The establishment of the infant gut microbiome in the first months of life

Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. Here we present two birth cohorts of newborns and their mothers from Finland and Boston with 44 and 73 families each, respectively. We compared bacterial strains across and within families and identified mother-to-child bacterial transmission events. We observed two inheritance patterns across multiple species, where often the mother`s dominant strain is transmitted to the child, but occasionally her secondary strains colonize the infant. In families where the secondary strain of B. uniformis was inherited, a starch-utilization gene cluster that was absent in the mother`s dominant strain was identified in the child, suggesting the selective advantage of a mother`s secondary strain in the infant gut.

We also examined the role of delivery mode on the infant gut microbiome, specifically focusing on infants born by non-elective C-sections, where the newborn was exposed to microbes in the birth canal, but was eventually extracted by section. We found the canonical microbial signature of infants born by C-section, namely the lack of Bacteroides species in the first months of life, was found in all C-sections, regardless if there was active labor involved or not, suggesting the microbial signature is not driven by exposure to the maternal vaginal microbiome. Surprisingly, we also noted that the canonical C-section microbial signature was not evident in the first week of life, and only detected in the second week of life, which raises many new questions about the factors that determine successful colonization of the infant gut.