Dutch mother-infant gut microbiome cohort (Lifelines NEXT)

The establishment of the infant gut microbiome is critical for later health, yet how it is shaped by maternal and early-life factors remains unclear. Here we metagenomically sequenced 4,526 longitudinal fecal samples from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT, spanning 12 weeks of pregnancy to one year postpartum. We integrated this data with 474 clinical and exposure variables and with ultra-deep sequencing of the breast milk and vaginal microbiomes. We observe that the maternal gut microbiome undergoes only subtle changes during pregnancy and postpartum and is influenced by dietary preferences, infections and pre-pregnancy smoking. The maternal gut microbiome is a major reservoir for infant gut strains, with only occasional transmission from vaginal and breast milk microbiomes. Mother-infant sharing of gut strains is time-dependent, and higher maternal abundances of gut species is linked to increased likelihood of strain transmission. Notably, we find the maternal gut microbiome to be a predictor of infant eczema. The primary factors shaping the infant gut microbiome and its carbohydrate-active enzyme profile were mode of delivery, followed by feeding mode. Of 585 vaginally delivered babies, 155 were born at home, but home delivery was only moderately associated with microbiome composition, similar to other birth parameters like duration of pushing and ruptured membranes. Overall, we highlight the central role of the mother and her microbiome in shaping the infant gut ecosystem and early health outcomes.

Classified as human gut / stool / vaginal / urogenital / human milk shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage verdict include”
• body site study.title · “influences on infant gut microbiome and health”
• body site study.description · “of the infant gut microbiome is critical”
• body site study.description · “breast milk and vaginal microbiomes. We observe”
• body site study.description · “sequencing of the breast milk and vaginal microbiomes.”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.title · “Maternal influences on infant gut microbiome and”
• life stage study.title · “Maternal influences on infant”
• life stage study.description · “is shaped by maternal and early-life factors”

4,749 runs over 4,749 samples · mean 3.91 Gbp per run (median 3.95 Gbp, total 18,560.85 Gbp; 4,749 runs with a base count) · layout PAIRED 4,749 · platform ILLUMINA 4,749 · models Illumina NovaSeq 6000 (4,749) · 0% of runs with a Sandpiper profile · first public 2026-05-31 – 2026-07-31

Sinha T first · Brushett S · Fernández-Pato A · Garmaeva S · Andreu-Sánchez S · Spreckels JE · Mallon CA · Kuzub N · Gois MB · Wu J · Kruk M · Jankipersadsing SA · Dekens JAM · Gacesa R · Vila AV · Bang C · Perenboom C · Franke A · Tytgat HLP · Mottaz SC · Peters L · de Jonge A · Verkade HJ · Swertz MA · Wijmenga C · Kuipers F · Scherjon S · Sikkema J · Sprikkelman AB · de Kroon MLA · Prins JR · Gordijn SJ · Koppelman GH · Reijneveld SA · Lifelines NEXT cohort study · Fu J · Yassour M · Kurilshikov A · Zhernakova A last

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

PRJNA1468137.csv.gz (145.5 KB) · parquet (320.2 KB) — all 4,749 samples, every field with route and confidence · PRJNA1468137_determinations.csv.gz (134.0 KB) — 18,996 evidence rows