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Fecal Transplant Facts, Potential Benefits, and Concerns

Linda Crampton is an experienced teacher with a first-class honors degree in biology. She writes about the scientific basis of disease.

The stomach leads to the small intestine, which in turn leads to the large intestine.

The stomach leads to the small intestine, which in turn leads to the large intestine.

The Importance of Bacteria in the Intestine

Many bacteria live in and on our body, especially in our large intestine. Good intestinal bacteria are so important in our lives that without their presence we may experience disease. Doctors have discovered that samples of feces containing the microbes from healthy people can be used to treat certain intestinal diseases in other people. The feces (or stool) is delivered to the patient as a fecal transplant. The process of transferring the stool is sometimes called fecal transplantation. It's very important that this procedure is performed under safe and medically supervised conditions. Stool may contain dangerous bacteria as well as helpful ones.

As unpleasant as fecal transplants may sound, they have been a wonderful boon for some people. The transplants have been most helpful for people suffering from a persistent intestinal infection by Clostridium difficile bacteria and have a high success rate in treating this illness. They have also helped some people with inflammatory bowel disease, or IBD. "Bowel" is another name for intestine. It's possible that fecal transplantation will eventually be useful for other disorders as researchers learn more about the composition and behaviour of our microbe community.

The tubular structure in which digestion occurs is called the gastrointestinal tract, GI tract, digestive tract, or gut. The tube runs from the mouth at the start to the anus at the end. The bacteria in the small and large intestine are known as gut or intestinal bacteria.

This is a colourized photo of E. coli cells. The normal strains of E. coli in our gut are different from the ones that make us sick.

This is a colourized photo of E. coli cells. The normal strains of E. coli in our gut are different from the ones that make us sick.

The Intestinal Microbiome

The bacteria that live in our large intestine are accompanied by a smaller number of yeasts and other microscopic organisms. Many of the microbes live in the colon, the longest part of the large intestine. Some live in the small intestine, however, especially in the ileum, or the last part. The sections of the large intestine and the end of the small one are labelled in the first image in this article, which may help people to visualize the structures.

It's thought that between 500 and 1000 different kinds of bacteria and trillions of individual ones normally live in the large intestine. Most of these microorganisms are helpful, but some are harmful. A healthy gut has far more beneficial microbes than harmful ones.

The community of microbes on or in the human body is called a microbiome. Some researchers believe that we may contain slightly more bacterial cells than human ones. This is possible because bacteria have smaller cells than humans and because the bacteria often colonize cavities in our bodies. The colony in the intestine is known as the intestinal microbiome.

Benefits of Intestinal Bacteria

The relationship between us and the helpful microbes in our gut is mutually beneficial. Colon bacteria feed on nutrients that enter the large intestine from the small intestine. The intestine also provides a warm and moist habitat for the bacteria. The microbes help us by producing nutrients that we absorb, such as vitamin K and biotin.

Another benefit of gut bacteria is that some ferment the soluble fibre that we eat into short-chain fatty acids. These acids are thought to have many helpful effects, including enhancing the activity of the immune system, improving the structure and function of the intestinal lining, lowering the blood cholesterol level, and helping to regulate the blood glucose level.

Good bacteria also help to prevent the growth of pathogens (disease-causing microbes) in the large intestine. In addition, they break down material that we are unable to digest. They may also reduce inflammation and have other health benefits.

Our microbiome is so important that the National Institutes of Health (NIH) has established a special project to study it. The goal of the Integrative Human Microbiome Project is to catalogue the microorganisms found on and in the body and to discover their role in health and disease.


The information below is given for general interest. Anyone with question about fecal transplantation or about intestinal problems that might be helped by the procedure should visit a doctor for advice. A fecal transplant must be performed by a doctor, who will know about all the necessary safety precautions.

Problems Treated by Fecal Transplantation

At the moment, most fecal transplants are performed to treat gut disorders caused or suspected to be caused by gut dysbiosis (an abnormal community of bacteria in the gut). The process of fecal transplantaction is sometimes known as fecal bacteriotherapy, fecal microbial transplantation, or FMT.

Some patients with a Clostridium difficile infection, Crohn’s disease, or ulcerative colitis have responded well to fecal transplantation. Clostridium difficile is an infectious bacterium and is one of the so-called "superbugs." Crohn’s disease and ulcerative colitis are forms of inflammatory bowel disease, or IBD. Researchers have discovered evidence suggesting that people with inflammatory bowel disease have an abnormal community of gut bacteria and that this community is determined by a person's genetic makeup.

Fecal transplants have about a 90% success rate in people with a persistent and serious Clostridium difficile infection. In addition, the improvement in the patient's condition may occur as soon as one to three days after treatment. Fecal transplants have about a 45% success rate for people with inflammatory bowel disease. The success rate is higher in some subgroups with IBD and lower in others. The lower success rate for IBD than for a Clostridium difficile infection may reflect the fact that IBD might involve more than just a gut bacteria problem.

The sections below discuss the three disorders that fecal transplants have helped. It’s important to remember that there is no guarantee that the treatment will be helpful in a specific case, however.

Clostrifium difficile or C. Diff Infections

Clostridium difficile is a bacterium that infects the large intestine, causing colitis (inflammation of the colon), severe diarrhea, nausea, vomiting, abdominal pain, dehydration, and a fever. Infection by Clostridium difficile, also known as C. difficile or C. diff, may occasionally be fatal.

