Infant gut and nasal metagenomes, PediCAP trial, 5 countries
631 samples from infants in South Africa, Uganda, Zambia, Zimbabwe, and Belgium, collected within the randomized PediCAP trial; peri-rectal swabs underwent shotgun metagenomic sequencing and nasopharyngeal swabs underwent metaserotyping. machine-written summary
631 samples · 682 runs · ZA, UG, ZM · Infant / toddler · 2026 · 0.13 Gbp / sample · cohort Impact of co-amoxiclav versus amoxicillin on the g
One study deposited as 2 BioProjects (1,313 catalog samples together): PRJEB90577 · PRJNA1277853 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,262 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,893 sample values (antibiotic exposure, health condition, health condition detail) · PMC13530132 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “Peri-rectal swabs at randomization, at hospital discharge, and at follow-up visit 4 weeks after randomization” (time origin: intervention start); stated follow-up 28 d.
Genera, mean relative abundance over 342 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 | 631 | 100% | ||||
| country | 631 | 100% | 631 | |||
| health_condition | 631 | 100% | 631 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 631 | 100% | 631 | |||
| collection_date | 631 | 100% | 631 | |||
| health_condition_detail | 631 | 100% | 631 |
- Impact of co-amoxiclav versus amoxicillin on the gastrointestinal microbiota in sub-Saharan children hospitalized with pneumonia. 2026 PMID 42168578 PMC13530132 own_data
Archive description
Raw reads of the samples sequenced within the PediCAP trial (RIA2017MC). Peri-rectal swabs were sequenced using a shotgun metagenomic approach on a NextSeq instrument. Nasopharyngeal swabs were sequenced using a metaserotyping approach on a MinION instrument.
How this project entered the registry
Classified as human gut / stool / nasal / nasopharyngeal 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.description · “trial (RIA2017MC). Peri- rectal swabs were sequenced”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “a NextSeq instrument. Nasopharyngeal swabs were sequenced”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA118568681 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.methods_results | Patients received initial WHO-standard IV therapy before being randomized to continue IV therapy or step-down to oral amoxicillin or co-amoxiclav |
| SAMEA118568681 | collection_date | 2022-01-12 | R1 | 0.85 | biosample.attribute:collection_date | 2022-01-12 |
| SAMEA118568681 | country | ZA | R1 | 0.90 | biosample_attr | South Africa |
| SAMEA118568681 | health_condition | other_infection | R3 | 0.70 | paper.fulltext.methods_results | 149 children (<6 years) from South Africa, Zambia, Zimbabwe and Uganda presenting with severe CAP |
| SAMEA118568681 | health_condition_detail | severe community-acquired pneumonia (CAP) | R3 | 0.70 | paper.fulltext.methods_results | 149 children (<6 years) from South Africa, Zambia, Zimbabwe and Uganda presenting with severe CAP |
Sequencing
682 runs over 631 samples · mean 1.54 Gbp per run (median 0.13 Gbp, total 1,050.39 Gbp; 682 runs with a base count) · layout PAIRED 682 · platform ILLUMINA 682 · models NextSeq 500 (682) · 52% of runs with a Sandpiper profile · first public 2026-01-12
Authors (0)
No author record.
Downloads
PRJEB90577.csv.gz (17.4 KB) · parquet (98.5 KB) — all 631 samples, every field with route and confidence · PRJEB90577_determinations.csv.gz (19.4 KB) — 3,155 evidence rows