The more this works, the more we'll be inclined to study it. We'll know eventually.
Even brewer's yeast is discarded after a few generations, usually, since it mutates enough to change the flavor of the resulting beer, and that's in an extremely well controlled environment.
Imagine that happening every six weeks in your gastrointestinal tract. Multiply by 6 billion people. I'd guess it's extremely unlikely we're going to thoroughly investigate all of those different variations on the theme.
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!
Your digestive tract is a jungle, with more species than man will ever fully know about. When too many of certain types go extinct, the ecosystem breaks down, and bad shit starts to happen (come to think of it, literally).
It may take decades to figure out all of the specific species that matter most, and in what proportions. We aren't even certain which bacteria are common to all people, and which are specific to certain cultures / races / geographies / genders / who-knows-what-else. I bet people who eat a lot of KFC have a very different personal biome than I do.
In the meantime, here's 'one weird trick' that seems to just work.