What to Expect From a Fecal Transplant

A Potential Cure for Severe Intestinal Conditions

A fecal transplant, also known as fecal bacteriotherapy or fecal microbiota transplant (FMT), is the process of restoring the bacteria commonly found in the digestive tract with an infusion of feces (stool) from a donor. When the bacteria in the digestive tract is destroyed as the result of an illness, it can be very difficult to get back. A fecal transplant can help with this.

A woman with abdominal pain on her couch
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While this may seem like a strange or unpleasant concept, it is important to remember that the body requires bacteria to digest food. Bacteria also helps maintain the normal movement of food and stool through the gut.

Reasons for a Fecal Transplant

In a normal digestive system, the hundreds of different bacteria that make up normal flora work to maintain balance, keeping any one bacteria from overgrowing. The balance, however, is a delicate one. When medications interfere, overgrowth can occur. The result can be devastating to the digestive system.

In most cases, the digestive system bounces back on its own, regrowing the normal flora. In others, the overgrowth results in repeated bouts of severe gastrointestinal distress and too little normal flora to be effective. For those, fecal bacteriotherapy is an important treatment option.

Feces are most commonly transplanted as a treatment for severe Clostridioides difficile colitis, commonly known as C. diff.

Infection can occur when the bacterial flora in the large intestine is altered, allowing the C. difficile to proliferate and produce toxins, which can cause severe and even life-threatening colitis and diarrhea. This typically results from a course of therapy with antibiotics that kill good bacteria in the process of killing bad bacteria.

The typical treatment for a C. diff infection is a 10- to 14-day course of anti-C. difficile antibiotics. Occasionally, C. difficile colitis can recur after therapy is complete. It is for these refractory cases that FMT has attracted the most attention.

Research has been done on using fecal transplants to treat ulcerative colitis and inflammatory bowel disease. Recently, the FDA approved Rebyota, a fecal microbiota product, to prevent the recurrence of C. diff infections in adults. It is for use after an individual has completed antibiotic treatment for recurrent C. diff infections.

Who Is Not a Good Candidate?

An FMT can be risky in some patients, and your healthcare provider may advise against the procedure under the following circumstances:

Donor Recipient Selection Process

Unlike many types of transplant procedures, fecal transplantation doesn't involve being added to a competitive waiting list. In fact, recipients aren't selected for a transplant so much as transplants are arranged when the need arises.

Most recipients receive a donation from someone they know after requesting such assistance.

Types of Donors

Typically, a healthy friend or relative is considered the ideal candidate for fecal donation, but any willing person may volunteer to contribute. There are stool banks that collect stool for this purpose.

The medical history of the donor will be examined, along with their current state of health, and blood tests will be done to rule out infections.

The donor must be free of infectious diseases, such as hepatitis A, B and C, and HIV. They must also be free of parasitic diseases, yeast overgrowth, celiac disease, and other digestive tract issues that could potentially be transmitted to the recipient.

In addition, a donor must not:

  • Have taken antibiotics for three weeks prior to the transplant
  • Have chronic diarrhea, inflammatory bowel disease, or colorectal cancer
  • Have engaged in (or be currently engaging in) sexual behavior that has a high risk of sexually-transmitted diseases
  • Be undergoing cancer treatment

Ongoing Research

Currently, scientists are researching so-called "super-donors," which refers to people whose gut bacteria is ideal for FMT. This would theoretically make some people more desirable donors than others.

Autologous restoration of gastrointestinal flora (ARGF) is another technique that is currently being studied. In this process, patients who are at risk for destruction of the normal flora of the intestine—such as those who undergo stem cell transplants—provide a sample of their own stool. The sample is stored, and if it is needed, it is filtered and freeze-dried.

A 2018 study done at Memorial Sloan-Kettering Cancer Center found that ARGF can restore important gut bacteria that may be destroyed in patients undergoing a stem cell transplant for a blood cancer.

Before the Procedure

The evening before the FMT procedure, the donor will take a laxative. The next morning, they will collect their stool in a container called a "hat" (obtained beforehand at a pharmacy) and deliver it to the outpatient facility where the transplant will occur.

