Gut metagenome in MSM before/after HIV seroconversion
Longitudinal study of 139 gut metagenome samples from men who have sex with men in Los Angeles, Chicago, and Peru, comparing those who acquired HIV to matched at-risk controls. machine-written summary
139 samples · 139 runs · US, PE · Adult · 2023 · 0.85 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,239 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 139 sample values (sex) · PMC13562672, PMC9520213 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 34 sample values (health condition) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
55 of 55 people sampled more than once (139 samples; median 2, up to 5 per person) · follow-up median 12 mo (max 2.0 y) · median interval between samples 6 mo (time from collection dates). Schedule stated by the source: “mSTUDY/HYM/RADAR visits every 6 months; Peru visits every 3 months; RevisedVisitNumber -2 to 3 relative to seroconversion”; stated follow-up 10 mo.
Each row is one person (36 shown of 55); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 109 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 | 139 | 100% | ||||
| country | 139 | 100% | 139 | |||
| health_condition | 139 | 100% | 105 | 34 | ||
| subject_id | 139 | 100% | 139 | |||
| health_condition_detail | 139 | 100% | 139 | |||
| latitude | 139 | 100% | 139 | |||
| longitude | 139 | 100% | 139 | |||
| sex | 139 | 100% | 139 | |||
| timepoint_label | 139 | 100% | 139 | |||
| collection_date | 116 | 83% | 116 | |||
| detailed_location | 92 | 66% | ||||
| location_locality | 92 | 66% | 92 | |||
| location_region | 92 | 66% | 92 |
- Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion. 2022 PMID 36179550 PMC9520213 own_data
- Commensal bacteria inhibit viral infections via a tryptophan metabolite. 2026 PMID 42722642 PMC13562672 unsure
Archive description
Alterations in the gut microbiome have been associated with HIV infection, but the relative impact of HIV versus other factors on the gut microbiome has been difficult to determine in cross-sectional studies using controls not at behavioral risk for HIV. To address this, we examined the gut microbiome, serum metabolome, and cytokines longitudinally within individuals before and after HIV seroconversion, and also compared those at risk who acquired HIV to matched control participants who did not.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut metagenome of MSM”
- body site study.description · “Alterations in the gut microbiome have been”
- body site study.description · “the gut microbiome, serum metabolome, and cytokines”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28157543 | collection_date | 2014-10-30 | R1 | 0.90 | biosample.attribute:collection_date | 2014-10-30 |
| SAMN28157543 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Los Angeles |
| SAMN28157545 | health_condition | other_infection | R1 | 0.90 | biosample_attr | Positive |
| SAMN28157543 | health_condition | other_infection | R2 | 0.75 | external.gmrepo source | phenotype: HIV Infections |
| SAMN28157543 | health_condition_detail | Negative | R1 | 0.90 | sample.attr.hivserostatus | Negative |
| SAMN28157543 | latitude | 34.0500 | R1 | 0.90 | biosample.attribute:lat_lon | 34.05 N 118.24 W |
| SAMN28157543 | location_locality | Los Angeles | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Los Angeles |
| SAMN28157543 | location_region | California | R1 | 0.60 | biosample.attribute:lat_lon | 34.05 N 118.24 W |
| SAMN28157543 | longitude | -118.2400 | R1 | 0.90 | biosample.attribute:lat_lon | 34.05 N 118.24 W |
| SAMN28157543 | sex | male | R3 | 0.60 | paper.fulltext.results | All participants were assigned male at birth |
| SAMN28157543 | subject_id | V140020 | R1 | 0.85 | sample.attr.pid | V140020 |
| SAMN28157543 | timepoint_label | revisedvisitnumber -2 | R1 | 0.85 | biosample.attribute:revisedvisitnumber | -2 |
Sequencing
139 runs over 139 samples · mean 1.07 Gbp per run (median 0.85 Gbp, total 149.30 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models Illumina HiSeq 4000 (139) · 78% of runs with a Sandpiper profile · first public 2023-06-05
Authors (36)
Fulcher JA first · Li F · Tobin NH · Zabih S · Elliott J · Clark JL · D'Aquila R · Mustanski B · Kipke MD · Shoptaw S · Gorbach PM · Aldrovandi GM last · Jiang D first · Soo N · Tan CY · Dankwa S · Wang HY · Theriot BS · Xue K · Hill D · Ardeshir A · Bain JR · Heston SM · Hurst JH · Siddiqui NY · Van Rompay KKA · Cervantes-Barragan L · Smith JP · Song R · Roper J · Kelly MS · Hudgens MG · De Paris K · Permar SR · Goswami R · Surana NK last
Downloads
PRJNA836336.csv.gz (5.5 KB) · parquet (77.6 KB) — all 139 samples, every field with route and confidence · PRJNA836336_determinations.csv.gz (11.3 KB) — 1,412 evidence rows