Human microbiota play an important role in the functioning of various organs, as well as the education of the immune system. Mammals have evolved to be born non-sterile, covered with the maternal vaginal bacteria that populate the maternal birth canal, as well as to exclusively breastfeed during early development. Unfortunately, these processes are substantially altered with modern Western practices, which may have health consequences. In particular, C-section is associated with an increased risk of immune diseases and allergies. This study explores the effects of exposing neonates to the vaginal environment at birth, perinatal antibiotics, and lactation on the acquisition of new microbial genes during the first year of infant microbiome development.