Fecal Transplant: What It Is & How It's Done

Dr. Antonio Carlos Moraes
Clinical review: Dr. Antonio Carlos Moraes Gastroenterologist CRM 436069-RJ
Created by: Jillian Kinton-Vieira Registered Nurse
Key points
  • Fecal transplant helps restore healthy gut bacteria and is mainly used for recurrent or hard-to-treat C. diff infection.
  • The procedure is done with stool from a carefully screened donor and may be given by colonoscopy, enema, tube, or oral capsules.
  • Recovery is usually quick, but mild side effects and rare complications can occur, so medical follow-up is important.

Fecal transplant, also called fecal microbiota transplantation (FMT), is a treatment used to help restore balance to the gut microbiota. It is mainly indicated for recurrent or refractory Clostridioides difficile (C. diff) infection, particularly when standard antibiotic therapy has failed or the infection keeps coming back.

This procedure may also help treat inflammatory bowel disease, especially mild to moderate ulcerative colitis. However, there are still no ideal protocols for using fecal transplant for this purpose.

Fecal transplant is done in hospitals or specialized clinics and involves transferring stool containing healthy bacteria from a screened stool donor into the patient’s intestines.

doctor discussing fecal transplant with a patient

What is a fecal transplant?

Fecal transplant is a therapy used to restore the balance of microbial flora in the gastrointestinal (GI) tract by replacing unhealthy microbiota with healthy microbiota from a selected stool donor.

Main indications

Fecal transplant may be indicated to treat conditions such as:

1. Clostridioides difficile infection

The main indication for fecal transplant is to treat recurrent intestinal infection caused by Clostridioides difficile (C. diff), such as in pseudomembranous colitis, by restoring healthy gut bacteria and preventing this bacterium from multiplying and causing damage.

According to the American Gastroenterological Association, fecal microbiota-based therapies may be used in select adults with recurrent C. difficile infection after completing standard antibiotic treatment to help prevent recurrence.

Fecal transplant may also be considered for hospitalized patients with severe or fulminant C. difficile infection who do not improve with antibiotic treatment and are not candidates for surgery.

2. Inflammatory bowel disease

Although ideal treatment protocols are still being studied, fecal transplant shows promising potential for treating inflammatory bowel disease, particularly mild to moderate ulcerative colitis.

3. Irritable bowel syndrome

Fecal transplant may help relieve symptoms such as fatigue, abdominal pain, and bloating, improving quality of life.

However, clinical results vary greatly between studies. More research is still needed to assess this possible benefit of fecal transplant.

4. SIBO

Fecal transplant may be a strategy to treat SIBO, or small intestinal bacterial overgrowth.

This is because this therapy may increase microbial diversity, restore biological balance, and relieve gastrointestinal symptoms such as bloating, abdominal pain, and diarrhea.

However, more robust studies are still needed to evaluate the possible benefits of fecal transplant in the treatment of SIBO.

Preparing for the procedure

Preparation for a fecal transplant usually includes stopping antibiotic medications 12 to 48 hours (up to 3 days) before the procedure, as directed by the doctor.

The doctor may also recommend bowel cleansing the day before the transplant to empty the colon and help the new bacteria establish themselves.

How it's done

The steps of a fecal transplant can vary based on the person’s clinical condition and the doctor’s preference, but it is generally performed as follows:

  1. A healthy donor is selected and undergoes a strict evaluation, including blood and stool tests.
  2. The donor’s stool is collected from a bowel movement in a controlled setting to reduce the risk of contamination.
  3. The stool is processed, which may involve mixing it with saline, filtering it, and/or encapsulating it, and it may then be frozen.
  4. The prepared material can be placed directly into the person’s colon during a colonoscopy or flexible sigmoidoscopy.
  5. It can also be administered as an enema, in which a liquid suspension is introduced into the rectum.

In some cases, the material is delivered through a nasogastric (NG) or nasoduodenal tube that runs from the nose to the stomach or small intestine.

Another option is oral capsules, which are swallowed and release the microbiota when they reach the intestine.

Recovery time

Recovery after fecal transplant is usually quick and well tolerated.

However, mild side effects are common and usually go away within 2 days. These can include abdominal discomfort, diarrhea, gas, constipation, nausea, vomiting, or a low-grade fever.

After the transplant, the person should be monitored for 8 weeks or longer to assess how well the treatment worked and to watch for possible side effects.

In some cases, the doctor may recommend avoiding antibiotics for at least 8 weeks after the transplant to avoid compromising the new microbiota.

Potential complications

Possible complications of fecal transplant include:

  • Infections caused by multidrug-resistant bacteria

  • Transmission of pathogens such as C. perfringens, Shiga toxin-producing E. coli, and viruses such as CMV, EBV, SARS-CoV-2, and mpox (formerly known as monkeypox)

  • Aspiration pneumonia and vomiting, in cases of administration by tube or endoscopy

  • Intestinal perforation and risks related to sedation, when the procedure is done by colonoscopy

In addition, people with inflammatory bowel disease may have worsening symptoms after the transplant.

Main contraindications

People with anaphylactic food allergies should not have fecal transplant due to the risk of transferring allergens present in the donor’s stool.

According to the American Gastroenterological Association, fecal microbiota-based therapies are not recommended for severely immunocompromised adults with recurrent C. difficile infection.

This includes people receiving active cytotoxic chemotherapy; those who have undergone CAR-T cell therapy or hematopoietic stem cell transplantation, particularly if neutropenic; and individuals with advanced or untreated HIV or severe primary immunodeficiency.

People with an intestinal perforation or obstruction should not undergo fecal transplant. This procedure should also be avoided via upper gastrointestinal routes, such as nasoenteric (NG) tubes or capsules, in people who are at risk of aspiration.

In addition, people who are pregnant or breastfeeding should only have fecal transplant after a doctor assesses the risks and benefits of this therapy.

Update History
We regularly update our content with the latest scientific information to maintain an exceptional level of quality.

References
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