The first colonizers of the baby’s gastrointestinal tract and skin actually come from the mother’s vagina. As the baby makes it’s way down the birth canal and out into the world, it is coated in it’s mother’s vaginal microbes, which then make the baby their new home. It is believed that this initial colonization is critical for kickstarting the baby’s immune system. What happens with cesarian sections? C-section babies still get colonized, but their bacteria more closely resembles that of mum’s skin and the hospital surrounds. Some people people believe that the microbiome might be responsible for the higher rate of immune-related disorders (e.g., asthma) that occur in C-section births. See post from Arielle Radin for some more information on a potential solution to this problem – vaginal swabs for C-section babies.