Children's Hospital Colorado
Doctor high-fiving her patient.


What is a fecal transplant?

Fecal microbiota transplantation (FMT) is a procedure that transfers a donor’s stool into the recipient’s digestive system. This procedure replaces infectious bacteria present in the digestive tract with healthy bacteria to eliminate an infection known as Clostridium difficile (C. diff).

At Children’s Hospital Colorado, our experts in the Digestive Health Institute and Infectious Disease Department use fecal microbiota transplantation to treat kids with C. diff whose bodies aren’t responding to antibiotics.

A feces transplant is not necessarily a new treatment. However, in the past few years, FMT has been gaining recognition for its effectiveness as more researchers have been studying the treatment. At Children’s Colorado, our experts see positive results in cases of C. diff where antibiotics have failed kids in the past.

What is Clostridium difficile (C. diff)?

Clostridium difficile, also known as C. diff, is a bacterium that can cause an aggressive infection in the digestive tract. A child may contract C. diff:

  • During hospitalization
  • From an imbalance of bacteria due to taking antibiotics
  • By chance alone 

Doctors treat C. diff with specific types of antibiotics to help eliminate the infectious bacteria from the digestive tract. However, in up to a one third of patients with C. diff, the infection returns after treatment with oral antibiotics. At Children’s Colorado, our experts at the Digestive Health Institute turn to FMT to treat these patients whose bodies aren’t responding to antibiotics.

Benefits of fecal microbiota transplantation

  • No side effects
  • Works for many patients, including those with conditions like cystic fibrosis or inflammatory bowel disease, where C. diff is more likely to cause infection
  • A quick outpatient procedure
  • Low (or no) odor
  • Costs less than some antibiotics
  • Covered by most insurance companies (please contact us to see if your insurance covers the procedure)

Where does Children’s Colorado get the stool?

The stool for your child’s transplant comes from a donor stool bank. The bank uses a rigorous screening process to ensure that donors are healthy and there isn’t an existing disease that could be spread in the stool. The fecal matter is shipped and delivered frozen to preserve the healthy bacteria. Before your child’s transplant, it is thawed.

What can patients and families expect from the fecal transplant procedure?

At Children’s Colorado, our pediatric nurses are trained and experienced in performing this procedure. When you arrive for your child’s appointment, the nurse will explain the procedure to you and your child in an age-appropriate way to help put them (and you) at ease.

Before the procedure, your child picks a scent (like Skittles) that is rubbed onto the upper lip to help mask any odor from the stool.

Then, the nurse places a nasogastric tube (NG tube) into your child’s nose. It is a very thin, soft, flexible tube that goes into the nose, through the throat and down into the stomach. Your child is awake for the tube insertion and may find the procedure to be unpleasant, but not painful. We then take X-rays to confirm that the tube is in exactly the right place for the transplant.

After we confirm the NG tube is properly placed, the nurse moves the end of the tube so your child doesn’t see the rest of the procedure. The nurse inserts 30 ml , roughly one ounce, of liquid stool into the NG tube. The donor stool is flushed into the stomach, where it passes through the intestinal tract over the next few hours.

After about 20 minutes, the tube is removed and your child can go home.

What happens when the tube cannot be placed through the nose?

If your child cannot pass an NG tube through their nose, then our team can deliver the fecal transplant by performing a procedure called a colonoscopy. During this procedure, a pediatric surgeon will place a thin tube directly into the colon. Patients are usually asleep (under anesthesia) for this procedure.

How long does a fecal microbiota transplantation take?

The FMT is done as an outpatient visit and takes around two hours to complete. The transplant portion of the visit is typically finished in less than 10 minutes.

Patient eligibility for FMT

Families considering FMT for your child’s C. diff infection will first have a consultation with either the gastroenterologists or infectious disease specialists at Children’s Colorado. During that consultation, we’ll discuss all of the options for treatment of C. diff infection.  If FMT is the best treatment option for your child, you will come back for the transplant at a second appointment.

To be considered for the transplant, children must:

  • Be one year of age or older
  • Have taken antibiotics, including 10 days of oral vancomycin (an antibiotic to treat bacterial infections) and have had C. diff infection return again

Life after fecal microbiota transplantation

After FMT, most children recover from C. diff within three to four days. They can resume eating a regular diet the same day of the procedure.

Once the symptoms disappear, you child can return to normal activities. A nurse in the Digestive Health Institute will follow up with your family one week, one month and six months after the transplant.

Why choose Children’s Hospital Colorado for fecal microbiota transplantation?

We are the only pediatric Fecal Microbiota Transplantation Program in Colorado

Our nationally recognized experts in the Digestive Health Institute are always looking for ways to help kids heal faster and easier. That’s why we are the first and only Fecal Microbiota Transplantation Program in Colorado treating kids for C. diff.

Our nurses have been awarded Magnet recognition

Not only are our nurses trained in providing pediatric care, but they have also received the prestigious recognition for excellence in nursing. When your child visits Children’s Colorado, they are in the best place for kids.

Helpful resources

  • A nonprofit organization dedicated to expanding safe access to fetal microbiota transplants

Compassionate care, wherever you are

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Get to know our pediatric experts.

David Brumbaugh, MD

David Brumbaugh, MD

Gastroenterology - Pediatric