Fecal Microbiota Transplant

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What is Fecal Microbiota Transplant?

In healthy children, there is a large community of bacteria in the colon (large intestine) called the Microbiota. When the Microbiota is damaged or replaced by unhealthy bacteria, a germ called Clostridioides difficile (C. difficile or C. diff), can grow in the colon and cause diarrhea. C. diff diarrhea can happen repeatedly, especially if the Microbiota is not repaired. When C. diff diarrhea keeps happening, this is called Recurrent C. diff. One way to treat Recurrent C. diff is by replacing the unhealthy microbiota in the colon with a healthy microbiota which prevents C. diff from growing again. The name of this treatment is called Fecal Microbiota Transplant.

Why might a child need a Fecal Microbiota Transplant?

Although it is not visible to the eye, C. diff can be found in a lot of places, including people’s homes and hospitals. When a person comes into contact with C. diff, it can infect the colon. Normally, we don’t even know it is there, and it does not cause any symptoms. However, when something damages the Microbiota, the C. diff can start to grow and make toxins in the colon that cause diarrhea. Many things can damage the Microbiota in the colon, especially antibiotics taken for an infection, but other medications and certain diseases can also harm the microbiota. Usually, another antibiotic is needed to treat the C. diff infection. When these antibiotics fail and the C. diff diarrhea keeps coming back, Fecal Microbiota Transplant may be used.

What happens in a Fecal Microbiota Transplant?

In a Fecal Microbiota Transplant, fecal material (stool or poop) is taken from a healthy person, called the donor. The liquid stool is then poured through a tube inserted in the child’s nose into the child’s intestines or squirted into the child’s colon through a device called a colonoscope. It is important that the donor who is providing the stool does not have any diseases or infections, so the donor is checked very carefully with blood and stool tests. Once the donor is found to be healthy and has passed the testing, a sample of their stool is processed and changed into liquid form so it can be given to the child with Recurrent C. diff.

How does Fecal Microbiota Transplant work?

Although it is not known exactly how Fecal Microbiota Transplant works, it is believed the healthy bacteria from the donor’s stool replaces the child’s damaged Microbiota and prevent the C. diff from growing back.

How do I prepare my child for a Fecal Microbiota Transplant?

Your doctor will provide specific instructions before the Fecal Microbiota Transplant. Usually, all antibiotics are stopped 48 hours before the Fecal Microbiota Transplant is performed. Your child may also be given instructions about when to stop eating and drinking before the transplant.

What can I expect if my child has had a Fecal Microbiota Transplant?

Most children can return home and resume their daily activities shortly after the transplant. If sedation (anesthesia) was used, your child may feel sleepy for a few hours after the transplant.

About 85% percent of children who receive a Fecal Microbiota Transplant are cured of their Recurrent C. diff diarrhea, but some children need a second Fecal Microbiota Transplant. Your physician will usually recommend avoiding more antibiotics and cleaning your home very well to prevent the C. diff infection from returning.

What are the side effects of Fecal Microbiota Transplant?

Fecal Microbiota Transplant is considered very safe, and most children who receive a Fecal Microbiota Transplant have no side effects, but some children may have mild symptoms, such as diarrhea, abdominal pain, bloating or vomiting. Very rarely, a child can get an infection from the donor stool.

What should I watch for after Fecal Microbiota Transplant?

Your child’s healthcare provider should discuss with your family signs and symptoms that require urgent medical attention. In general, you should contact your child’s healthcare provider/gastroenterologist or go to the nearest emergency department if your child experiences any of the following :

  • Pain that wakes your child from sleep
  • Severe pain that is different from your child’s usual pain
  • Fever higher than 101ºF
  • blood in stools
  • Persistent or severe vomiting


Bernard R et al. (2021) Fecal Microbiota Transplantation and Microbial Therapeutics for the Treatment of Clostridioides difficile Infection in Pediatric Patients. J Pediatric Infect Dis Soc. 10(Supplement_3):S58-S63.

Davidovics ZH et al. (2019) Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection and Other Conditions in Children: A Joint Position Paper From the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition. J Pediatr Gastroenterol Nutr. 68(1):130-143

Nicholson MR et al. (2020) Efficacy of Fecal Microbiota Transplantation for Clostridium difficile Infection in Children. Clin Gastroenterol Hepatol. 18(3):612-619

Author: Jonathan Gisser, MD
Editor: Christine Waasdorp, MD
September 2023

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North American Society for Pediatric Gastroenterology, Hepatology and Nutrition
The Association of Pediatric Gastroenterology and Nutrition Nurses
North American Society for Pediatric Gastroenterology, Hepatology and Nutrition Foundation
The NASPGHAN Council For Pediatric Nutrition Professionals
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