HIV Gut Microbiota Before and During ART, USA
75 shotgun metagenome samples from USA participants with HIV, studying intestinal microbiota at baseline, 24 weeks, and 48 weeks of antiretroviral therapy; longitudinal design. machine-written summary
75 samples · 75 runs · US · Age unknown · 2020 · 1.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 525 sample values (collection date, country, health condition, health condition detail, intervention, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention · arms resolved
10 people have samples in more than one arm.
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · Antiretroviral therapy (ART) initiation, sampled baseline/24wk/48wk
“Pre and Post Initiation of Antiretroviral Therapy” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
10 of 10 people sampled more than once (45 samples; median 5, up to 5 per person) · follow-up median 11 mo (max 11 mo) · median interval between samples 6 mo (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Baseline, 24 weeks ART, and 48 weeks ART per participant” (time origin: intervention_start); stated follow-up 11 mo.
Each row is one person (10 shown); dots are samples at days since that person's first sample.
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 | 0 | 0% | ||||
| country | 75 | 100% | 75 | |||
| health_condition | 75 | 100% | 75 | |||
| subject_id | 75 | 100% | 75 | |||
| collection_date | 75 | 100% | 75 | |||
| health_condition_detail | 75 | 100% | 75 | |||
| intervention | 75 | 100% | 75 | |||
| timepoint_label | 75 | 100% | 75 |
Archive description
Shotgun human metagenome raw sequence reads. Baseline, 24wks ART, and 48wk ART.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “Shotgun human metagenome raw sequence reads”
- body site study.title · “HIV Intestinal Microbiota”
- body site sample.attr.host_body_product · “Saliva (n=30/75)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14657279 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN14657279 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN14657279 | health_condition | other_infection | R1 | 0.85 | biosample_attr | HIV |
| SAMN14657279 | health_condition_detail | HIV | R1 | 0.90 | sample.attr.host_disease | HIV |
| SAMN14657279 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:description | description: Baseline |
| SAMN14657279 | subject_id | HIV001 | R1 | 0.70 | sample.name_rule:alias | A01_HIV001_0_136 |
| SAMN14657279 | timepoint_label | Baseline | R1 | 0.85 | biosample.attribute:description | description: Baseline |
Sequencing
75 runs over 75 samples · mean 1.26 Gbp per run (median 1.23 Gbp, total 94.55 Gbp; 75 runs with a base count) · layout PAIRED 75 · platform ILLUMINA 75 · models Illumina HiSeq 4000 (75) · 81% of runs with a Sandpiper profile · first public 2020-04-24
Authors (0)
No author record.
Downloads
PRJNA627223.csv.gz (2.7 KB) · parquet (72.7 KB) — all 75 samples, every field with route and confidence · PRJNA627223_determinations.csv.gz (4.0 KB) — 525 evidence rows