The sample will be prepared for transplantation by mixing it with sterile water and filtering it repeatedly to remove the solids. Once prepared, it must be transplanted within six hours. 

As the recipient, you must not have taken antibiotics for two weeks prior to the procedure. Assuming this is the case, you will take a laxative (or an enema) the night beforehand so that your bowels are empty.

On the day of the transplant, you will be given a proton-pump inhibitor (PPI) to prevent the beneficial bacteria from being killed by stomach acids, as well as an anti-diarrheal medication (e.g., loperamide) to keep the transplanted stool in your gut while it takes hold.

Make sure to arrange for someone to take you home after the procedure.

Do Not Try This at Home

Fecal transplants should never be done at home, even after reading instructions or watching a video of how one is done. The risks include perforating your colon or damaging your rectum, as well as introducing harmful bacteria into your system.

The Transplant Process

FMTs typically take place in an outpatient facility. The stool can be transplanted in a variety of ways. The severity of your digestive disease, your overall health, and your personal preference will all be considered when determining which method of delivery is most appropriate for you.

Via Enema

If the enema method is used, the stool sample is placed into the enema bag or bottle, then infused into the rectum where it is held as long as possible.

This may need to be done repeatedly over the course of a few days in order to sufficiently introduce the normal flora back into the intestinal tract.

Via Colonoscopy

An enema only extends so far up into the colon, so performing the transplant via a colonoscopy is another method that may be used.

With this, the stool sample is placed in a colonoscope, which is inserted into the anus and slowly advanced into the colon, where the stool sample is released.

The procedure takes around 30 minutes, and you will be given a sedative.

Via Upper Endoscopy

If there are contraindications for a colonoscopy, the transplant may be done via an upper endoscopy.

For this procedure, you will be given a sedative. An endoscope is inserted into your mouth, and air is used to fully open the esophagus, stomach, and intestine. The stool is then placed into your small intestine.

The procedure lasts approximately 15 to 20 minutes.

Via Capsule

With this method, the stool is encapsulated within three layers of gelatin. You are required to ingest as many as 40 capsules—each roughly the size of a large multi-vitamin—over the course of a day or several days; you will be monitored by your healthcare provider for any side effects.

One study found this method's effectiveness to be comparable to the colonoscopy procedure.

Via Feeding Tube

Another method uses a feeding tube to infuse the stool sample directly into the intestine. This is typically used for patients who cannot tolerate other methods. The fecal sample is infused through a nasal tube and placed directly into the intestine.

After any procedure, you will be asked to hold your stool for at least two hours to prevent eliminating the new bacteria.


Following a fecal transplant, you may experience side effects, including:

  • Abdominal discomfort or cramping
  • Constipation
  • Bloating
  • Diarrhea
  • Belching or flatulence
  • A reaction to the sedative

More serious risks can occur when a colonoscopy or endoscopy is used, including bleeding and perforation of the intestine or bowel.

Fecal transplants are not without very serious risks. In April 2020, the FDA released a statement saying that six patients who received stool from a certain stool bank contracted serious infections and an additional two patients died.

After Surgery

Fecal transplants are outpatient procedures, and you will go home the same day. If you have received a sedative, you will be monitored until it wears off before you can leave the facility.

You may have diarrhea for a few days, but most people experience relief of gastrointestinal symptoms within 48 hours; it can take up to three months for the gut bacteria to resemble that of the donor.

If symptoms recur within four weeks, the procedure is thought to have failed. In some cases, it will be repeated in the future, though there are currently no specific guidelines for optimal timing for a second FMT.


According to a 2019 review, fecal bacteriotherapy has been found to have a 70% to 93% cure rate in patients who have experienced repeated C. difficile overgrowth and the symptoms associated with it.

The success rate is generally lowest with the capsule delivery method and highest with the colonoscopy method. 

A Word From Verywell

Fecal microbiota transplants have become an accepted and effective method for treating serious and intractable C. difficile infections. Your healthcare provider can advise you on the risks and benefits and advise you on the procedure that is likely to be most effective in your case.

13 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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Additional Reading

By Jennifer Whitlock, RN, MSN, FN
Jennifer Whitlock, RN, MSN, FNP-C, is a board-certified family nurse practitioner. She has experience in primary care and hospital medicine.