Babies get their intestinal bacteria during the birthing process from the vagina, their mother, the mother's feces, etc. That's why C-section infants have vastly different gut flora initially. They never made that trip down the vagina to be exposed to vaginal bacteria and are exposed to different types of bacteria during the first few weeks of life. I'm not sure the effect of antibiotics are the same or similar to that of a c-section baby. I'm not sure we know the long term effects of c-section babies and gut flora especially later in life. I would think c-section would be much more disturbing to gut flora than antibiotics.

http://en.wikipedia.org/wiki/Gut_flora#Acquisition_of_gut_fl...