Gut/oral microbiome in MSM before HIV-1 infection, USA
463 gut and oral samples from men who have sex with men (MSM) in the USA, comparing those who later acquired HIV-1 to those who remained uninfected, in a longitudinal design. machine-written summary
463 samples · 463 runs · US · Adult · 2025 · 4.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 926 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 463 sample values (sex) · PMC12635353 |
| ○ 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 |
Genera, mean relative abundance over 211 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 | 463 | 100% | ||||
| country | 463 | 100% | 463 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 463 | 100% | 463 | |||
| sex | 463 | 100% | 463 |
- A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection. 2025 PMID 41266305 PMC12635353 own_data
Archive description
This study aims to characterize gut and oral microbial profiles in Men who have Sex with Men (MSM) prior to HIV-1 infection.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- life stage study.description · “Men who have Sex with Men (MSM)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN50500414 | collection_date | 1984/1985 | R1 | 0.90 | biosample.attribute:collection_date | 1984/1985 |
| SAMN50500414 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN50500414 | sex | male | R3 | 0.70 | paper.fulltext.methods | 239 MSM enrolled in the MACS |
Sequencing
463 runs over 463 samples · mean 4.75 Gbp per run (median 4.59 Gbp, total 2,197.27 Gbp; 463 runs with a base count) · layout PAIRED 463 · platform ILLUMINA 463 · models Illumina NovaSeq X (463) · 93% of runs with a Sandpiper profile · first public 2025-10-23
Authors (12)
Fouladi F first · Chen Y · Bera S · Jarmusch AK · Van Tyne D · Palella FJ · Margolick JB · Chew KW · Sun J · Martinson J · Rinaldo CR · Peddada SD last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1303200.csv.gz (10.8 KB) · parquet (85.3 KB) — all 463 samples, every field with route and confidence · PRJNA1303200_determinations.csv.gz (5.9 KB) — 1,389 evidence rows