Stephen J. Dubner explained the process of fecal transplants a couple months ago:
[M]any maladies — from intestinal problems to obesity to disorders like multiple sclerosis and Parkinson’s and Alzheimer’s and perhaps even cancer — are related to damaged or missing gut bacteria; the solution therefore may lie in transplanting healthy bacteria into a sick person. How is this accomplished? (Okay, hold your nose for a moment.) A fecal transplant. Yes, you read right: taking the stool from a healthy person, mixing it with a saline solution, and injecting it into an ill person. The procedure resembles a colonoscopy; it’s a sort of combination of organ transplant and blood transfusion, which one doctor in our podcast calls a “transpoosion.”
One woman's success story is here. Earlier coverage of this novel treatment here.