Gut microbiome and HIV-1 reservoir size in PLWH on ART, Sweden
Cross-sectional shotgun metagenomic study of 30 fecal samples from people living with HIV on long-term ART in Sweden, examining links between gut microbiome composition and blood HIV-1 reservoir size. machine-written summary
30 samples · 30 runs · SE · Adult · 2025 · 10.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (age, collection date, country, health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 90 sample values (antibiotic exposure, location locality, location site) · PMC13063484 |
| ○ 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 |
Genera, mean relative abundance over 29 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 | 30 | 100% | ||||
| country | 30 | 100% | 30 | |||
| health_condition | 30 | 100% | 30 | |||
| subject_id | 30 | 100% | 30 | |||
| age_at_collection_days | 30 | 100% | 30 | |||
| antibiotic_exposure | 30 | 100% | 30 | |||
| collection_date | 30 | 100% | 30 | |||
| detailed_location | 30 | 100% | ||||
| health_condition_detail | 30 | 100% | 30 | |||
| location_locality | 30 | 100% | 30 | |||
| location_site | 30 | 100% | 30 | |||
| sex | 30 | 100% | 30 |
- Linking gut microbiome to HIV-1 reservoir size in people living with HIV. 2026 PMID 41913289 PMC13063484 own_data
Archive description
Whole genome sequencing analysis of fecal samples collected from people living with HIV. Aim to identify microbial taxa and functional pathways that correlate with the size of the intact HIV reservoir, with the goal of uncovering novel microbiome-based targets for reservoir modulation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “fecal samples collected from people living with HIV”
- life stage sample.attr.age · “54 (n=21/30)”
- life stage sample.attr.age · “68 (n=9/30)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48534839 | age_at_collection_days | 12053.2 | R1 | 0.70 | sample.attr.age | 33 |
| SAMN48534839 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | excluding nine individuals who had received antibiotic treatment within three months |
| SAMN48534839 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMN48534839 | country | SE | R1 | 0.90 | sample.attr.geo_loc_name | Sweden |
| SAMN48534839 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:isolate | People living with HIV |
| SAMN48534839 | health_condition_detail | People living with HIV | R1 | 0.85 | biosample.attribute:isolate | People living with HIV |
| SAMN48534839 | location_locality | Stockholm | R3 | 0.70 | paper.fulltext.methods | Karolinska University Hospital, Stockholm, Sweden |
| SAMN48534839 | location_site | Karolinska University Hospital outpatient HIV clinic | R3 | 0.70 | paper.fulltext.methods | followed at the outpatient HIV clinic |
| SAMN48534839 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN48534839 | subject_id | 1 | R1 | 0.85 | sample.attr.subject_id | 1 |
Sequencing
30 runs over 30 samples · mean 10.92 Gbp per run (median 10.88 Gbp, total 327.70 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ILLUMINA 30 · models Illumina NovaSeq 6000 (30) · 97% of runs with a Sandpiper profile · first public 2025-09-03 – 2025-09-21
Authors (8)
Kieri O first · Narayanan A · Jütte BB · Svensson P · Aleman S · Sönnerborg A · Ray S · Nowak P last
Downloads
PRJNA1263627.csv.gz (2.0 KB) · parquet (71.9 KB) — all 30 samples, every field with route and confidence · PRJNA1263627_determinations.csv.gz (2.9 KB) — 300 evidence rows