The microbiome and vaginal seeding
A real biological difference. Not a proven cause, and not a recommended treatment.
Babies born by cesarean acquire a different early bacterial population. In a study of 596 newborns, cesarean birth was associated with reduced transmission of maternal gut bacteria and more colonization by hospital organisms. The same disruption also appeared, to a lesser degree, in vaginally born babies whose mothers received antibiotics in labor and in babies who were not breastfed, which means antibiotics and feeding are doing part of the work usually attributed to the cesarean.
Vaginal seeding means swabbing a newborn's mouth, face or skin with the mother's vaginal fluid. ACOG guidance states it should not be performed outside an approved research protocol, because efficacy and safety data are inadequate and there is a risk of transmitting infection.