Gut virome in HIV-1 patients on ART vs controls, Sweden
Case-control study of 24 gut metagenome samples from Sweden (13 from HIV-1-infected individuals on antiretroviral therapy, 11 HIV-negative controls), profiling the gut DNA virome using shotgun metagenomic sequencing. machine-written summary
24 samples · 24 runs · SE · Age unknown · 2021 · 12.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 48 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 61 sample values (location locality, medication, subject id) · PMC11320835, PMC13285549, PMC8267369 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 120 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 22 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 | 24 | 100% | ||||
| country | 24 | 100% | 24 | |||
| health_condition | 24 | 100% | 24 | |||
| subject_id | 24 | 100% | 24 | |||
| age_at_collection_days | 24 | 100% | 24 | |||
| antibiotic_exposure | 24 | 100% | 24 | |||
| collection_date | 24 | 100% | 24 | |||
| detailed_location | 24 | 100% | ||||
| health_condition_detail | 24 | 100% | 24 | |||
| location_locality | 24 | 100% | 24 | |||
| sex | 24 | 100% | 24 | |||
| medication | 13 | 54% | 13 |
- Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. 2021 PMID 34248876 PMC8267369 own_data
- Species-level virome profiling reveals compositional differences in the gut prokaryotic DNA virome of people with HIV-1 on antiretroviral therapy. 2026 PMID 42339316 PMC13285549 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
Gut microbiome plays a significant role in HIV-1 immunopathogenesis as well as in HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene amplicon sequencing, which is limited in taxonomic resolution at bacterial genus level at best, and inferred functionality. In this study, we performed Shotgun metagenome sequencing in HIV-1 infected individuals on antiretroviral therapy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host study.title · “HIV-1 infected individuals”
- host run.host_tax_id · “9606”
- body site study.title · “gut microbiome”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17372208 | age_at_collection_days | 15705.75 | R2 | 0.75 | external.cmd source | age: 43; age_unit: (empty); age_group: Adult |
| SAMN17372208 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN17372208 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN17372208 | country | SE | R1 | 0.90 | sample.attr.geo_loc_name | Sweden |
| SAMN17372208 | health_condition | other_infection | R2 | 0.75 | external.cmd source | disease: HIV Infection |
| SAMN17372208 | health_condition_detail | HIV Infection | R2 | 0.75 | external.cmd source | disease: HIV Infection |
| SAMN17372208 | location_locality | Stockholm | R3 | 0.70 | paper.fulltext.methods | Karolinska University Hospital, Stockholm, Sweden |
| SAMN17372208 | medication | antiretroviral | R3 | 0.85 | paper.body.TABLE 1[ART at sampling date] | Abacavir/Lamivudine/Dolutegravir |
| SAMN17372208 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMN17372208 | subject_id | SAMN17372208 | R3 | 0.75 | design.one_sample_per_subject:fulltext | This cross-sectional study included HIV-1-ART patients who were recruited from the outpatient clinic |
Sequencing
24 runs over 24 samples · mean 12.66 Gbp per run (median 12.53 Gbp, total 303.77 Gbp; 24 runs with a base count) · layout PAIRED 24 · platform ILLUMINA 24 · models Illumina NovaSeq 6000 (24) · 92% of runs with a Sandpiper profile · first public 2021-07-04
Authors (43)
Bai X first · Narayanan A · Nowak P · Ray S · Neogi U · Sönnerborg A last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M 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 · Zhang J first · Matussek A
Downloads
PRJNA692830.csv.gz (1.7 KB) · parquet (71.3 KB) — all 24 samples, every field with route and confidence · PRJNA692830_determinations.csv.gz (3.4 KB) — 229 evidence rows