Cotrimoxazole trial, HIV-exposed infants, S. Africa
165 gut microbiome samples from HIV-exposed, uninfected infants and neonates in Durban, KwaZulu-Natal, South Africa, from a randomized controlled trial on prophylactic cotrimoxazole (antibiotic) effects. machine-written summary
165 samples · 165 runs · ZA · Infant / toddler · 2019 · 1.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,210 sample values (age, antibiotic exposure, collection date, country, delivery mode, intervention, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 208 sample values (feeding mode, location locality) · PMC10092070, PMC10175488, PMC10269646, PMC11019788, PMC11322291, PMC11494892, PMC11929092, PMC12769767, PMC7778358, PMC8518733, PMC9512645, PMC9622858 |
| ✓ Supplementary tables | 569 sample values (diet, feeding mode, preterm status, sex, timepoint) |
| – 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 resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · Prophylactic cotrimoxazole vs no cotrimoxazole in HEU infants
“Randomized control trial on the effects of prophylactic cotrimoxazole” — bioproject.description (study level; per-sample arms are in the intervention column below)
sex: supplementary table and sequence archive disagree for 7 samples (e.g. male vs female) — withheld.
The sources disagree on 7 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (7)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN12097529 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
| SAMN12097530 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
| SAMN12097531 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
| SAMN12097555 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
| SAMN12097556 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
| SAMN12097557 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
| SAMN12097558 | sex | male (supplementary table) | female (sequence archive) | withheld: neither value published |
longitudinal
61 of 64 people sampled more than once (162 samples; median 3, up to 4 per person) · follow-up median 4 mo (max 6 mo) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “archive time labels: pre-weaning, post-weaning, B, C, 1, A, Neonatal”.
Each row is one person (36 shown of 61); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 91 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 | 165 | 100% | ||||
| country | 165 | 100% | 165 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 165 | 100% | 165 | |||
| age_at_collection_days | 165 | 100% | 165 | |||
| antibiotic_exposure | 165 | 100% | 165 | |||
| collection_date | 165 | 100% | 165 | |||
| detailed_location | 165 | 100% | ||||
| feeding_mode | 165 | 100% | 122 | 43 | ||
| intervention | 165 | 100% | 165 | |||
| location_locality | 165 | 100% | 165 | |||
| timepoint_label | 165 | 100% | 21 | 144 | ||
| delivery_mode | 164 | 99% | 164 | |||
| sex | 157 | 95% | 35 | 122 | ||
| diet | 122 | 74% | 122 | |||
| preterm_status | 59 | 36% | 59 |
- Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants. PMID 31832638 PMC7778358 curated
- Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire. PMID 34152069 PMC8518733 curated
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858 curated
7 more
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
Archive description
Randomized control trial on the effects of prophylactic cotrimoxazole on developing HIV-exposed, uninfected infant gut microbiomes
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “HIV-exposed, uninfected infant gut microbiomes”
- body site study.description · “HIV-exposed, uninfected infant gut microbiomes”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “African HIV-exposed, uninfected infant gut microbiomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12097426 | age_at_collection_days | 43 | R1 | 0.90 | biosample_attr | 43 |
| SAMN12097426 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:CTX | y |
| SAMN12097426 | collection_date | 2014-05-20 | R1 | 0.85 | biosample.attribute:collection_date | 2014-05-20 |
| SAMN12097426 | country | ZA | R1 | 0.90 | biosample_attr | South Africa:Durban in KwaZulu-Natal |
| SAMN12097426 | delivery_mode | c_section | R1 | 0.90 | biosample_attr | 1 |
| SAMN12097428 | diet | exclusive_breast_milk | R2 | 0.85 | paper.supp.41522_2025_868_MOESM2_ESM.xlsx[Data S1!Feeding type] | Breast Milk |
| SAMN12097428 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Feeding type=Breast Milk |
| SAMN12097426 | feeding_mode | exclusive_breast | R3 | 0.40 | paper.fulltext.methods | all infants were exclusively breastfed |
| SAMN12097426 | intervention | antibiotic | R1 | 0.85 | biosample.attribute:CTX | y |
| SAMN12097426 | location_locality | Durban | R3 | 0.70 | paper.fulltext.methods | Cato Manor and Lancers Road Clinics in Durban |
| SAMN12097426 | preterm_status | term | R2 | 0.75 | paper.supp.table | premature=no |
| SAMN12097432 | sex | male | R1 | 0.85 | biosample.attribute:FemaleInfant | 0 |
| SAMN12097426 | sex | male | R2 | 0.75 | paper.supp.table | gender=male |
| SAMN12097426 | subject_id | 100 | R1 | 0.85 | biosample_attr | 100 |
| SAMN12097427 | timepoint_label | B | R1 | 0.85 | biosample.attribute:time | time: B |
| SAMN12097426 | timepoint_label | 1 | R2 | 0.75 | paper.supp.table | visit_number=1 |
Sequencing
165 runs over 165 samples · mean 1.08 Gbp per run (median 1.15 Gbp, total 178.52 Gbp; 165 runs with a base count) · layout PAIRED 165 · platform ILLUMINA 165 · models NextSeq 500 (165) · 55% of runs with a Sandpiper profile · first public 2019-11-01
Authors (59)
D'Souza AW first · Moodley-Govender E · Berla B · Kelkar T · Wang B · Sun X · Daniels B · Coutsoudis A · Trehan I · Dantas G last · Fontana F first · Mancabelli L · Lugli GA · Taracchini C · Alessandri G · Longhi G · Anzalone R · Viappiani A · Famo R · Brognan M · Micondo KH · Turroni F · Ventura M · D'Alfonso R · Milani C last · Tarracchini C · Bianchi MG · Rizzo SM · Argentini C · Vergna LM · Taurino G · Chiu M · Bussolati O · van Sinderen D · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Valles-Colomer M · Debelius J · Kurilshikov A · Pettersen VK last · Gennaioli E · Muscò A · Vitale SG · Angioni S
Downloads
PRJNA549787.csv.gz (7.1 KB) · parquet (79.8 KB) — all 165 samples, every field with route and confidence · PRJNA549787_determinations.csv.gz (16.3 KB) — 1,987 evidence rows