Strain tracking in children/mothers, urban/rural Kenya
511 stool samples from children and mothers in urban and rural communities in Kenya, longitudinal cohort design, studying bacterial strain-sharing and the impact of community-level water chlorination. machine-written summary
511 samples · 511 runs · KE · Infant / toddler · 2026 · 11.83 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,533 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
households — not resolvedmother–infant — not resolved
511 stool samples from children and mothers in Kenyan households/communities; strain-sharing studied within/between households and communities..
Genera, mean relative abundance over 496 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 | 0 | 0% | ||||
| country | 511 | 100% | 511 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 511 | 100% | 511 | |||
| collection_date | 511 | 100% | 511 |
- Metagenomic strain tracking reveals patterns of bacterial spread and the impact of water chlorination 2026 own_data
Archive description
Childhood bacterial enteric infections remain a significant public health challenge in low- and middle-income countries. However, the mechanisms underlying bacterial exchange among humans are poorly understood. Here, we collected 511 stool samples from children and mothers across urban and rural communities in Kenya and applied a machine learning-based strain-tracking framework to investigate bacterial strain-sharing dynamics and evaluate the impact of community-level water chlorination. This study provides new insights into how bacterial strains disseminate within and between households and communities in low- and middle-income settings. By integrating metagenomic sequencing with machine learning, it elucidates both the microbial dissemination dynamics and the extent to which community-scale water treatment can disrupt microbial spread, informing strategies to mitigate pathogen transmission in vulnerable populations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and 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.description · “we collected 511 stool samples from children”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage study.title · “strain tracking among children in urban and”
- life stage study.description · “Childhood bacterial enteric infections”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “from children and mothers across urban and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN53062846 | collection_date | 2019-06-20 | R1 | 0.85 | biosample.attribute:collection_date | 2019-06-20 |
| SAMN53062846 | country | KE | R1 | 0.90 | biosample_attr | Kenya |
| SAMN53062846 | subject_id | stools_11001501 | R1 | 0.85 | biosample_attr | stools_11001501 |
Sequencing
511 runs over 511 samples · mean 11.68 Gbp per run (median 11.83 Gbp, total 5,970.73 Gbp; 511 runs with a base count) · layout PAIRED 511 · platform ILLUMINA 511 · models Illumina NovaSeq 6000 (511) · 97% of runs with a Sandpiper profile · first public 2026-02-22 – 2026-02-23
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1356541.csv.gz (16.2 KB) · parquet (94.9 KB) — all 511 samples, every field with route and confidence · PRJNA1356541_determinations.csv.gz (12.2 KB) — 1,533 evidence rows