Mother-infant dyads & breast milk antibiotic exposure, US
Longitudinal cohort of 572 fecal, breast milk, and skin swab samples from mothers and infants in San Diego, USA, studying indirect antibiotic exposure through breast milk and its impact on microbiome and metabolome. machine-written summary
572 samples · 665 runs · US · Infant / toddler · 2026 · 2.57 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,839 sample values (age, antibiotic exposure, collection date, country, family id, family role, sex, 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
age: two sequence archives disagree for 273 samples (e.g. 86 vs 1033.7) — withheld.
The sources disagree on 273 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 273)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA121748174 | age | 86 (sequence archive) | 1033.7 (sequence archive) | withheld: neither value published |
| SAMEA121748175 | age | 89 (sequence archive) | 1070.2 (sequence archive) | withheld: neither value published |
| SAMEA121748176 | age | 92 (sequence archive) | 1106.7 (sequence archive) | withheld: neither value published |
| SAMEA121748177 | age | 84 (sequence archive) | 1008.1 (sequence archive) | withheld: neither value published |
| SAMEA121748182 | age | 196 (sequence archive) | 2348.6 (sequence archive) | withheld: neither value published |
| SAMEA121748183 | age | 199 (sequence archive) | 2385.1 (sequence archive) | withheld: neither value published |
| SAMEA121748184 | age | 202 (sequence archive) | 2421.6 (sequence archive) | withheld: neither value published |
| SAMEA121748185 | age | 138 (sequence archive) | 1654.6 (sequence archive) | withheld: neither value published |
| SAMEA121748190 | age | 146 (sequence archive) | 1753.2 (sequence archive) | withheld: neither value published |
| SAMEA121748191 | age | 148 (sequence archive) | 1775.1 (sequence archive) | withheld: neither value published |
| SAMEA121748192 | age | 150 (sequence archive) | 1800.7 (sequence archive) | withheld: neither value published |
| SAMEA121748193 | age | 117 (sequence archive) | 1409.9 (sequence archive) | withheld: neither value published |
| SAMEA121748198 | age | 136 (sequence archive) | 1629.0 (sequence archive) | withheld: neither value published |
| SAMEA121748199 | age | 138 (sequence archive) | 1654.6 (sequence archive) | withheld: neither value published |
| SAMEA121748200 | age | 140 (sequence archive) | 1680.1 (sequence archive) | withheld: neither value published |
| SAMEA121748201 | age | 108 (sequence archive) | 1300.3 (sequence archive) | withheld: neither value published |
| SAMEA121748205 | age | 117 (sequence archive) | 1409.9 (sequence archive) | withheld: neither value published |
| SAMEA121748207 | age | 312 (sequence archive) | 3747.5 (sequence archive) | withheld: neither value published |
| SAMEA121748209 | age | 301 (sequence archive) | 3616.0 (sequence archive) | withheld: neither value published |
| SAMEA121748210 | age | 303 (sequence archive) | 3637.9 (sequence archive) | withheld: neither value published |
| SAMEA121748211 | age | 307 (sequence archive) | 3689.0 (sequence archive) | withheld: neither value published |
| SAMEA121748212 | age | 34 (sequence archive) | 412.7 (sequence archive) | withheld: neither value published |
| SAMEA121748216 | age | 197 (sequence archive) | 2359.5 (sequence archive) | withheld: neither value published |
| SAMEA121748217 | age | 200 (sequence archive) | 2396.0 (sequence archive) | withheld: neither value published |
| SAMEA121748218 | age | 202 (sequence archive) | 2421.6 (sequence archive) | withheld: neither value published |
| SAMEA121748219 | age | 187 (sequence archive) | 2239.0 (sequence archive) | withheld: neither value published |
| SAMEA121748224 | age | 85 (sequence archive) | 1022.7 (sequence archive) | withheld: neither value published |
| SAMEA121748225 | age | 149 (sequence archive) | 1789.7 (sequence archive) | withheld: neither value published |
| SAMEA121748226 | age | 153 (sequence archive) | 1837.2 (sequence archive) | withheld: neither value published |
| SAMEA121748231 | age | 318 (sequence archive) | 3820.5 (sequence archive) | withheld: neither value published |
| SAMEA121748232 | age | 49 (sequence archive) | 584.4 (sequence archive) | withheld: neither value published |
| SAMEA121748235 | age | 154 (sequence archive) | 1848.2 (sequence archive) | withheld: neither value published |
| SAMEA121748237 | age | 190 (sequence archive) | 2275.5 (sequence archive) | withheld: neither value published |
| SAMEA121748238 | age | 194 (sequence archive) | 2323.0 (sequence archive) | withheld: neither value published |
| SAMEA121748239 | age | 200 (sequence archive) | 2396.0 (sequence archive) | withheld: neither value published |
| SAMEA121748240 | age | 117 (sequence archive) | 1398.9 (sequence archive) | withheld: neither value published |
| SAMEA121748245 | age | 377 (sequence archive) | 4529.1 (sequence archive) | withheld: neither value published |
| SAMEA121748246 | age | 380 (sequence archive) | 4565.6 (sequence archive) | withheld: neither value published |
| SAMEA121748247 | age | 382 (sequence archive) | 4587.5 (sequence archive) | withheld: neither value published |
| SAMEA121748248 | age | 59 (sequence archive) | 704.9 (sequence archive) | withheld: neither value published |
longitudinalmother–infant
160 of 160 people sampled more than once (572 samples; median 4, up to 7 per person) · follow-up median 3 mo (max 10.5 y) · median interval between samples 4 d (time from collection dates). Schedule stated by the source: “Longitudinal fecal, breast milk, and skin swabs collected from 120 mother/infant dyads; no specific timepoint intervals stated”.
