Gut microbiome in HIV patients before/after ART, Mali
Case-control study of 82 gut microbiome samples from adults in Mali, comparing people living with HIV (pre-ART, 6 and 12 months post-ART) to HIV-negative individuals using whole-genome metagenomic sequencing. machine-written summary
82 samples · 82 runs · ML · Age unknown · 2025 · 7.28 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 328 sample values (collection date, country, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 82 sample values (antibiotic exposure) · PMC12323315 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Stool collected at enrollment/pre-ART (M0), 6 months (M6), and 12 months (M12) after ART initiation; healthy controls sampled at matching M0/M6/M12 visits” (time origin: enrolment); stated follow-up 12 mo.
Genera, mean relative abundance over 76 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 | 82 | 100% | ||||
| country | 82 | 100% | 82 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 82 | 100% | 82 | |||
| collection_date | 82 | 100% | 82 | |||
| latitude | 82 | 100% | 82 | |||
| longitude | 82 | 100% | 82 |
- The human gut microbiome and its metabolic pathway dynamics before and during HIV antiretroviral therapy. 2025 PMID 40522093 PMC12323315 own_data
Archive description
The human gut microbiome consists of highly complex microbial populations that play important roles in disease pathogenesis. Changes in the gut microbiome are associated with HIV infection. However, it is unclear whether the gut microbiome dysbiosis is causally linked to disease or whether it simply reflects disease-induced changes in the host immune and metabolic systems. This study aims to describe and compare intestinal microbial compositions and derived metabolic pathways in people living with HIV (PL-HIV) from prior to antiretroviral therapy (ART) to six and twelve months after ART initiation, compared to HIV-negative individuals. Whole-genome microbiome sequencing coupled with bioinformatics analysis was used to characterize participants' intestinal microbial structures and derived metabolic pathways.</p><p>Pre- and post-ART gut microbiota characterization of PL-HIV revealed substantial dysbiosis compared to HIV-negative people. An enrichment of pro-inflammatory microorganisms was the hallmark of dysbiosis in the PL-HIV pre-ART, with a decline in Proteobacteria at six months of ART, continuing until twelve months of ART. Lower proportions of Bacteroidetes were noted pre-ART, but they increased slightly at six months of ART before decreasing again at twelve months of ART. Additionally, we reported metabolic changes that are particularly important for health and are associated with dysbiosis both before and post-ART. Alteration of the pyruvate fermentation to the isobutanol metabolic pathway persisted in PL-HIV after twelve months of ART, and this mechanism was correlated with a decrease in Ruminococcus bromii species. ART initiation appears to lead to changes in several crucial metabolic pathways and may not entirely restore the dysbiosis of the gut microbiota caused by HIV.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “The Human Gut Microbiome”
- body site study.title · “Human Gut Microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48287807 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic treatment in the 4 weeks prior to enrollment |
| SAMN48287807 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN48287807 | country | ML | R1 | 0.90 | sample.attr.geo_loc_name | Mali |
| SAMN48287807 | latitude | 17.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 17.57 N 3.99 W |
| SAMN48287807 | longitude | -3.9900 | R1 | 0.90 | biosample.attribute:lat_lon | 17.57 N 3.99 W |
Sequencing
82 runs over 82 samples · mean 7.91 Gbp per run (median 7.28 Gbp, total 648.85 Gbp; 82 runs with a base count) · layout PAIRED 82 · platform ILLUMINA 82 · models Illumina HiSeq 4000 (82) · 93% of runs with a Sandpiper profile · first public 2025-05-04
Authors (18)
Dolo O first · Coulibaly F · Somboro AM · Sun S · Diarra M · Maiga A · Bore S · Fofana DB · Marcelin AG · Diakite B · Kassogue Y · Holl JL · Calvez V · Traoré CB · Murphy R · Fodor AA · Maiga M · Maiga AI last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1257948.csv.gz (2.8 KB) · parquet (72.5 KB) — all 82 samples, every field with route and confidence · PRJNA1257948_determinations.csv.gz (2.5 KB) — 410 evidence rows