What to Expect From a Fecal Transplant

A Potential Cure for Severe Intestinal Conditions

Woman with abdominal pain Woman with abdominal pain at home

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A fecal transplant, also known as fecal bacteriotherapy or fecal microbiata transplant (FMT), is the process of restoring the bacteria commonly found in the digestive tract with an infusion of feces (stool) from a donor. 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.

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.

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 Clostridium difficile colitis, commonly known as C. diff. A C. difficile 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 FB has attracted the most attention.

Research has been done on using fecal transplants to treat ulcerative colitis and inflammatory bowel disease. But for now, the use of FMT for these conditions is considered experimental.

According to one study, fecal bacteriotherapy has a 91% success rate for patients who experience repeated C. difficile overgrowth and the extreme symptoms associated with it.

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.

The medical history of the donor will be examined, along with their current state of health. 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, and other digestive tract issues that could potentially be transmitted to the fecal recipient.

Autologous restoration of gastrointestinal flora (ARGF) is a 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 person who is donating their stool collects it over a few days.The fecal matter is tested for anything that might prove harmful, such as a disease, foreign bacteria or parasites. After the stool is determined to be safe for implantation, it can then be used for FMT.

Prior to the procedure, you will need to stop any antibiotic therapy and follow a liquid diet followed by an enema or laxative preparation the night beforehand. Your doctor will instruct you regarding any prescription medication you take.

Make sure a responsible adult accompanies you on the day of the procedure to take you home after it is finished.

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. It's not the "how" to do it that is the hard part. The part that is still being studied is what makes a good donor and how donated gut bacteria will interact with and change that of the recipient. Patients have died after using "do-it-yourself" fecal transplants. Others have experienced unintended effects such as new bowel diseases or weight gain.

The Transplant Process

The fecal sample is obtained from a donor within six hours of the transplant procedure. It is examined and tested for intestinal parasites and other signs of illness that might rule out the donor. If the sample is appropriate, it is prepared for transplantation, typically by mixing it with sterile water and filtering it repeatedly to remove the solids.

This sample is then infused into the recipient using one of three methods. You will be given anesthesia, with the specific type determined by the method of transplantation.

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 is done repeatedly over the course of no less than five to 10 days, directly introducing the normal flora back into the intestinal tract.

Via Feeding Tube

Another method uses a feeding tube to infuse the stool sample directly into the intestine. This tube is typically used for feeding patients who are unable to tolerate typical types of food or tube feeding. It is inserted into the nose and down into the stomach, and it then continues to advance until it stops in the intestine. The fecal sample prepared for transplant is then infused through the tube, allowing it to be placed directly into the intestine.

In some cases, both the enema and the feeding tube methods may be used to reintroduce normal flora into the digestive tract.

Via Colonoscopy

An enema only extends so far up into the colon, so administering the transplantation via a colonoscopy is another method that may be used. When the procedure is done through a colonoscope, the fecal matter can be spread throughout the colon, which is thought to be more effective.

proton-pump inhibitor is usually given at the same time in order to prevent the beneficial bacteria from being killed by stomach acids.


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

  • Abdominal discomfort or cramping
  • Constipation
  • Bloating
  • Diarrhea
  • Belching or flatulence

Contact your healthcare provider right away if the pain becomes severe or you also experience:

  • Severe abdominal swelling
  • Vomiting
  • Blood in your stool

After Surgery

Fecal transplants are outpatient procedures, and you will go home the same day. Most people experience relief of gastrointestinal symptoms within 48 hours, but it can take up to three months for the gut bacteria to resemble that of the donor.

In some cases, the FMT procedure will be repeated at some point, depending on how effective the first one was.

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  1. Liubakka A, Vaughn BP. Clostridium difficile Infection and Fecal Microbiota Transplant. ACN Adv Crit Care. 2016;27(3):324-337. doi:10.4037/aacnacc2016703

  2. Fischer M, Sipe B, Cheng YW, et al. Fecal microbiota transplant in severe and severe-complicated Clostridium difficile: A promising treatment approach. Gut Microbes. 2017;8(3):289-302. doi:10.1080/19490976.2016.1273998

  3. Narula N, Kassam Z, Yuan Y, et al. Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis. Inflamm Bowel Dis. 2017;23(10):1702-1709. doi:10.1097/MIB.0000000000001228

  4. Browne AS, Kelly CR. Fecal Transplant in Inflammatory Bowel Disease. Gastroenterol Clin North Am. 2017;46(4):825-837. doi:10.1016/j.gtc.2017.08.005

  5. Woodworth MH, Neish EM, Miller NS, et al. Laboratory Testing of Donors and Stool Samples for Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection. J Clin Microbiol. 2017;55(4):1002-1010. doi:10.1128/JCM.02327-16

  6. Taur Y, Coyte K, Schluter J, et al. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci Transl Med. 2018;10(460). doi:10.1126/scitranslmed.aap9489

  7. Chapman BC, Moore HB, Overbey DM, et al. Fecal microbiota transplant in patients with Clostridium difficile infection: A systematic review. J Trauma Acute Care Surg. 2016;81(4):756-64. doi:10.1097/TA.0000000000001195

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