Each row is one person (36 shown of 160); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
80 mother–infant dyads (80 mothers, 80 infants) linked by user_id; Mom/Infant from BioSample 'source' · 80 families with 160 sampled people (80 with a parent and a child).
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 80 families (one per family structure, then more). 160 people in the project overall.
Families (25 of 80)
Genera, mean relative abundance over 519 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 | 561 | 98% | ||||
| country | 572 | 100% | 572 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 572 | 100% | 572 | |||
| collection_date | 572 | 100% | 572 | |||
| family_id | 572 | 100% | 572 | |||
| family_role | 572 | 100% | 572 | |||
| antibiotic_exposure | 414 | 72% | 414 | |||
| sex | 288 | 50% | 288 | |||
| age_at_collection_days | 277 | 48% | 277 |
Archive description
Newborns and infants are commonly exposed to antibiotics. Evidence is mounting that disruption of the developing microbiome through antibiotic exposure leads to long term adverse immunological, neurological and metabolic outcomes. While direct antibiotic exposure has been shown to alter the microbiome and metabolome, much less is known about indirect antibiotic exposure such as through breast milk. In this project, we aim to address the impact of antibiotic exposure through breast milk on the infant microbiome and metabolome and to determine if we can monitor antibiotic exposure through noninvasive skin swabs. Longitudinal fecal, breast milk, and skin swabs have been collected from 120 mother/infant dyads. Untargeted metabolomics analysis will be conducted to analyze changes in metabolites shotgun metagenomics analysis will be used to analyze changes in maternal and infant microbial communities.
How this project entered the registry
Classified as human gut / stool / skin / human milk 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 · “skin swabs. Longitudinal fecal , breast milk,”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “exposure through noninvasive skin swabs. Longitudinal fecal,”
- body site study.description · “such as through breast milk . In this”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “MPRINT: mother- infant dyads and antibiotic”
- life stage study.description · “Newborns and infants are”
- life stage study.description · “analyze changes in maternal and infant microbial”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA121748178 | age_at_collection_days | 13226 | R1 | 0.90 | sample.attr.host_age | 36.21 |
| SAMEA121748174 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | Cephalexin |
| SAMEA121748174 | collection_date | 2022-06-04 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2022-06-04 |
| SAMEA121748174 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMEA121748174 | family_id | 12121 | R1 | 0.85 | biosample.attribute:user_id | user_id: 12121 |
| SAMEA121748174 | family_role | child | R1 | 0.85 | biosample.attribute:source | source: Infant |
| SAMEA121748178 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMEA121748174 | subject_id | 12121.Infant | R1 | 0.85 | biosample_attr | 12121.Infant |
Sequencing
665 runs over 572 samples · mean 2.16 Gbp per run (median 2.57 Gbp, total 1,438.42 Gbp; 665 runs with a base count) · layout PAIRED 665 · platform ILLUMINA 665 · models Illumina NovaSeq X (665) · 78% of runs with a Sandpiper profile · first public 2026-02-24 – 2026-02-25
Authors (0)
No author record.
Downloads
PRJEB108678.csv.gz (21.2 KB) · parquet (99.4 KB) — all 572 samples, every field with route and confidence · PRJEB108678_determinations.csv.gz (30.1 KB) — 3,839 evidence rows