Infant and maternal gut microbiota, longitudinal cohort
108 stool samples from healthy, term-born breastfed infants and their mothers, collected longitudinally, studying how human milk oligosaccharides mediate mutualism between Escherichia coli and Bifidobacterium bifidum in the gut. machine-written summary
108 samples · 108 runs · NL · Infant / toddler · 2026 · 7.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 216 sample values (collection date, country) |
| ✓ Abstract / description | 216 sample values (feeding mode, preterm status) |
| ✓ Full text | 108 sample values (location region) · PMC13103366 |
| ○ 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 |
longitudinal — not resolvedmother–infant — not resolved
Schedule stated by the source: “stool at two, six, and eleven months post-delivery” (time origin: birth).
41 infants sampled; 30 of their mothers also sampled per paper, but maternal samples are not among this project's BioSamples.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 108 | 100% | ||||
| country | 108 | 100% | 108 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 108 | 100% | 108 | |||
| detailed_location | 108 | 100% | ||||
| feeding_mode | 108 | 100% | 108 | |||
| location_region | 108 | 100% | 108 | |||
| preterm_status | 108 | 100% | 108 |
- Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum. PMID 42020426 PMC13103366 curated
- Mutualistic interactions between Escherichia coli and Bifidobacterium bifidum enable degradation of human milk oligosaccharides in healthy infants curated
Archive description
The development of the human gut microbiota during infancy is marked by frequent colonization of Enterobacteriaceae, a bacterial family notoriously associated with various diseases. Yet, despite their prominence in the absence of illness, their exact ecological role during healthy maturation of the infant gut remains poorly explored. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed neonates (n=41) at two, six, and eleven months post-delivery, as well as microbiota of related mothers (n=30) with shotgun metagenomic sequencing, complemented by novel computational approaches and experimentation.
How this project entered the registry
Classified as human gut / stool / 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 · “of the human gut microbiota during infancy”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.title · “Human milk oligosaccharide mediates mutualism”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “gut microbiota during infancy is marked by”
- life stage study.description · “healthy, term-born, breastfed neonates (n=41) at two,”
- life stage study.description · “microbiota of related mothers (n=30) with shotgun”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN51274603 | collection_date | 2020 | R1 | 0.85 | biosample.attribute:collection_date | 2020 |
| SAMN51274603 | country | NL | R1 | 0.90 | biosample_attr | Netherlands |
| SAMN51274603 | feeding_mode | exclusive_breast | R4 | 0.50 | study.description | healthy, term-born, breastfed neonates |
| SAMN51274603 | location_region | South Limburg | R3 | 0.70 | paper.fulltext.methods | residing in the South Limburg region of the Netherlands |
| SAMN51274603 | preterm_status | term | R4 | 0.50 | study.description | healthy, term-born, breastfed neonates |
Sequencing
108 runs over 108 samples · mean 7.91 Gbp per run (median 7.88 Gbp, total 854.65 Gbp; 108 runs with a base count) · layout PAIRED 108 · platform ILLUMINA 108 · models NextSeq 2000 (108) · 0% of runs with a Sandpiper profile · first public 2026-03-23
Authors (16)
Seki D first · Pollak S · Kujawska M · Kiu R · Acuna-Gonzalez A · Crouch LI · Bakshani CR · Chivers PT · Mommers M · van Best N · Penders J · Hall LJ last · Acuna-Gonzales A · Crouch L · Bakshani C · Chivers P
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1230889.csv.gz (3.7 KB) · parquet (74.1 KB) — all 108 samples, every field with route and confidence · PRJNA1230889_determinations.csv.gz (2.9 KB) — 540 evidence rows