MILK study: human milk and infant feces metagenomics, USA
MILK study metagenomic sequencing of human milk and infant feces
Longitudinal cohort study of 497 samples from paired human milk and infant fecal specimens in the USA; milk sampled at 1 month (and 3 months for a subset), infant feces at 1 and 6 months. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinalmother–infant
151 of 183 people sampled more than once (302 samples; median 2, up to 2 per person) · follow-up median 5 mo (max 5 mo) · median interval between samples 5 mo(time from age at collection).
Schedule stated by the source: “Milk at 1 month (subset also 3 months); infant feces at 1 and 6 months” (time origin: birth (postpartum)); stated follow-up 6 mo.
Each row is one person (36 shown of 151); 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).
189 mother-infant couples (couple_id); 131 with both maternal milk and infant stool sequenced · 131 families with 262 sampled people (131 with a parent and a child).
131 × mother + 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 131 families (one per family structure, then more). 183 people in the project overall.
Bifidobacterium 37.4%Escherichia 8.8%Bacteroides 7.5%Klebsiella 7.2%Phocaeicola 4.7%Clostridium 4.1%Veillonella 3.9%Streptococcus 2.3%Parabacteroides 1.7%Veillonella_A 1.6%Mediterraneibacter 1.6%Thomasclavelia 1.3%not assigned to a genus 4.1%other genera 13.7%
Genera, mean relative abundance over 290 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth. PMID 39043677PMC11266569curated
Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome. PMID 39265573PMC11602576curated
Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk. PMID 41274878PMC12749357curated
Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis. PMID 42171373PMC13288982curated
Details
Archive description
Metagenomic sequencing was performed for paired human milk and infant fecal samples from the MILK study. Milk sequencing was performed at 1 month postpartum (and 3 months for a subset of samples), and infant fecal sequencing was performed at 1 and 6 months.
How this project entered the registry
Classified as human gut / stool / human milk shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
body sitestudy.description · “milk and infant fecal samples from the”
body sitestudy.title · “MILK study metagenomic sequencing”
body sitestudy.description · “performed for paired human milk and infant fecal”
life stageexternal_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stagestudy.title · “human milk and infant feces”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN37492489
age_at_collection_days
183
R3
0.40
paper.fulltext.methods
collected at one and six months of age
SAMN37492488
country
US
R1
0.90
biosample_attr
USA
SAMN37492488
family_id
p0019
R1
0.85
biosample.attribute:couple_id
couple_id: p0019
SAMN37492488
family_role
mother
R1
0.70
biosample.attribute:tissue
tissue: Milk
SAMN37492489
preterm_status
term
R3
0.80
paper.fulltext.methods
born at term with a birth weight
SAMN37492488
sex
female
R1
0.90
biosample_attr
female
SAMN37492488
subject_id
p0019_mother
R2
0.80
archive
SAMN37492488
timepoint_label
1M
R1
0.80
biosample_attr
1M
Sequencing
507 runs over 507 samples · mean 2.40 Gbp per run (median 2.60 Gbp, total 1,217.69 Gbp; 507 runs with a base count) · layout PAIRED 507 · platform ILLUMINA 507 · models Illumina NovaSeq 6000 (507) · 66% of runs with a Sandpiper profile · first public 2024-01-10 – 2024-01-28