Admittedly, a fecal transplant—putting someone else’s poop into your body—sounds unpleasant. However, it may be the only way to cure some very serious gastrointestinal conditions that resist conventional treatment. And the procedure is not really as gross as what you’re probably imagining.

The medical name for the procedure is fecal microbiota transplantation (or FMT)—and the serious condition it most commonly treats is C. difficile (C. diff), a bacterial infection that sickens half a million Americans and kills up to 30,000 each year. In fact, both the Infectious Diseases Society of America and The Society for Healthcare Epidemiology of America have recently added FMT to their official guidelines for treating C. diff. 

An Ancient Therapy Made Modern

The concept of curing illness with donor fecal matter dates back to 4th-century China, when a cruder version of the procedure (which truly was gross—it involved making a soup!) was used to treat severe food poisoning and diarrhea. Today’s procedure administers FMT via colonoscopy, enema or a tube run through the nose and into the stomach. (An oral capsule is being tested in clinical trials.) The procedure is simple and usually performed outpatient. In most cases, the patient leaves the hospital the same day and C. diff symptoms ease within days.

The fecal matter used in FMT comes from either a local donor (someone you know or the hospital’s donor program) or from a national nonprofit stool bank called OpenBiome. In all cases, donors are screened first for illnesses, the same as for blood donors. With a local donor, medical staff mixes the stool with saline (often in a basic kitchen blender) to prepare for a transplant. OpenBiome stool donations are filtered and homogenized, then sealed and kept frozen. 

The risk for side effects is low—for instance, abdominal discomfort or a mild fever. FMT has become so accepted as a treatment for C. diff that 97% of Americans live within two hours of a facility that performs the procedure, according to OpenBiome.

How FMT Works

The main culprit behind C. diff and many other gastrointestinal upsets is a disruption of the gut microbiome. This can be caused by medical conditions, such as a compromised immune system, diabetes or obesity…or from taking certain drugs, such as antibiotics. FMT transplants gut organisms from a healthy donor into a sick patient’s gut, repopulating the disrupted gut and helping to restore the natural balance. Numerous studies show FMT to be about 70% to 90%—or more—effective for treating recurrent C. diff infections. (If you’re wondering why probiotics don’t help, they contain only a few strains of microorganisms, not the wide, diverse spectrum contained in the stool of a healthy donor.)  

C. diff bacteria actually are present in a normal, healthy gut in small numbers. But when antibiotics—even a single course—kill off healthy gut bacteria while they’re killing the pathogens that made you sick, C. diff can take over, triggering severe diarrhea. Ironically, the standard first line of treatment for C. diff is more antibiotics, which explains why recurrent C. diff is a common problem. Especially vulnerable are children, people over age 65 and those who have a compromised immune system.

The FMT Frontier

While the effectiveness of FMT has only been established for treating C. diff—which is the only FDA-approved use outside of research—the procedure shows promise for other conditions. Because your gut microbiome is critical to your whole immune system and your general health, scientists are studying how FMT might also treat irritable bowel syndrome (IBS), Crohn’s disease, diabetes, obesity, peanut allergies and melanoma.

The National Institutes of Health is currently funding a large study that is being conducted by the Fecal Microbiota Transplantation National Registry under the guidance of the American Gastroenterological Association’s Center for Gut Microbiome Research and Education. 

The study plans to track about 4,000 FMT patients for a decade after their transplants. The researchers will be gathering data on FMT’s effectiveness for C. diff and other illnesses, including information on the short- and long-term effects. Currently, more than 20 hospitals, medical centers and medical schools across the country are participating—a number that’s expected to grow to 75.

Meanwhile, you can search for a doctor who performs FMT by going to

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