Infant Gut Microbiota Cohort, Dhaka, Bangladesh
1347 fecal samples from infants and neonates in Nandipara, Dhaka, Bangladesh, collected birth to two years as part of a longitudinal community-based cohort study of gut microbial diversity and metabolism. machine-written summary
1,347 samples · 1,347 runs · BD · Infant / toddler · 2022 · 3.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,388 sample values (age, country, subject id, timepoint) |
| ✓ Abstract / description | 4,041 sample values (collection date, location locality, location site) |
| ○ Full text | read; no usable statement or table · PMC11445081 |
| ○ 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
222 of 223 people sampled more than once (1,346 samples; median 6, up to 11 per person) · follow-up median 22 mo (max 2.0 y) · median interval between samples 4 mo (time from age at collection). Schedule stated by the source: “at birth, during subsequent scheduled visits, and when possible during illness episodes” (time origin: birth); stated follow-up 2.0 y.
Each row is one person (36 shown of 222); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 1,233 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 | 1,347 | 100% | ||||
| country | 1,347 | 100% | 1,347 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,347 | 100% | 1,347 | |||
| age_at_collection_days | 1,347 | 100% | 1,347 | |||
| collection_date | 1,347 | 100% | 1,347 | |||
| detailed_location | 1,347 | 100% | ||||
| location_locality | 1,347 | 100% | 1,347 | |||
| location_site | 1,347 | 100% | 1,347 | |||
| timepoint_label | 1,347 | 100% | 1,347 |
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. PMID 39242817 PMC11445081 curated
Archive description
The Microbiota and Health Study (clinicaltrials.gov: NCT02361164) was a longitudinal, community-based cohort study in Nandipara, a peri-urban community of Dhaka, Bangladesh conducted from April 2013 to October 2016. 267 newborns born to healthy mothers were followed from birth to two years of age. Fecal samples were collected at birth, during subsequent scheduled visits, and when possible during illness episodes. Active surveillance of diarrheal and respiratory infections was conducted by a community-based team of nurses supervised by a physician. Fecal samples of 222 participants were analyzed using metagenomic sequencing to characterize any undescribed gut microbial diversity and downstream contributions to gut metabolism.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “years of age. Fecal samples were collected”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “October 2016. 267 newborns born to healthy”
- life stage study.description · “born to healthy mothers were followed from”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN26285829 | age_at_collection_days | 304 | R1 | 0.90 | biosample_attr | 10 months |
| SAMN26285829 | collection_date | 2013-04/2016-10 | R4 | 0.45 | ena.study_description | conducted from April 2013 to October 2016 |
| SAMN26285829 | country | BD | R1 | 0.90 | biosample_attr | Bangladesh: Dhaka |
| SAMN26285829 | location_locality | Nandipara, Dhaka | R4 | 0.45 | ena.study_description | Nandipara, a peri-urban community of Dhaka |
| SAMN26285829 | location_site | Nandipara community | R4 | 0.45 | ena.study_description | community-based cohort study in Nandipara |
| SAMN26285829 | subject_id | R140 | R1 | 0.85 | biosample.attribute:misc_param | subject ID: R140 |
| SAMN26285829 | timepoint_label | 10 months | R1 | 0.70 | sample.title | Stool sample collected at the age of 10 months from subject R140 |
Sequencing
1,347 runs over 1,347 samples · mean 3.63 Gbp per run (median 3.27 Gbp, total 4,894.16 Gbp; 1,347 runs with a base count) · layout PAIRED 1,347 · platform ILLUMINA 1,347 · models Illumina NovaSeq 6000 (1,347) · 92% of runs with a Sandpiper profile · first public 2022-11-02
Authors (23)
Shao Y first · Garcia-Mauriño C · Clare S · Dawson NJR · Mu A · Adoum A · Harcourt K · Liu J · Browne HP · Stares MD · Rodger A · Brocklehurst P · Field N · Lawley TD last · Vidal K first · Sultana S · Patron AP · Binia A · Rahman M · Deeba IM · Brüssow H · Sakwinska O · Sarker SA last
Downloads
PRJNA806984.csv.gz (42.7 KB) · parquet (125.2 KB) — all 1,347 samples, every field with route and confidence · PRJNA806984_determinations.csv.gz (54.0 KB) — 9,429 evidence rows