Is it out of the question for people to be consistently pooping & supplying this data so we have ongoing tracking of the ratios of the various bacteria present in the population? Some clear patterns may arise.
http://academy.asm.org/images/stories/documents/FAQ_Human_Mi...
That represents the consensus view (ie no exotic theories). The really good stuff starts on page 10.
They talk about mother's milk/breast milk being a source of microbes for babies at birth. I have heard this before and I wonder if it could be an alternative to this pill/fecal transplants?
Mother's milk is mostly viruses, so it's unlikely this would work against CDiff. For other users is sounds interesting though!