Gut microbiome in HIV-1 infection, Barcelona
156 fecal samples from HIV-1-infected and HIV-negative control subjects in Barcelona, examining gut microbiome composition and bacterial richness in relation to HIV-1 status and risk factors; cross-sectional design. machine-written summary
156 samples · 156 runs · ES · Adult · 2018 · 3.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,759 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality) |
| ✓ Abstract / description | 156 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC11899578, PMC4816837, PMC6050633, PMC6629854, PMC9744196 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 156 sample values (antibiotic exposure) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “BCN0 subjects sampled once; 110 of them provided a second fecal sample 1 month later for internal validation; Stockholm cohort sampled once (external validation).” (time origin: enrolment); stated follow-up 30 d.
Genera, mean relative abundance over 145 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 | 156 | 100% | ||||
| country | 156 | 100% | 156 | |||
| health_condition | 156 | 100% | 156 | |||
| subject_id | 156 | 100% | 156 | |||
| age_at_collection_days | 156 | 100% | 156 | |||
| antibiotic_exposure | 156 | 100% | 156 | |||
| collection_date | 156 | 100% | 156 | |||
| detailed_location | 156 | 100% | ||||
| health_condition_detail | 156 | 100% | 156 | |||
| latitude | 156 | 100% | 156 | |||
| location_locality | 156 | 100% | 156 | |||
| location_region | 156 | 100% | 156 | |||
| longitude | 156 | 100% | 156 | |||
| sex | 156 | 100% | 156 | |||
| bmi | 138 | 88% | 138 | |||
| stool_consistency_bristol | 61 | 39% | 61 |
- Gut Microbiota Linked to Sexual Preference and HIV Infection. 2016 PMID 27077120 PMC4816837 own_data
- Balances: a New Perspective for Microbiome Analysis. 2018 PMID 30035234 PMC6050633 own_data
- Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data. 2019 PMID 31308384 PMC6629854 own_data
- SCNIC: Sparse correlation network investigation for compositional data. 2023 PMID 36001047 PMC9744196 own_data
- Disrupted microbial cross-feeding and altered L-phenylalanine consumption in people living with HIV. 2025 PMID 40072847 PMC11899578 own_data
4 more
- Pathogen elimination by probiotic Bacillus via signalling interference. 2018 PMID 30305736 PMC6202238
- Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation. 2020 PMID 33102244 PMC7546801
- Impaired gut microbiota-mediated short-chain fatty acid production precedes morbidity and mortality in people with HIV. 2023 PMID 37918403 PMC10872975
- Proportion-based normalizations outperform compositional data transformations in machine learning applications 2024 PMC10913632
Archive description
The precise effects of HIV-1 on the human microbiome are unclear. Initial cross-sectional studies provided contradictory associations between microbial richness and HIV status and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection, which have not been found in animal models or in studies matched for HIV-1 risk groups.</p><p>This was a cross-sectional study where we first tested 129 HIV-1-infected subjects and 27 HIV-negative controls in Barcelona (BCN0). Findings were internally validated in 110 subjects from BCN0 providing a second fecal sample 1 month later. External validation was obtained in 77 HIV-1-infected and 7 non-infected subjects from Stockholm. In all study participants, we produced MiSeq 16S rRNA data on fecal microbiomes and collected comprehensive metadata.
How this project entered the registry
Classified as human gut / stool 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 · “Human feces metagenome 16s rDNA”
- body site study.description · “providing a second fecal sample 1 month”
- 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 |
|---|---|---|---|---|---|---|
| SAMN04382182 | age_at_collection_days | 20434.0 | R1 | 0.85 | sample.attr.host_age | 56 |
| SAMN04382182 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN04382182 | bmi | 22.4 | R1 | 0.90 | sample.attr.host_body_mass_index | 22.4 |
| SAMN04382182 | collection_date | 2014-01-18 | R1 | 0.90 | biosample.attribute:collection_date | 2014-01-18 |
| SAMN04382182 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain: Barcelona |
| SAMN04382182 | health_condition | other_infection | R1 | 0.90 | biosample_attr | positive |
| SAMN04382185 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:hiv_serostatus | negative |
| SAMN04382182 | health_condition_detail | positive | R1 | 0.90 | sample.attr.hiv_serostatus | positive |
| SAMN04382182 | latitude | 41.3900 | R1 | 0.90 | biosample.attribute:lat_lon | 41.39 N 2.15 E |
| SAMN04382182 | location_locality | Barcelona | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Barcelona |
| SAMN04382182 | location_region | Catalonia | R1 | 0.60 | biosample.attribute:lat_lon | 41.39 N 2.15 E |
| SAMN04382182 | longitude | 2.1500 | R1 | 0.90 | biosample.attribute:lat_lon | 41.39 N 2.15 E |
| SAMN04382182 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN04382182 | stool_consistency_bristol | 2 | R1 | 0.70 | biosample.attribute:stool_consistency | hard |
| SAMN04382182 | subject_id | SAMN04382182 | R4 | 0.60 | design.one_sample_per_subject:description | we first tested 129 HIV-1-infected subjects and 27 HIV-negative controls in Barcelona (BCN0) |
Sequencing
156 runs over 156 samples · mean 3.87 Gbp per run (median 3.63 Gbp, total 604.16 Gbp; 156 runs with a base count) · layout PAIRED 156 · platform ILLUMINA 156 · models Illumina HiSeq 2500 (156) · 93% of runs with a Sandpiper profile · first public 2018-03-31
Authors (55)
Rivera-Pinto J first · Egozcue JJ · Pawlowsky-Glahn V · Paredes R · Noguera-Julian M · Calle ML last · Shaffer M first · Thurimella K · Sterrett JD · Lozupone CA last · Sereti I first · Verburgh ML · Gifford J · Lo A · Boyd A · Verheij E · Verhoeven A · Wit FWNM · Schim van der Loeff MF · Giera M · Kootstra NA · Reiss P · Vujkovic-Cvijin I last · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · Nguyen HD first · Kim WK last · Huang S first · Chaudhari DS · Shukla R · Kanani P · Zeidan RS · Lin Y · Burrow W · Mankowski RT · Jain S · Yadav H last · Yerke A first · Fry Brumit D · Fodor A last
Downloads
PRJNA307231.csv.gz (6.3 KB) · parquet (80.1 KB) — all 156 samples, every field with route and confidence · PRJNA307231_determinations.csv.gz (17.2 KB) — 2,071 evidence rows