Strain-level identification of mother-to-child bacterial transmission during the first few months of life

Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child’s life. We identified mother-to-child microbial transmission events and describe the incidence of family-specific antibiotic resistance genes. Across multiple species, we identified two inheritance patterns, where often the mother’s dominant strain is transmitted to the child, but occasionally her minor strains colonize the infant gut. We observed both inheritance patterns for Bacteroides uniformis strains. In families where the minor strain was inherited, we identified a starch utilization gene cluster that was absent in the mother’s dominant strain, suggesting the selective advantage of her minor strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high-resolution and give insights into early colonization of the infant gut.