Mother-infant sharing of gut and vaginal microbes at the species and strain level

Mother-to-offspring microbial transmission is a foundational process for seeding the infant gut microbiome, yet the relative contributions of maternal body sites and the influence of birth delivery mode remain incompletely understood. We use shotgun metagenomic sequencing in 68 mother-infant dyads to investigate species- and strain-level sharing of the maternal gut and vaginal microbiomes with the infant gut during the first year of life. At 2–4 months of age, infants share an average of 35% of species with their mother's microbiomes, with markedly greater sharing from the maternal gut than the vagina. Vaginally delivered infants exhibit higher levels of sharing than those born by cesarean section (C-section). Strain-level analyses reveal persistent mother-infant transmission across multiple Bacteroides and Bifidobacterium species genome bins, with strain-sharing frequencies varying by species and birth mode. C-section reduces the extent of mother-infant species- and strain-level sharing.