There is a new procedure in which microbiota (the microbes) from a healthy individual are introduced into the gastrointestinal system of a diseased individual via a fecal transplant. The purpose of the fecal transplant is to replace good bacteria which has been suppressed or killed (usually by antibiotics) , and which has caused bad bacteria, such as Clostridium difficile, to overpopulate the gut. This is having amazing success rates. It has been used the most for Clostridium difficile (C. difficile) infections, which sickens about half a million Americans annually. This infection can be so debilitating and so resistant to all antibiotics that about 14,000 Americans die each year from it. Even though not that many have been done, fecal transplants are gaining in popularity (some even being done by do-it-yourselfers using fecal enemas at home) because fecal transplants can have a 95 to 98% success rate.
New research is starting to see if the fecal transplant can be made even easier (via a "poop pill"), and also if fecal transplants will work for Inflammatory Bowel Diseases (IBD). This would mean the future treatment possibility of transplanting microbiota from healthy individuals to individuals sick with IBD. From the October 4, 2013 Science Daily:
Fecal Transplant Pill Knocks out Recurrent C. Diff Infection
C. diff infection can occur after people take antibiotics, wiping out the good bacteria in the gastrointestinal (GI) system, allowing C. diff to flourish and leading to severe diarrhea. In some patients, infection continues to recur despite standard treatment with antibiotics. For patients trapped in that cycle, doctors have transplanted feces from healthy donors into their GI system to rebalance the bacteria and stop infections from recurring.
University of Calgary researchers reported a 100 percent success rate -- none of the 27 patients who took the tablet-sized pills had a recurrence of C. diff, even though all of them previously had had at least four bouts of the infection. Patients ingested between 24 and 34 capsules containing fecal bacteria, often donated by family members.
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There is even the site The Power of Poop which calls itself a "patient information resource dedicated to promoting safe accessible Fecal Microbiota Transplant (FMT) and to raising awareness of the role of the human microbiome in digestive illness." http://thepowerofpoop.com