Longitudinal gut metagenomes from mothers and their infants in the EDIA study

In a cohort consisting of 70 mother-infant dyads, we profiled the fecal microbiome and in late pregnancy and different stages of infancy. We used longitudinal sampling to investigate the vertical transmission of species, strains, and individual genes. We discovered hundreds of mother-to-infant gene transmission events in the absence of maternal carrier strains in the infant gut. Key maternal donor species in these events belonged to the Bacteroidales order. Although these species were rarely transmitted to infants, their relative abundance in maternal samples exerted a significant influence on infant gut microbial structure and functional potential, including HMO utilization capacity. Hence, apart from classical vertical transmission of strains and species, the maternal microbiome may also shape the infant gut microbiome through lateral gene transfer events.