Gut microbiome in late-presenting HIV, DTG vs DRV/r trial, Spain
271 faecal samples from adults with advanced HIV-1 infection in Spain, collected during a randomized trial comparing dolutegravir vs. ritonavir-boosted darunavir as first-line antiretroviral therapy. machine-written summary
271 samples · 271 runs · ES · Adult · 2024 · 6.72 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,355 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 16 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12960958 |
| ✓ Supplementary tables | 2,348 sample values (age, bmi, health condition, health condition detail, intervention, medication, sex, subject id) |
| – 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 not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design randomized_controlled_trial · population other_infection · Lamivudine/abacavir plus dolutegravir vs ritonavir-boosted darunavir (ART)
“randomized (1:1) to initiate lamivudine/abacavir plus either dolutegravir or ritonavir-boosted darunavir” — abstract:41781390 (study level; per-sample arms are in the intervention column below)
longitudinal
79 of 88 people sampled more than once (254 samples; median 3, up to 4 per person) · follow-up median 22 mo (max 22 mo) · median interval between samples 11 mo (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Faecal samples at day 1 (baseline) and weeks 24, 48 and 96”; stated follow-up 22 mo.
Each row is one person (36 shown of 79); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 243 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 | 271 | 100% | ||||
| country | 271 | 100% | 271 | |||
| health_condition | 271 | 100% | 263 | 8 | ||
| subject_id | 263 | 97% | 263 | |||
| collection_date | 271 | 100% | 271 | |||
| detailed_location | 271 | 100% | ||||
| health_condition_detail | 271 | 100% | 263 | 8 | ||
| latitude | 271 | 100% | 271 | |||
| location_region | 271 | 100% | 271 | |||
| longitude | 271 | 100% | 271 | |||
| age_at_collection_days | 263 | 97% | 263 | |||
| intervention | 263 | 97% | 263 | |||
| medication | 263 | 97% | 263 | |||
| sex | 263 | 97% | 263 | |||
| timepoint_label | 263 | 97% | 263 | |||
| bmi | 244 | 90% | 244 |
- Dolutegravir restores gut microbiota in late-stage HIV-1 unlike darunavir: an open-label, randomized clinical trial. 2026 PMID 41781390 PMC12960958 own_data
Archive description
This was a substudy of the ADVANZ-4 trial (EudraCT: 2014-002281-70, ClinicalTrials.gov: NCT02337322), an open-label 2-arm randomized clinical trial where ART-naïve subjects with CD4+<100 cells/ml at diagnosis were randomised 1:1 to initiate dolutegravir (50 mg QD) or ritonavir-boosted darunavir (800/100 mg QD) in addition to co-formulated lamivudine (300 mg QD) / abacavir (150 mg QD). All subjects received cotrimoxazole prophylaxis until their CD4+ counts improved >200 cells/mm3. Study participants were followed prospectively for 96 weeks. Faecal samples were collected on day 1 of study medication intake (baseline) and on weeks 24, 48 and 96. For this microbiome analysis we used a modified intention to treat (mITT2) approach where only study participants who provided faecal samples at baseline or in at least two timepoints during the study follow-up were analysed.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “ART-naïve subjects with CD4+<100 cells/ml”
- body site run.scientific_name · “feces metagenome”
- body site study.description · “Faecal samples were collected on day 1”
- life stage study.description · “CD4+<100 cells/ml at diagnosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115761322 | age_at_collection_days | 10957.5 | R2 | 0.75 | paper.supp.sup_fig_4C_rmcorr.tsv[!age] | age=30 |
| SAMEA115761322 | bmi | 23.9 | R2 | 0.85 | paper.supp.sup_fig_1ABC_marker_abundance.tsv[!BMI] | 23.880301228695995 |
| SAMEA115761322 | collection_date | 2017-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-01 |
| SAMEA115761322 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA115761322 | health_condition | other_infection | R2 | 0.85 | paper.supp.fig_3D_dissimilarity.tsv[!HIV_Status] | ADZ4_100: HIV_Status=positive |
| SAMEA115761332 | health_condition | other_infection | R4 | 0.50 | paper.abstract | advanced HIV-1 infection |
| SAMEA115761322 | health_condition_detail | HIV_Status: positive | R2 | 0.85 | paper.supp.fig_3D_dissimilarity.tsv[!HIV_Status] | ADZ4_100: HIV_Status=positive |
| SAMEA115761332 | health_condition_detail | advanced HIV-1 infection with median CD4+ T cells of 34 cells/mm3 | R4 | 0.50 | paper.abstract | advanced HIV-1 infection |
| SAMEA115761322 | intervention | drug_therapy | R2 | 0.85 | paper.supp.fig_3D_dissimilarity.tsv[!type] | ADZ4_100: type=DTG |
| SAMEA115761322 | latitude | 40.4637 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 40.463667 -3.74922 |
| SAMEA115761322 | location_region | Madrid | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 40.463667 -3.74922 |
| SAMEA115761322 | longitude | -3.7492 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 40.463667 -3.74922 |
| SAMEA115761322 | medication | antiretroviral | R2 | 0.85 | paper.supp.sup_fig_1ABC_marker_abundance.tsv[!treatment] | ADZ4_100: treatment=DTG |
| SAMEA115761322 | sex | male | R2 | 0.80 | paper.supp.fig_3G_rmcorr_treatment.tsv[!gender] | gender=male |
| SAMEA115761322 | subject_id | A020 | R2 | 0.85 | paper.supp.sup_fig_1ABC_marker_abundance.tsv[!record_id] | A020 |
| SAMEA115761322 | timepoint_label | 24 | R2 | 0.85 | paper.supp.sup_fig_1ABC_marker_abundance.tsv[!time_point] | 24 |
Sequencing
271 runs over 271 samples · mean 6.73 Gbp per run (median 6.72 Gbp, total 1,824.63 Gbp; 271 runs with a base count) · layout PAIRED 271 · platform ILLUMINA 271 · models Illumina HiSeq 2500 (271) · 90% of runs with a Sandpiper profile · first public 2024-10-10
Authors (17)
Català-Moll F first · Blázquez-Bondia C · Farré-Badia J · Torres F · Manzardo C · Bonfill E · Curran A · Domingo P · Podzamczer D · Force L · Falcó V · Parera M · Casadellà M · Miró JM · Noguera-Julian M · Paredes R · ADVANZ-4 MISTRAL investigators last
Downloads
PRJEB76817.csv.gz (10.0 KB) · parquet (82.7 KB) — all 271 samples, every field with route and confidence · PRJEB76817_determinations.csv.gz (31.1 KB) — 3,719 evidence rows