C. diff is responsible for half a million infections, more than 20,000 deaths and at least $1 billion in health care costs in the U.S. per year, according to the Centers for Disease Control and Prevention.

Many of the infections are contracted in hospitals and nursing homes, with the highest risk among patients who take antibiotics for other conditions. Antibiotics, designed to kill harmful bacteria, also can deplete beneficial bacteria that keep C. diff in check.

Unsavory but powerful

At Meriter, fecal transplants cost $1,300 and have been covered by insurance, Griglione said.

Most of the cost is for screening the donor for parasites, unwanted bacteria and viruses such as hepatitis and HIV. The donor doesn't have to be related or blood-matched to the patient.

The stool is put into a blender and filtered to remove solids, resulting in a brown liquid.

Griglione gives one dose of the liquid at the hospital, and the patient administers a second dose at home the same day. Unlike probiotics, which generally contain a limited number of a few freeze-dried bacteria, fecal material has a high volume of a wide range of live bacteria, he said.