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Fecal Microbiota Transplants: What are they and how are they done?

Updated: Oct 31, 2023

Poop transplants are the real deal, and they are saving lives across the country. Fecal microbiota transplantation (FMT) is the formal term for the process of taking poop from a healthy person and putting it into the colon of a sick person to restore their gut microbiome and help them recover from certain diseases or infections.

The first FMT dates back to 4th century China, where “yellow soup” (ya they are talking about poop here) was applied in cases of severe food poisoning and diarrhea (1). YUMMY.

Bedouin groups have also been said to eat their camels stool as an ancient remedy for bacterial dysentery.

FMT has also been used in veterinary medicine for a long time to heal sick animals. Vets would infuse a healthy animals poop into a sick animal. And if you haven’t noticed, many animal species practice coprophagia, which is a Greek word for “eating poop”. The evolutionary idea behind coprophagia is that it helps create a robust and diverse gut microbiome… maybe our pets are on to something?

Today, fecal transplants are used to treat medication resistant Clostridium difficile (C. diff) infections. C diff is a serious infection of the intestines that causes diarrhea and colitis. Cure rates for C. diff using FMT are typically over 90%.

The standard of care treatment for C. diff is a course of antibiotics like vancomycin. One study compared the use of FMT with vancomycin in patients with recurrent C. diff (they had had the infection previously and treatment failed). 90% of people treated with FMT exhibited resolution of C. difficile‐associated diarrhea, while only 26% of people treated with vancomycin experienced resolution of diarrhea (2). But vancomycin is still the standard of care….

To be fair- in first time infections vancomycin is about 90% effective as well, but about 25% of people with C. diff will experience a recurrence of the infection. So do we just keep hitting them with broad-spectrum antibiotics that create superbugs and antibiotics resistance? That’s not my idea of restoring health!

C. diff is the only FDA approved condition for the use of FMT in the United States, but in other countries they are using FMT for the treatment of other conditions that look really promising.

Other potential uses of FMT:

  • Weight-loss: It has been shown that gastric bypass may actually cause weight loss in part due to the changes in the gut microbiome. And when FMT is done on obese mice using the feces from mice that have undergone a bypass, the obese mice loose weight (despite no gastric bypass surgery). Weight loss has not been shown in human models yet, however I believe this may be seen in the future when we discover what the ideal microbiome is for metabolism optimization.

  • Inflammatory bowel disease (IBD): Ulcerative colitis and Crohn’s disease are two conditions that share similarities with C. diff infections due to the colitis aspect. Studies have shown that FMT induced clinical remission was achieved in 28% patients in the donor FMT groups compared with 9% of patients in the placebo groups (3)

- A smaller study looked at the efficacy of FMT in children and young adults with mild- moderate ulcerative colitis. 67% of subjects maintained positive clinical response 9 months after FMT was administered (4).

You might be thinking, what does this fecal transplant process actually consist of. Here is the basic concept:

  1. In a fecal transplant, stool from a healthy donor is used to replace a patient’s gut microbial flora.

  2. Exact preparations vary, but usually the stool is blended with saline and put through a strainer. It can be frozen before use.

  3. The stool can be applied into the small intestine via a tube through the nose or mouth or deep into the colon, using a colonoscopy. Enemas are popular for at-home treatments, but they only reach the lower end of the colon.

Is FMT safe to do at home by yourself?

Not really. If you don’t have a C. diff infection but think you could benefit from FMT then you need to work with a doctor who can screen your donor to makes sure they are healthy and free of any diseases or infections that can be transmitted through poop. Poop is a biological agent just like semen, vaginal fluid, blood, and saliva, so working with a qualified practitioner is important.

If you want to find out more information on FMT, become a patient today. We love talking about poop!!!


  1. Uwlfoh SS, Dgglwlrqdo RU, Derxw L, Duwlfoh W, Lewin RA. More on Merde. 2016

  2. Cammarota, Giovanni, et al. "Randomised clinical trial: faecal microbiota transplantation by colonoscopy vs. vancomycin for the treatment of recurrent Clostridium difficile infection." Alimentary pharmacology & therapeutics 41.9 (2015): 835-843.

  3. Costello, S. P., et al. "Systematic review with meta‐analysis: faecal microbiota transplantation for the induction of remission for active ulcerative colitis." Alimentary pharmacology & therapeutics 46.3 (2017): 213-224.

  4. Moayyedi, Paul, et al. "Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial." Gastroenterology 149.1 (2015): 102-109.

  5. Moayyedi, Paul, et al. "Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial." Gastroenterology 149.1 (2015): 102-109.

  6. Paramsothy, Sudarshan, et al. "Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial." The Lancet 389.10075 (2017): 1218-1228.

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