Gut metagenome in HIV-1 patients on ART, China, case-control
71 fecal samples from HIV-1 patients (on antiretroviral therapy) and healthy controls in China, comparing gut microbiota between immune responders and non-responders in a case-control design. machine-written summary
71 samples · 71 runs · CN · Age unknown · 2017 · 6.92 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 497 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ✓ Abstract / description | 71 sample values (subject id) |
| ✓ Full text | 223 sample values (antibiotic exposure, location locality, location site, sex) · PMC11320835, PMC6043814, PMC8191414 |
| ✓ Supplementary tables | 183 sample values (age, bmi, sex) |
| – 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 62 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 | 71 | 100% | ||||
| country | 71 | 100% | 71 | |||
| health_condition | 71 | 100% | 71 | |||
| subject_id | 71 | 100% | 71 | |||
| antibiotic_exposure | 71 | 100% | 71 | |||
| collection_date | 71 | 100% | 71 | |||
| detailed_location | 71 | 100% | ||||
| health_condition_detail | 71 | 100% | 71 | |||
| latitude | 71 | 100% | 71 | |||
| location_locality | 71 | 100% | 71 | |||
| location_region | 71 | 100% | 71 | |||
| location_site | 71 | 100% | 71 | |||
| longitude | 71 | 100% | 71 | |||
| sex | 71 | 100% | 61 | 10 | ||
| age_at_collection_days | 61 | 86% | 61 | |||
| bmi | 61 | 86% | 61 |
- Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients. 2018 PMID 30034377 PMC6043814 own_data
- Gut lactate-producing bacteria promote CD4 T cell recovery on Anti-retroviral therapy in HIV-infected patients. 2021 PMID 34141131 PMC8191414 own_data
- Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs. 2024 PMID 39138568 PMC11320835 unsure
Archive description
The study is set to sequencing the feces from HIV-1 patients to find out the difference in the taxonomy and pathway
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “sequencing the feces from HIV-1 patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07285620 | age_at_collection_days | 12418 | R2 | 0.85 | paper.supp.Table_1.XLSX[Table S1!Age] | 34 |
| SAMN07285610 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | Subjects who have used antibiotics, probiotics, or prebiotics |
| SAMN07285620 | bmi | 24.62 | R2 | 0.85 | paper.supp.Table_1.XLSX[Table S1!BMI (kg/m2)] | 24.622960911049557 |
| SAMN07285610 | collection_date | 2016-01-07 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01-07 |
| SAMN07285610 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN07285610 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | Control01 |
| SAMN07285610 | health_condition_detail | Control01 | R1 | 0.70 | sample.name_rule:title | Control01 |
| SAMN07285610 | latitude | 39.9200 | R1 | 0.90 | biosample.attribute:lat_lon | 39.92 N 116.42 E |
| SAMN07285610 | location_locality | Beijing | R3 | 0.70 | paper.fulltext.methods | Peking Union Medical College Hospital, China |
| SAMN07285610 | location_region | Beijing | R1 | 0.60 | biosample.attribute:lat_lon | 39.92 N 116.42 E |
| SAMN07285610 | location_site | Department of Infectious Diseases, Peking Union Medical College Hospital | R3 | 0.70 | paper.fulltext.methods | recruited from the Department of Infectious Diseases, Peking Union Medical College Hospital |
| SAMN07285610 | longitude | 116.4200 | R1 | 0.90 | biosample.attribute:lat_lon | 39.92 N 116.42 E |
| SAMN07285620 | sex | male | R2 | 0.80 | paper.supp.Table_1.XLSX[Table S1][Gendar] | Male |
| SAMN07285610 | sex | male | R3 | 0.60 | paper.fulltext.results | This study included 61 male subjects who had sex with men |
| SAMN07285610 | subject_id | SAMN07285610 | R4 | 0.65 | design.one_sample_per_subject:abstract | cross-sectional study on 30 healthy controls (HC) and 61 HIV-infected individuals |
Sequencing
71 runs over 71 samples · mean 7.23 Gbp per run (median 6.92 Gbp, total 513.60 Gbp; 71 runs with a base count) · layout PAIRED 71 · platform ILLUMINA 71 · models HiSeq X Ten (71) · 87% of runs with a Sandpiper profile · first public 2017-07-13
Authors (44)
Lu W first · Feng Y · Jing F · Han Y · Lyu N · Liu F · Li J · Song X · Xie J · Qiu Z · Zhu T · Routy B · Routy JP · Li T · Zhu B last · Lyu W first · Meng Q · Xiao J · Wang J · Zhu H · Shao C · Chu Y · Zhou Q · Jean-Pierre R · Yu J · Kang Y last · Belda E first · Capeau J · Zucker JD · Chatelier EL · Pons N · Oñate FP · Quinquis B · Alili R · Fellahi S · Katlama C · Clément K · Fève B · Jaureguiberry S · Goujard C · Lambotte O · Doré J · Prifti E · Bastard JP last
Downloads
PRJNA391226.csv.gz (3.7 KB) · parquet (76.6 KB) — all 71 samples, every field with route and confidence · PRJNA391226_determinations.csv.gz (9.3 KB) — 974 evidence rows