commensal strains with resistance mutations reestablishing dominance. FMT of the antibiotic-resistant commensal microbiome in mice recapitulates resistance to further antibiotic disruption. These findings demonstrate that antimicrobial resistance mutations in commensals can have paradoxically beneficial effects by promoting microbiome resilience to antimicrobials and identify microbiome dynamics as a predictor of disease resolution in antibiotic therapy of a chronic infection.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host run.scientific_name · “mouse gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “20 months of multi-drug-resistant tuberculosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN37719770 | country | HT | R1 | 0.90 | sample.attr.geo_loc_name | Haiti |
| SAMN37719770 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: human stool metagenome HRZE |
| SAMN37719770 | health_condition_detail | human stool metagenome HRZE | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: human stool metagenome HRZE |
| SAMN37719770 | latitude | 18.5900 | R1 | 0.90 | biosample.attribute:lat_lon | 18.59 N 72.31 W |
| SAMN37719770 | location_locality | Port-au-Prince | R3 | 0.70 | paper.fulltext.methods | GHESKIO) Centers (Port-au-Prince, Haiti) |
| SAMN37719770 | location_region | Ouest | R1 | 0.60 | biosample.attribute:lat_lon | 18.59 N 72.31 W |
| SAMN37719770 | longitude | -72.3100 | R1 | 0.90 | biosample.attribute:lat_lon | 18.59 N 72.31 W |
| SAMN37719770 | subject_id | 1830023T | R1 | 0.85 | sample.attr.patient_id | 1830023T |
Sequencing
367 runs over 263 samples · mean 0.93 Gbp per run (median 0.66 Gbp, total 342.50 Gbp; 367 runs with a base count) · layout SINGLE 263, PAIRED 104 · platform ILLUMINA 367 · models NextSeq 500 (367) · 92% of runs with a Sandpiper profile · first public 2024-01-24
Authors (15)
Bhattarai SK first · Du M · Zeamer AL · M Morzfeld B · Kellogg TD · Firat K · Benjamin A · Bean JM · Zimmerman M · Mardi G · Vilbrun SC · Walsh KF · Fitzgerald DW · Glickman MS · Bucci V last
Downloads
PRJNA1025016.csv.gz (6.5 KB) · parquet (78.9 KB) — all 263 samples, every field with route and confidence · PRJNA1025016_determinations.csv.gz (12.4 KB) — 2,104 evidence rows