I haven't read through all of the responses, but I'm just going to assume that no one has suggested FMT (fecal microbial transplantation), ie: putting a healthy donor's stool in your bum. :D. I've been doing lots of research about it lately and getting more and more convinced that its an excellent way to repopulate the gut after Antibiotics .
Here's some of the links I've been collecting:
An article by the mayo clinic about FMT:
"The microbiome of the gut is not inactive; it's diverse and plays many roles in health and well-being that are just now being explored," Dr. Orenstein points out. "With molecular biology and the sequencing of these species, this can only get bigger. It's like the beginning of the space program."
And here's an article by The New York Times on how the lack of certain gut microbes might cause celiac disease and other auto immune diseases in general:
And finally, here's a link to a podcast by a girl who did one FMT the DIY way and cured herself of fibromyalgia, lost weight, cleared her complexion and stopped being sensitive to certain foods: