MILK study human milk metagenome, USA, longitudinal cohort
10 human milk samples from the USA MILK study, collected at 1 month postpartum, as part of a longitudinal cohort design. machine-written summary
10 samples · 30 runs · US · Infant / toddler · 2024 · 46.1 Mbp / sample · cohort MILK study
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 30 sample values (country, sex, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 30 sample values (collection date, location locality, location site) · PMC12749357 |
| ✓ Supplementary tables | 20 sample values (antibiotic exposure, subject id) |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 10 | 100% | 10 | |||
| antibiotic_exposure | 10 | 100% | 10 | |||
| collection_date | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| location_locality | 10 | 100% | 10 | |||
| location_site | 10 | 100% | 10 | |||
| sex | 10 | 100% | 10 | |||
| timepoint_label | 10 | 100% | 10 |
- Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk. PMID 41274878 PMC12749357 curated
Archive description
Metagenomic sequencing was performed for human milk samples from the MILK study. Milk samples were collected at 1 month postpartum.
How this project entered the registry
Classified as human human milk / 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 · “MILK study metagenomic re-sequencing”
- body site study.description · “was performed for human milk samples from the”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN37492531 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.41467_2025_66497_MOESM4_ESM.csv[Abx_exposure_any] | p0255: No |
| SAMN37492531 | collection_date | 2014/2023 | R3 | 0.70 | paper.fulltext.methods | Samples were collected between 2014 and 2023 |
| SAMN37492531 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN37492531 | location_locality | Minneapolis | R3 | 0.60 | paper.fulltext.results | recruited in Minneapolis, USA |
| SAMN37492531 | location_site | University of Minnesota / HealthPartners Institute | R3 | 0.70 | paper.fulltext.methods | enrolled prenatally at the University of Minnesota |
| SAMN37492531 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN37492531 | subject_id | Mother_Infant_Pair_52 | R2 | 0.85 | paper.supp.41467_2025_66497_MOESM4_ESM.csv[Mother Infant Pair] | p0255: Mother_Infant_Pair_52 |
| SAMN37492531 | timepoint_label | 1M | R1 | 0.80 | biosample_attr | 1M |
Sequencing
30 runs over 30 samples · mean 72.8 Mbp per run (median 46.1 Mbp, total 2.18 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ELEMENT 30 · models Element AVITI (30) · 0% of runs with a Sandpiper profile · first public 2024-12-15
Authors (12)
Ferretti P first · Allert M · Johnson KE · Rossi M · Heisel T · Gonia S · Knights D · Fields DA · Albert FW · Demerath EW · Gale CA · Blekhman R last
Downloads
PRJNA1198101.csv.gz (1.3 KB) · parquet (70.7 KB) — all 10 samples, every field with route and confidence · PRJNA1198101_determinations.csv.gz (1.2 KB) — 80 evidence rows