Maternal-infant gut microbiome and neurodevelopment, Rochester NY
315 samples from mothers, infants, and neonates in Rochester, NY, examining mother-to-infant microbiome transfer and neuroactive metabolites in relation to prenatal anxiety and infant neurocognitive development; longitudinal cohort design. machine-written summary
1,109 samples · 1,109 runs · US · Infant / toddler · 2026 · 16.07 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 7,762 sample values (age, 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 |
age: two sequence archives disagree for 1 sample (e.g. 700 vs 10166.0) — withheld.
The sources disagree on 1 sample. 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 (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN47931211 | age | 700 (sequence archive) | 10166.0 (sequence archive) | withheld: neither value published |
longitudinalmother–infant
231 of 267 people sampled more than once (835 samples; median 4, up to 5 per person) · follow-up median 12 mo (max 3.9 y) · median interval between samples 5 mo (time from age at collection). Schedule stated by the source: “Infants sampled at multiple ages (e.g. 0, 30.4, 182.6, 273.9, 365.2 days); host_age attribute includes 0,1,6,12,5,11,13 months indicating repeated postnatal timepoints per infant.” (time origin: birth).
Each row is one person (36 shown of 231); 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).
292 mother–infant dyad ids (host_subject_id prefix); 214 dyads with both mother and infant sampled, 53 infant-only, 25 mother-only · 214 families with 428 sampled people (214 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 214 families (one per family structure, then more). 267 people in the project overall.
Families (25 of 214)
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 1,109 | 100% | ||||
| country | 1,109 | 100% | 1,109 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,109 | 100% | 1,109 | |||
| collection_date | 1,109 | 100% | 1,109 | |||
| family_id | 1,109 | 100% | 1,109 | |||
| family_role | 1,109 | 100% | 1,109 | |||
| sex | 1,109 | 100% | 1,109 | |||
| age_at_collection_days | 1,108 | 100% | 1,108 |
Archive description
There is compelling evidence, particularly from pre-clinical studies, for a critical role of the maternal and infant gut microbiome in early postnatal neurodevelopment. Temporal milestones in postnatal infant gut microbiome development align with changes in early infant brain development, suggesting a functional relationship between the gut-brain axis. There is reliable evidence linking maternal prenatal factors such as prenatal anxiety to the vaginal and gut microbiome as well as to child neurodevelopment. This proposal will test the hypothesis that infant neurocognitive development is shaped by mother-to-infant microbiome transfer and postnatal development and biosynthesis of microbiota-derived neuroactive metabolites, with the functional characteristics of this relationship shaped by prenatal anxiety.
How this project entered the registry
Classified as human gut / stool / vaginal / urogenital shotgun DNA metagenome of infant / toddler and child and adult and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “maternal and infant gut microbiome in early”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “anxiety to the vaginal and gut microbiome”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “the maternal and infant gut microbiome in”
- life stage study.description · “well as to child neurodevelopment. This proposal”
- life stage study.description · “role of the maternal and infant gut”
- life stage sample.attr.host_age · “0 months (n=287/794)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47890478 | age_at_collection_days | 182.6 | R1 | 0.85 | sample.attr.host_age | 6 months |
| SAMN47890512 | age_at_collection_days | 365.2 | R1 | 0.95 | biosample.attribute:host_age | host_age: 12 months |
| SAMN47923111 | age_at_collection_days | 30 | R1 | 0.90 | biosample_attr | 1 months |
| SAMN47890478 | collection_date | 2018-03-09 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2018-03-09 |
| SAMN47890478 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Rochester, NY |
| SAMN47922927 | country | US | R1 | 0.90 | biosample_attr | USA: Rochester, NY |
| SAMN47890478 | family_id | 085 | R1 | 0.70 | biosample.attribute:host_subject_id | 085-2 |
| SAMN47890478 | family_role | child | R1 | 0.70 | biosample.attribute:host_subject_id | 085-2 |
| SAMN47890478 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN47922927 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN47890478 | subject_id | 085-2 | R1 | 0.85 | biosample.attribute:host_subject_id | host_subject_id: 085-2 |
| SAMN47922927 | subject_id | 085-1 | R1 | 0.85 | biosample_attr | 085-1 |
Sequencing
1,109 runs over 1,109 samples · mean 15.92 Gbp per run (median 16.07 Gbp, total 17,651.99 Gbp; 1,109 runs with a base count) · layout PAIRED 1,109 · platform ILLUMINA 1,109 · models Illumina NovaSeq 6000 (1,109) · 0% of runs with a Sandpiper profile · first public 2026-04-19
Authors (0)
No author record.
Downloads
PRJNA1249435.csv.gz (38.1 KB) · parquet (123.0 KB) — all 1,109 samples, every field with route and confidence · PRJNA1249435_determinations.csv.gz (72.7 KB) — 7,762 evidence rows