Infant gut microbiome maturation during weaning in Denmark
A longitudinal cohort study of 108 infant gut samples from Denmark, examining how weaning (introduction of solid foods and cessation of breastfeeding) drives gut microbiome maturation during the first year of life. machine-written summary
108 samples · 108 runs · DK · Infant / toddler · 2025 · 12.22 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 648 sample values (collection date, country, family id, family role, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 540 sample values (delivery mode, feeding mode, hmo supplementation, location locality, location site) · PMC13388695 |
| ✓ Supplementary tables | 108 sample values (antibiotic exposure) |
| – 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 |
longitudinal — not resolvedmother–infant
13 of 13 people sampled more than once (108 samples; median 3, up to 19 per person). Schedule stated by the source: “stool at pre-weaning, early weaning, and late weaning stages”.
Milkome infant–mother dyad cohort: 7 infants, 6 with their mother sampled (mother at early weaning) · 6 families with 12 sampled people (6 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: 6 families. 13 people in the project overall.
Families (6)
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 | 108 | 100% | 108 | |||
| antibiotic_exposure | 108 | 100% | 108 | |||
| collection_date | 108 | 100% | 108 | |||
| delivery_mode | 108 | 100% | 108 | |||
| detailed_location | 108 | 100% | ||||
| family_id | 108 | 100% | 108 | |||
| family_role | 108 | 100% | 108 | |||
| feeding_mode | 108 | 100% | 108 | |||
| hmo_supplementation | 108 | 100% | 108 | |||
| location_locality | 108 | 100% | 108 | |||
| location_site | 108 | 100% | 108 | |||
| timepoint_label | 108 | 100% | 108 |
- Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome. PMID 42203770 PMC13388695 curated
Archive description
The infant gut microbiome develops dynamically during the first year of life, with the introduction of solid foods and the gradual cessation of breastfeeding marking key milestones. This study investigated how the weaning drives the maturation of the infant gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Infant gut microbiome maturation during”
- body site study.description · “The infant gut microbiome develops dynamically”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant gut microbiome maturation”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120234870 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.table | antibiotics=False |
| SAMEA120234870 | collection_date | 2023 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2023 |
| SAMEA120234870 | country | DK | R1 | 0.90 | biosample_attr | Denmark |
| SAMEA120234870 | delivery_mode | vaginal | R3 | 0.80 | paper.fulltext.results | vaginally delivered and exclusively breastfed infants |
| SAMEA120234870 | family_id | PRJEB97976:dyad_B | R1 | 0.70 | biosample.attribute:host subject id | host subject id: I_B |
| SAMEA120234870 | family_role | child | R1 | 0.70 | biosample.attribute:host subject id | host subject id: I_B |
| SAMEA120234870 | feeding_mode | exclusive_breast | R3 | 0.80 | paper.fulltext.results | vaginally delivered and exclusively breastfed infants |
| SAMEA120234870 | hmo_supplementation | no | R3 | 0.40 | paper.fulltext.results | did not receive antibiotics or formula |
| SAMEA120234870 | location_locality | Copenhagen | R3 | 0.70 | paper.fulltext.methods | recruited at Copenhagen University Hospital, Rigshospitalet (Copenhagen, Denmark) |
| SAMEA120234870 | location_site | Copenhagen University Hospital, Rigshospitalet | R3 | 0.70 | paper.fulltext.methods | recruited at Copenhagen University Hospital, Rigshospitalet |
| SAMEA120234870 | subject_id | I_B | R1 | 0.85 | biosample_attr | I_B |
| SAMEA120234870 | timepoint_label | T3 | R1 | 0.80 | biosample_attr | T3 |
Sequencing
108 runs over 108 samples · mean 12.41 Gbp per run (median 12.22 Gbp, total 1,340.01 Gbp; 108 runs with a base count) · layout PAIRED 108 · platform DNBSEQ 108 · models DNBSEQ-T7 (108) · 0% of runs with a Sandpiper profile · first public 2025-11-11
Authors (15)
So Y first · Pichler MJ · Kappel SS · Jin C · Eriksen C · Chatzigiannidou I · Andersen MHB · Tsiamis V · Lukassen MV · Skytthe LE · Teneberg S · Kristiansen K · Brix S · Aunsholt L · Abou Hachem M last
Downloads
PRJEB97976.csv.gz (3.9 KB) · parquet (75.3 KB) — all 108 samples, every field with route and confidence · PRJEB97976_determinations.csv.gz (8.9 KB) — 1,296 evidence rows