Infant gut microbiome, Zimbabwe, randomized trial
875 stool samples from rural Zimbabwean infants (and some neonates) studying gut microbiome maturation in relation to sanitation/nutrition interventions and maternal HIV infection, in a randomized trial with dietary supplement intervention. machine-written summary
875 samples · 1,750 runs · ZW · Infant / toddler · 2023 · 3.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,609 sample values (age, country, sex) |
| ✓ Abstract / description | 875 sample values (lifestyle detail) |
| ✓ Full text | 2,625 sample values (collection date, lifestyle, location region) · PMC11467582, PMC11929092, PMC9929340 |
| ✓ Supplementary tables | 3,636 sample values (antibiotic exposure, birth weight grams, delivery mode, preterm status, subject id, 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 not resolved
Non-microbial dietary supplement (vitamins design randomized_controlled_trial · population malnutrition · IYCF intervention with SQ-LNS vs WASH, growth trial
“randomized trial in rural Zimbabwe” — abstract:39341154 (study level; per-sample arms are in the intervention column below)
longitudinal
23 of 583 people sampled more than once (46 samples; median 2, up to 2 per person) · follow-up median 6 mo (max 18 mo) · median interval between samples 6 mo (time from age at collection).
Each row is one person (23 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 864 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 | 859 | 98% | ||||
| country | 875 | 100% | 875 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 606 | 69% | 606 | |||
| collection_date | 875 | 100% | 875 | |||
| detailed_location | 875 | 100% | ||||
| lifestyle | 875 | 100% | 875 | |||
| lifestyle_detail | 875 | 100% | 875 | |||
| location_region | 875 | 100% | 875 | |||
| sex | 875 | 100% | 875 | |||
| age_at_collection_days | 859 | 98% | 859 | |||
| antibiotic_exposure | 606 | 69% | 606 | |||
| birth_weight_grams | 606 | 69% | 606 | |||
| delivery_mode | 606 | 69% | 606 | |||
| preterm_status | 606 | 69% | 606 | |||
| timepoint_label | 606 | 69% | 606 |
- The gut microbiome and early-life growth in a population with high prevalence of stunting. PMID 36788215 PMC9929340 curated
- Bifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants. PMID 39341154 PMC11467582 curated
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092 curated
- Temperate phage microdiversity reflects infant gut microbiome maturation independent of chronic undernutrition curated
Archive description
The gut microbiome of rural Zimbabwean infants undergoes programmed maturation that is unresponsive to sanitation and nutrition interventions but is comprehensively modified by maternal HIV infection and can moderately predict linear growth.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Infant stool metagenomic datasets”
- body site study.description · “The gut microbiome of rural”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant stool metagenomic datasets”
- life stage study.description · “comprehensively modified by maternal HIV infection and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112437701 | age_at_collection_days | 36 | R1 | 0.90 | biosample_attr | 36 |
| SAMEA112437701 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.table | abx_ever=no |
| SAMEA112437701 | birth_weight_grams | 2900 | R2 | 0.75 | paper.supp.table | birth_weight=2900 |
| SAMEA112437701 | collection_date | 2012/2017 | R3 | 0.70 | paper.fulltext.methods | conducted between 2012 and 2017 |
| SAMEA112437701 | country | ZW | R1 | 0.90 | biosample_attr | Zimbabwe |
| SAMEA112437701 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | born_method=vaginal |
| SAMEA112437701 | lifestyle | rural_non_industrialized | R3 | 0.70 | paper.fulltext.abstract | rural Zimbabwean districts, Chirumanzu and Shurugwi |
| SAMEA112437701 | lifestyle_detail | rural Zimbabwean infants | R4 | 0.45 | ena.study_description | rural Zimbabwean infants undergoes programmed maturation |
| SAMEA112437701 | location_region | Chirumanzu and Shurugwi districts | R3 | 0.70 | paper.fulltext.methods | two rural Zimbabwean districts, Chirumanzu and Shurugwi |
| SAMEA112437701 | preterm_status | term | R2 | 0.75 | paper.supp.table | premature=no |
| SAMEA112437701 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMEA112437701 | subject_id | ERR10901352 | R2 | 0.75 | paper.supp.table | sequence_id=ERR10901352 |
| SAMEA112437701 | timepoint_label | 3 | R2 | 0.85 | paper.supp.mmc1.xlsx[Table S2!visit_number] | SHINE_00003: 3 |
Sequencing
1,750 runs over 875 samples · mean 1.60 Gbp per run (median 1.65 Gbp, total 2,802.79 Gbp; 1,750 runs with a base count) · layout PAIRED 1,750 · platform ILLUMINA 1,750 · models Illumina HiSeq X (1,202), Illumina HiSeq 2500 (548) · 91% of runs with a Sandpiper profile · first public 2023-02-14 – 2023-02-16
Authors (34)
Robertson RC first · Edens TJ · Carr L · Mutasa K · Gough EK · Evans C · Geum HM · Baharmand I · Gill SK · Ntozini R · Smith LE · Chasekwa B · Majo FD · Tavengwa NV · Mutasa B · Francis F · Tome J · Stoltzfus RJ · Humphrey JH · Prendergast AJ · Manges AR last · Mbuya MNN · Tavengwa N · Kosek M · Sanitation Hygiene Infant Nutrition Efficacy (SHINE) Trial Team last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Valles-Colomer M · Debelius J · Kurilshikov A · Pettersen VK last
Downloads
PRJEB51728.csv.gz (31.0 KB) · parquet (116.4 KB) — all 875 samples, every field with route and confidence · PRJEB51728_determinations.csv.gz (73.0 KB) — 9,745 evidence rows