Human milk milk
Breast-milk and colostrum shotgun metagenomes.
Membership rule (config/scope.yaml): milk in body_sites. Memberships derive deterministically from host, body sites, life stages and assay; a study can belong to several scopes.
64
studies
22,569
runs
20,282
BioSamples
4,065
BioSamples with harvested attributes — site known 24 %, age 18 %, sex 0 %
6,873
runs with a Sandpiper profile (30 %)
64
classified · 0 pending
Open in the registry explorer (pre-filtered) All scopes
Body sites and life stages within the scope
Primary body site (body_site_primary)
| value | studies | runs |
|---|---|---|
| gut_stool | 47 | 19,751 |
| milk | 14 | 1,588 |
| multi_site | 3 | 1,230 |
Primary life stage (life_stage_primary)
| value | studies | runs |
|---|---|---|
| infant | 43 | 19,012 |
| adult | 10 | 2,757 |
| unknown_age | 5 | 82 |
| mixed_ages | 3 | 114 |
| child | 2 | 503 |
| neonate | 1 | 101 |
Assay (assay)
| value | studies | runs |
|---|---|---|
| shotgun_dna | 51 | 17,435 |
| amplicon_misfiled | 5 | 3,029 |
| other | 3 | 137 |
| amplicon | 2 | 1,364 |
| isolate_genome | 2 | 9 |
| unknown | 1 | 595 |
Classification stage (classification_stage)
| value | studies | runs |
|---|---|---|
| deterministic_prior | 43 | 17,124 |
| sonnet_x2 | 10 | 668 |
| opus_adjudicated | 4 | 336 |
| curator_audit | 3 | 1,384 |
| owner_decision | 3 | 2,462 |
| deterministic_rule | 1 | 595 |
Largest studies by BioSamples (top 25)
| study | title | BioSamples | runs | sites | stages | assay | stage |
|---|---|---|---|---|---|---|---|
| PRJNA1468137 ENA | Maternal influences on infant gut microbiome and health | 4,749 | 4,749 | gut_stool;vaginal_urogenital;milk | infant;adult | shotgun_dna | deterministic_prior |
| PRJEB83236 ENA | SEPSIS Human Microbiome Study | 1,917 | 1,917 | gut_stool;milk;oral;skin | infant;child;adult | shotgun_dna | deterministic_prior |
| PRJEB111647 ENA | Restoration of Microbiota in Newborns | 1,441 | 1,441 | gut_stool;skin;vaginal_urogenital;milk | infant;neonate;child;adult | shotgun_dna | deterministic_prior |
| PRJEB14941 ENA | The microbiota at multiple body sites during pregnancy in a rural Tanzanian population and the effects of... | 1,118 | 1,118 | gut_stool;oral;vaginal_urogenital;milk | adult;infant | amplicon | curator_audit |
| PRJEB62690 ENA | Infant stool, 5-HMO supplemented formula vs. control formula vs. breastfed | 1,110 | 1,110 | gut_stool;milk | infant | shotgun_dna | deterministic_prior |
| PRJEB79896 ENA | PRIMAL fecal samples shotgun metagenome sequencing | 948 | 1,712 | gut_stool;milk | infant;neonate | shotgun_dna | deterministic_prior |
| PRJNA1404625 ENA | Investigating the role of the infant gut microbiome in rotavirus vaccine efficacy | 928 | 928 | gut_stool;milk | infant | shotgun_dna | deterministic_prior |
| PRJEB77729 ENA | First-Year Dynamics of the Microbiome in Infants’ Oral and Gastrointestinal Systems | 840 | 1,787 | gut_stool;oral;milk | infant | amplicon_misfiled | owner_decision |
| PRJEB108678 ENA | MPRINT: mother-infant dyads and antibiotic exposure | 665 | 665 | gut_stool;skin;milk | infant;neonate;adult | shotgun_dna | deterministic_prior |
| PRJEB52093 ENA | Gut microbiome response to a fermented milk product in subjects exposed to H pylori eradication treatment | 539 | 539 | gut_stool;milk | adult | shotgun_dna | deterministic_prior |
| PRJNA1019702 ENA | MILK study metagenomic sequencing of human milk and infant feces | 507 | 507 | gut_stool;milk | infant | shotgun_dna | deterministic_prior |
| PRJNA1464060 ENA | Efficacy of Bifidobacterium lactis BLa80 in Preventing Early Childhood Eczema and Respiratory Infections... | 488 | 488 | gut_stool;nasal_nasopharyngeal;milk | child;infant | amplicon_misfiled | owner_decision |
| PRJNA1356526 ENA | Breastmillk microbiome sequecing from mothers with and without T1D | 443 | 443 | milk | adult | amplicon_misfiled | sonnet_x2 |
| PRJNA1010893 ENA | MILK-Omics: Systems Biology of Human Milk and its Links to Maternal and Infant Health | 346 | 595 | milk | infant;adult | unknown | deterministic_rule |
| PRJNA630999 ENA | Premature infant microbiome Metagenome | 293 | 293 | gut_stool;milk | infant;neonate | shotgun_dna | deterministic_prior |
| PRJNA976196 ENA | Impact of soymilk-burkina intake on gut microbiome and nutritional status of Ghanaian women | 246 | 246 | gut_stool;milk;blood_tissue | adult | amplicon | curator_audit |
| PRJNA633576 ENA | Metagenomic survey of the gut microbiome of term infants in the United States reveals widespread... | 227 | 227 | gut_stool;milk | infant;neonate | shotgun_dna | deterministic_prior |
| PRJNA1086674 ENA | The Impact of Oral Feedings on the Preterm Infant Microbiome and Metabolome | 193 | 193 | oral;gut_stool;milk | infant;neonate;adult | shotgun_dna | deterministic_prior |
| PRJNA802048 ENA | Insights into the infant gut microbiome composition after bovine lactoferrin oral administration over time | 187 | 187 | gut_stool;milk | infant;neonate | amplicon_misfiled | owner_decision |
| PRJEB74322 ENA | Spanish mother and infants metagenomes of stool and milk samples | 182 | 182 | gut_stool;milk;vaginal_urogenital | infant;adult | shotgun_dna | deterministic_prior |
| PRJEB63183 ENA | Interactions Between Bifidobacterium and Bacteroides and Human Milk Oligosaccharides and Their... | 170 | 170 | milk;gut_stool | infant;child;adult | shotgun_dna | deterministic_prior |
| PRJEB54991 ENA | Shotgun metagenomics of infant formula study | 162 | 162 | gut_stool;milk | infant | shotgun_dna | deterministic_prior |
| PRJNA906107 ENA | Characterizing microbiome dynamics among maternal and donor breastmilk and infants | 156 | 156 | milk;gut_stool;vaginal_urogenital | infant;adult | shotgun_dna | deterministic_prior |
| PRJNA1169661 ENA | Infamilk | 152 | 152 | gut_stool;milk | infant;adult | shotgun_dna | deterministic_prior |
| PRJNA1227883 ENA | Metagenomes from mother-infant fecal and breastmilk samples of the MAMI cohort Metagenome | 146 | 146 | gut_stool;milk | infant | shotgun_dna | deterministic_prior |
Counts are computed from data/registry_studies.parquet at build time (release R2026.25).