Gut microbiota and early-life adversity, mother-child dyads
183 samples from mother-child dyads, case-control design, comparing gut microbiota between dyads with high versus low social disadvantage and psychological stress exposure in utero and early life. machine-written summary
183 samples · 183 runs · US · Infant / toddler · 2023 · 6.73 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 549 sample values (family id, family role, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10509221 |
| ✓ Supplementary tables | 361 sample values (age, antibiotic exposure, sex) |
| ✓ External resources | 183 sample values (country) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
mother–infant
92 mother–child dyads (91 complete, 1 mother only) via Dyad id and Mother/Child status · 91 families with 182 sampled people (91 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 91 families (one per family structure, then more). 183 people in the project overall.
Families (25 of 91)
Genera, mean relative abundance over 162 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 | 179 | 98% | ||||
| country | 183 | 100% | 183 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 183 | 100% | 183 | |||
| family_id | 183 | 100% | 183 | |||
| family_role | 183 | 100% | 183 | |||
| age_at_collection_days | 179 | 98% | 179 | |||
| sex | 179 | 98% | 179 | |||
| antibiotic_exposure | 3 | 2% | 3 |
- Social and psychological adversity are associated with distinct mother and infant gut microbiome variations. PMID 37726348 PMC10509221 curated
Archive description
Social disadvantage (SD) and psychological stressors (PS) trap some populations in poverty, resulting in health inequities. How these two factors become biologically embedded and the pathways leading to adverse health outcomes is unclear, especially in infants exposed to psychosocial adversity in utero and during early life. Variation in gut microbiome structure and functions offers a possible causative pathway. The whole metagenome shotgun datasets and 16S microbiome datasets here are used to interrogate the gut microbiome of mother-child dyads and compare high-SD/high-PS dyads to pairs with low-SD/Low-PS, and demonstrate that the GM of high-SD and high-PS mothers may already be compromised, resulting in the lowest observed inter-individual similarity in that group.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child 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 · “with variation in gut microbiota”
- body site study.description · “life. Variation in gut microbiome structure and”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “in utero and early life is associated with”
- life stage study.description · “microbiome of mother- child dyads and compare”
- life stage study.description · “high-SD and high-PS mothers may already be”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32165274 | age_at_collection_days | 29.0 | R2 | 0.85 | paper.supp.41467_2023_41421_MOESM5_ESM.xlsx[Supp Table 2 all data][Age at time of sampling] | 4.2 weeks |
| SAMN32165346 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.41467_2023_41421_MOESM5_ESM.xlsx[Supp Table 2 all data][Antibiotic] | azithromycin (Zithromax) |
| SAMN32165274 | country | US | R2 | 0.60 | external.bugsigdb source | Location of subjects: United States of America |
| SAMN32165274 | family_id | 150 | R1 | 0.85 | biosample.attribute:Dyad id | Dyad id: 150 |
| SAMN32165274 | family_role | child | R1 | 0.85 | biosample.attribute:Mother/Child status | Mother/Child status: Child |
| SAMN32165274 | sex | female | R2 | 0.85 | paper.supp.41467_2023_41421_MOESM5_ESM.xlsx[Supp Table 2 all data][Sex] | Female |
| SAMN32165274 | subject_id | 150_Child | R1 | 0.85 | biosample.attribute:Dyad id+Mother/Child status | Dyad id: 150; Mother/Child status: Child |
Sequencing
183 runs over 183 samples · mean 8.07 Gbp per run (median 6.73 Gbp, total 1,476.13 Gbp; 183 runs with a base count) · layout PAIRED 183 · platform ILLUMINA 183 · models Illumina NovaSeq 6000 (183) · 89% of runs with a Sandpiper profile · first public 2023-02-27
Authors (19)
Warner BB first · Rosa BA · Ndao IM · Tarr PI · Miller JP · England SK · Luby JL · Rogers CE · Hall-Moore C · Bryant RE · Wang JD · Linneman LA · Smyser TA · Smyser CD · Barch DM · Miller GE · Chen E · Martin J · Mitreva M last
Downloads
PRJNA911205.csv.gz (7.2 KB) · parquet (79.4 KB) — all 183 samples, every field with route and confidence · PRJNA911205_determinations.csv.gz (11.0 KB) — 1,093 evidence rows