Gut microbiome, drinking water chlorine, infants in Haiti
16 rectal swab samples from infants, young children, and one neonate in Mirebalais, Haiti, examining association between household drinking water free chlorine residue levels and gut microbiome composition; cross-sectional design. machine-written summary
137 samples · 137 runs · HT · Infant / toddler · 2025 · 0.84 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 335 sample values (age, country, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 411 sample values (collection date, location locality, location region) · PMC11500667 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Other administered intervention (see intervention_detail) design observational_with_procedure · population healthy_control · Household water chlorination (free chlorine residue levels) observed, not investigator-assigned
“association of free chlorine residue levels in the household drinking water” — bioproject.description (study level; per-sample arms are in the intervention column below)
age: two sequence archives disagree for 91 samples (e.g. 243.5 vs 2922.0) — withheld.
The sources disagree on 91 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 (40 of 91)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN39534460 | age | 243.5 (sequence archive) | 2922.0 (sequence archive) | withheld: neither value published |
| SAMN39534461 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN39534462 | age | 121.8 (sequence archive) | 1461.0 (sequence archive) | withheld: neither value published |
| SAMN39534463 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN39534464 | age | 456.6 (sequence archive) | 5479.0 (sequence archive) | withheld: neither value published |
| SAMN39534465 | age | 213.1 (sequence archive) | 2554.0 (sequence archive) | withheld: neither value published |
| SAMN39534466 | age | 578.3 (sequence archive) | 6939.0 (sequence archive) | withheld: neither value published |
| SAMN39534468 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534469 | age | 121.8 (sequence archive) | 1461.0 (sequence archive) | withheld: neither value published |
| SAMN39534472 | age | 608.8 (sequence archive) | 7305.0 (sequence archive) | withheld: neither value published |
| SAMN39534473 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN39534474 | age | 730.5 (sequence archive) | 8766.0 (sequence archive) | withheld: neither value published |
| SAMN39534476 | age | 882.7 (sequence archive) | 10601.0 (sequence archive) | withheld: neither value published |
| SAMN39534477 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN39534478 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534479 | age | 730.5 (sequence archive) | 8766.0 (sequence archive) | withheld: neither value published |
| SAMN39534480 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN39534482 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534483 | age | 1126.2 (sequence archive) | 13504.0 (sequence archive) | withheld: neither value published |
| SAMN39534484 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534485 | age | 730.5 (sequence archive) | 8766.0 (sequence archive) | withheld: neither value published |
| SAMN39534487 | age | 608.8 (sequence archive) | 7305.0 (sequence archive) | withheld: neither value published |
| SAMN39534490 | age | 121.8 (sequence archive) | 1461.0 (sequence archive) | withheld: neither value published |
| SAMN39534493 | age | 182.6 (sequence archive) | 2192.0 (sequence archive) | withheld: neither value published |
| SAMN39534494 | age | 1126.2 (sequence archive) | 13504.0 (sequence archive) | withheld: neither value published |
| SAMN39534495 | age | 334.8 (sequence archive) | 4019.0 (sequence archive) | withheld: neither value published |
| SAMN39534497 | age | 1156.6 (sequence archive) | 13878.5 (sequence archive) | withheld: neither value published |
| SAMN39534498 | age | 1369.7 (sequence archive) | 16436.2 (sequence archive) | withheld: neither value published |
| SAMN39534499 | age | 1308.8 (sequence archive) | 15696.8 (sequence archive) | withheld: neither value published |
| SAMN39534502 | age | 1126.2 (sequence archive) | 13504.0 (sequence archive) | withheld: neither value published |
| SAMN39534504 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN39534507 | age | 821.8 (sequence archive) | 9857.0 (sequence archive) | withheld: neither value published |
| SAMN39534508 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534510 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534511 | age | 913.1 (sequence archive) | 10957.5 (sequence archive) | withheld: neither value published |
| SAMN39534512 | age | 1430.6 (sequence archive) | 17151.0 (sequence archive) | withheld: neither value published |
| SAMN39534514 | age | 121.8 (sequence archive) | 1461.0 (sequence archive) | withheld: neither value published |
| SAMN39534515 | age | 365.2 (sequence archive) | 4383.0 (sequence archive) | withheld: neither value published |
| SAMN39534516 | age | 517.4 (sequence archive) | 6205.8 (sequence archive) | withheld: neither value published |
| SAMN39534518 | age | 1704.5 (sequence archive) | 20434.0 (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 14 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 | 137 | 100% | ||||
| country | 137 | 100% | 137 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 16 | 12% | 16 | |||
| collection_date | 137 | 100% | 137 | |||
| detailed_location | 137 | 100% | ||||
| location_locality | 137 | 100% | 137 | |||
| location_region | 137 | 100% | 137 | |||
| sex | 136 | 99% | 136 | |||
| age_at_collection_days | 46 | 34% | 46 |
- Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study. 2024 PMID 38977240 PMC11500667 own_data
Archive description
Safe drinking water is critical for prevention of enteric infections and diarrheal diseases. However, the effect of safe household water, sanitation, and hygiene interventions on the gut microbiome is not well understood. We accessed the association of free chlorine residue levels in the household drinking water with microbiome composition using rectal swabs of infants and young children in Haiti.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child and adult and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Gut microbiome of children”
- body site study.description · “interventions on the gut microbiome is not”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “rectal swabs of infants and young children”
- life stage study.title · “Gut microbiome of children in Haiti”
- life stage study.description · “infants and young children in Haiti.”
- life stage sample.attr.host_age · “24 (n=76/121)”
- life stage sample.attr.host_age · “12 (n=15/121)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39534467 | age_at_collection_days | 639.2 | R1 | 0.80 | biosample.attribute:host_age | host_age: 21 (months; 131 children from one month to five years of age living in |
| SAMN39534481 | age_at_collection_days | 1126 | R1 | 0.70 | sample.attr.host_age | 37 |
| SAMN39534460 | collection_date | 2017-05/2017-07 | R3 | 0.70 | paper.body.text | Participants were recruited in Mirebalais, a community in the Central Plateau of Haiti, between May and July 2017 |
| SAMN39534460 | country | HT | R1 | 0.90 | sample.attr.geo_loc_name | Haiti: Mirebalais |
| SAMN39534481 | country | HT | R1 | 0.90 | biosample_attr | Haiti: Mirebalais |
| SAMN39534460 | location_locality | Mirebalais | R3 | 0.70 | paper.body.text | Participants were recruited in Mirebalais, a community in the Central Plateau of Haiti, between May and July 2017 |
| SAMN39534460 | location_region | Centre | R3 | 0.70 | paper.body.text | We enrolled 131 participants <1 to 59 months of age from 108 households in the Centre Department of Haiti |
| SAMN39534460 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN39534481 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN39534481 | subject_id | 5910-DS-22 | R1 | 0.85 | biosample_attr | 5910-DS-22 |
Sequencing
137 runs over 137 samples · mean 0.82 Gbp per run (median 0.84 Gbp, total 111.69 Gbp; 137 runs with a base count) · layout PAIRED 137 · platform ILLUMINA 137 · models Illumina NovaSeq 6000 (137) · 88% of runs with a Sandpiper profile · first public 2025-01-02
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1067625.csv.gz (4.5 KB) · parquet (76.1 KB) — all 137 samples, every field with route and confidence · PRJNA1067625_determinations.csv.gz (5.0 KB) — 746 evidence rows