The number of legitimate scientific studies and publications over the last three years has increased exponentially. What started the trend is the government funded Human Microbiome Project http://en.wikipedia.org/wiki/Human_Microbiome_Project
Even NASA is looking into reasons why astronauts have a tendency to develop Candidiasis when spending long durations in space stations.
The title of this NASA press release is: "Yeast Studies in Microgravity Raising New Treatment Potential For Infections on Earth" The date is very recent 9-12-2012.
So finally, the medical Science community is recognizing the importance of Gut Microbiota on overall health, and it is likely going to lead to some successful treatments. it sounds kind of disgusting, but fecal transplants are already being used to restore healthy intestinal flora.