How a Poop Transplant Cures Infection

They’re called fecal microbiota transplantations—and they can knock out a common, dangerous illness.

Medically reviewed in February 2022

Every year, about 500,000 Americans become sick with Clostridium difficile (C. diff) infections, caused by bacteria that invades the colon. But the most stubborn of these infections may have met their match with a procedure known as a fecal microbiota transplantation (FMT). If you’re thinking that sounds suspiciously like putting someone else’s poop into your intestines, you’re right.

That may seem odd, but one recent study was halted early because FMT proved to be so much more effective than the two other treatments in the study. In fact, a participant who had a C. diff relapse after using one of the other treatments was cured with FMT.

Though it's not a typical treatment recommendation—yet—FMT can be a safe and effective method for getting rid of recurring C. diff infections. Here’s how it’s done, and what the future may hold for the procedure.

What is C. diff?  
“C. diff is not normally part of the gastrointestinal flora,” says gastroenterologist Bahri Bilir, MD, of Presbyterian/Saint Luke’s Medical Center in Denver, Colorado. It usually makes its way into your gut through contact with other people or via contaminated food and surfaces. Touch a table with C. diff and then eat a sandwich? You’ve just been colonized by the bacteria. C. diff is particularly common in hospitals—in fact, it’s the most common hospital-acquired infection in the US. 

Once it’s in your intestines, C. diff bacteria can multiply if you’ve been on antibiotics that destroy other bacteria in your gut, but don’t kill C. diff. “Normal flora has an anti-C. diff effect,” Dr. Bilir explains. When the other bacteria are gone, that allows C. diff to grow unchecked, leading to watery diarrhea, nausea and abdominal pain. Left untreated, it can progress to life-threatening complications such as inflammation of the colon, kidney failure or a hole in the colon wall.

C. diff is normally treated with antibiotics. But between 10 and 25 percent of people have a recurrence of C. diff, and this is where FMT is most useful. FMT is done to re-introduce the good bacteria into the digestive tract, which tamps down on C. diff’s growth.

How an FMT is done
The fecal material for FMT comes from donors, who are screened for parasites and infectious diseases like HIV and hepatitis. There are a number of ways to deliver the donor feces, including:

  • A tube down the throat and into the stomach—a nasogastric tube
  • An enema into the lower colon
  • A colonoscopy through the entire colon

Some researchers are even exploring FMT via frozen capsules.

Colonoscopy is the most common method. A tube is snaked through the colon, and as it’s withdrawn, it deposits the donor material. Side effects are generally short-lived and can include belching, nausea, vomiting, abdominal cramps, diarrhea and constipation. All of the delivery methods have been shown to be safe and effective in studies.

No one is sure how many FMT procedures have been performed, but they likely number in the thousands. As FMT becomes more common, the Food and Drug Administration has moved to regulate it more closely.

You’re a good candidate for FMT if:

  • You’ve had at least three mild-to-moderate C. diff infections that didn’t respond to a six- to eight-week course of antibiotics
  • You’ve had at least two C. diff infections that have sent you to the hospital
  • You’ve had a severe C. diff infection that didn’t respond to antibiotics after two days

If you have no C. diff relapse for eight weeks after a procedure, then the FMT is considered successful.

The future of fecal transplants
Though FMT is considered safe and effective, it’s still relatively rare. Expanded donor screening would make Bilir more comfortable with recommending FMT more often. “Right now we only check for obvious infections, and that concerns me,” he says. “If you can get the right bacteria made in a test tube you may have better control over safety, but no one is really doing that right now.” 

Researchers are exploring the use of FMT to treat inflammatory bowel disease (IBD), as well. Antibiotics—and the way they clear the gut of bacteria—may play a similar role in IBD as they do in C. diff infections. According to a 2016 Gastroenterology and Hepatology roundup of research, however, FMT is not nearly as effective in treating IBD as it is in treating C. diff. That’s likely because IBD is a more complex group of diseases than a C. diff infection, say researchers.

Bilir would also like to see more research on the effectiveness and safety of FMT. “Will it become a viable method of treatment? I would like to say yes, but I would like to see more studies,” he says. But with the rate of recurrent C. diff infections soaring and FMT's potential uses expanding, expect this odd-but-effective treatment to only become more common.

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