An interesting aside - as you may have read, FMT is being investigated as a treatment for autism. The thinking here is as follows. Babies are born with a certain level of Clostridium species (not necessarily C. diff). Clostridium are very good at producing toxins (botulism and the toxins involved in C.diff). Normally the level of clostridium in babies drops on its own. It's believed that in some babies, this drop never happens. These babies are then therefore continually exposed to toxins from these clostridium bugs, some of which may have neurotoxic properties and can result in autism. The goal of FMT is to alter the gut flora enough to get rid of these Clostridium species and stop the toxin from reaching the brain. There has been success in young children. What we need to keep in mind though is that autism is a spectrum of not only symptoms, but also a spectrum of causes as well, so FMT won't necessarily work for everyone.

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...