Gut microbiome in virally suppressed PLHIV, Nijmegen
Cross-sectional study of 143 samples from adults with HIV on long-term antiretroviral therapy (virally suppressed) in Nijmegen, Netherlands, examining gut microbiome dysbiosis and cytokine production capacity. machine-written summary
143 samples · 143 runs · NL · Adult · 2022 · 7.35 Gbp / sample · cohort Gut dysbiosis associates with cytokine production
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what each source gave
| ✓ Sequence archive | 1,001 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ✓ Abstract / description | 429 sample values (health condition, health condition detail, location site) |
| – 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 |
Genera, mean relative abundance over 129 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 | 143 | 100% | ||||
| country | 143 | 100% | 143 | |||
| health_condition | 143 | 100% | 143 | |||
| subject_id | 143 | 100% | 143 | |||
| collection_date | 143 | 100% | 143 | |||
| detailed_location | 143 | 100% | ||||
| health_condition_detail | 143 | 100% | 143 | |||
| latitude | 143 | 100% | 143 | |||
| location_locality | 143 | 100% | 143 | |||
| location_region | 143 | 100% | 143 | |||
| location_site | 143 | 100% | 143 | |||
| longitude | 143 | 100% | 143 |
- Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV. 2023 PMID 37583444 PMC10425223 unsure
Archive description
Raw metagenomic sequencing data of 143 people living with HIV (PLHIV). The included PLHIV were on long-term anti-virus treatment (median 6.35 years) and were virally suppressed (plasma HIV-RNA < 200 copies/mL). All participants are Caucasian individuals recruited from the HIV clinic of the Radboud University Medical Center between December 2015 and February 2017.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut microbiome in viral-suppressed”
- body site external_curation.infant_catalog · “body_site_call gut”
- body site study.description · “virally suppressed ( plasma HIV-RNA < 200”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27015179 | collection_date | 2015-12-21 | R1 | 0.90 | biosample.attribute:collection_date | 2015-12-21 |
| SAMN27015179 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands: Nijmegen |
| SAMN27015179 | health_condition | other_infection | R4 | 0.50 | study.description | virally suppressed (plasma HIV-RNA < 200 copies/mL) |
| SAMN27015179 | health_condition_detail | viral-suppressed people living with HIV on long-term antiretroviral therapy | R4 | 0.50 | study.description | virally suppressed (plasma HIV-RNA < 200 copies/mL) |
| SAMN27015179 | latitude | 51.8449 | R1 | 0.90 | biosample.attribute:lat_lon | 51.8449 N 5.8428 E |
| SAMN27015179 | location_locality | Nijmegen | R1 | 0.85 | biosample.attribute:geo_loc_name | Netherlands: Nijmegen |
| SAMN27015179 | location_region | Gelderland | R1 | 0.60 | biosample.attribute:lat_lon | 51.8449 N 5.8428 E |
| SAMN27015179 | location_site | HIV clinic of the Radboud University Medical Center | R4 | 0.45 | ena.study_description | recruited from the HIV clinic of the Radboud University Medical Center |
| SAMN27015179 | longitude | 5.8428 | R1 | 0.90 | biosample.attribute:lat_lon | 51.8449 N 5.8428 E |
| SAMN27015179 | subject_id | Individual 1 | R1 | 0.85 | biosample.attribute:differentiating information | Individual 1 |
Sequencing
143 runs over 143 samples · mean 7.53 Gbp per run (median 7.35 Gbp, total 1,077.30 Gbp; 143 runs with a base count) · layout PAIRED 143 · platform ILLUMINA 143 · models Illumina HiSeq 2000 (143) · 90% of runs with a Sandpiper profile · first public 2022-04-01
Authors (15)
Zhang Y first · Andreu-Sánchez S · Vadaq N · Wang D · Matzaraki V · van der Heijden WA · Gacesa R · Weersma RK · Zhernakova A · Vandekerckhove L · de Mast Q · Joosten LAB · Netea MG · van der Ven AJAM · Fu J last
Downloads
PRJNA820547.csv.gz (5.0 KB) · parquet (77.7 KB) — all 143 samples, every field with route and confidence · PRJNA820547_determinations.csv.gz (10.1 KB) — 1,430 evidence rows