C. diff infections tend to develop in hospitals and other medical facilities, although they appear in the general community as well. Like other superbugs, the bacterium is resistant to many antibiotics and is difficult to kill. In fact, the infection often appears in patients who have been taking antibiotics for a different infection. The antibiotics kill other bad bacteria and good bacteria as well, but don't affect C. diff. significantly. Without good bacteria to keep C. diff under control, the Clostridium difficile population may increase and cause unpleasant effects. In some places, a fecal transplant may be offered to people when antibiotics don't get rid of C. diff.

Fecal Transplants and the Immune System

There might be more to the effects of fecal transplantion in a C. diff infection than an increase in the concentration of beneficial bacteria in a person’s large intestine. Researchers at the University of Virginia School of Medicine have discovered that a fecal transplant also raises the level of an important immune system molecule called IL-25. The increase in the molecule’s concentration is accompanied by a decrease in inflammation in the intestine. The researchers suspect that the increase in good bacteria and the increase in IL-25 both play a role in a patient’s improvement in the infection.

Crohn's Disease Facts

Crohn's disease is a disorder involving inflammation of the gastrointestinal tract. Any section of the GI tract may be inflamed, from the mouth to the anus. The lower part of the small intestine and the first part of the large intestine are the most common sites affected, however. Patches of inflamed tissue appear on the intestinal lining and may be deep.

The cause of Crohn's disease isn't known. It is known that the patient's immune system behaves abnormally, which results in damage to the GI tract. The immune system may be responding to the presence of certain bacteria in the gut and may stay active even when these bacteria are destroyed. There seems to be a genetic tendency to develop the disease when the right environmental trigger appears.

Patients with Crohn’s disease may have mild symptoms or severe ones that make life very difficult and unpleasant. Gastrointestinal tract problems often include bloody diarrhea and abdominal pain. Symptoms may extend beyond the GI tract. The patient may suffer from loss of appetite, weight loss, fatigue, joint pain, fever, nausea, vomiting, skin problems, and eye inflammation.

People with Crohn's disease generally experience flare-ups, or periods when their symptoms are severe, alternating with periods of remission when their symptoms are weaker or absent.

Ulcerative Colitis Facts

Ulcerative colitis produces similar symptoms to those caused by Crohn’s disease, but the intestinal effects are slightly different. The inflamed tissue in the intestine generally appears only in the colon and the rectum (the chamber at the the end of the large intestine that stores the feces before it's eliminated). In addition, only the surface layer of the intestinal lining tends to be affected in ulcerative colitis, while in people with Crohn's disease the damage goes deeper into the lining.

As in Crohn's disease, the immune system behaves abnormally in a person with ulcerative colitis. Also as in Crohn's disease, the cause of the disorder isn't known for certain. It may be due to either the presence of harmful bacteria or an inappropriate immune response to healthy ones.

People with ulcerative colitis experience flare-ups and remissions. They are said to be more like to experience an absence of symptoms during remissions than people with Crohn's disease.

Fecal Transplantation

Fecal transplantation is an attempt to correct a health problem by improving the composition of the gut flora. The goal is to insert beneficial microoganisms into the large intestine. The transplanted microbes will hopefully reproduce, fighting or crowding out dangerous bacteria.

Fecal transplantation is not a new technique. It's been performed since the 1950s. The process has only recently begun to be seriously investigated by researchers, however.

Dr. Thomas Borody, an Australian gastroenterologist, is a leading practitioner of fecal transplants. He is not only treating gut disorders with the transplants but is also investigating whether other disorders such as multiple sclerosis, chronic fatigue syndrome, and Parkinson's disease can be improved by fecal transplantation. Other doctors are trying to find out if transplantation of beneficial bacteria from the stool of lean people into overweight people can treat obesity.

The transplanted stool is inserted into the colon or occasionally through a tube inserted into the nose or mouth. The recipient doesn't smell or taste the stool that is administered by the second method. Some companies are exploring the use of a capsule containing the bacteria that could be swallowed. A research team has discovered that in the patients that they studied, the donated bacteria were still present in the intestine two years after a transplant.

Safety Concerns

Fecal transplants are simple to perform and often have rapid benefits. However, the transplantation must be done by a doctor or under a doctor’s guidance. Safety is extremely important. The sample of feces must be prepared properly. In addition, donors and their feces need to be screened for the presence of parasites so that the recipient doesn't develop a serious or even deadly infection as a result of the transplant.

It's vital that an expert checks donated feces for the presence of harmful bacteria and other parasites before a fecal transplant is performed. If this isn't done, the patient may become sicker than they were before the transplant and may become dangerously ill. Unfortunately, as described below, not all of the harmful bacterial in the donated stool may be detected.

A Cautionary Tale

As wonderful as fecal transplantation may sound, there could be a problem with ensuring that the donated stool is completely free of harmful bacteria. In mid 2019, a patient in the United States died when given a fecal transplant in a clinical trial. The donated stool contained a multidrug-resistant bacterium that hadn't been detected when the stool was analyzed. The infection killed the recipient, despite efforts to save them. The patient was suffering from another disease, but they weren't near death when they received the stool.

A patient in a different clinical trial and with a different pre-existing illness also received a donation from the contaminated stool sample. They became infected by the multidrug-resistant bacterium, but they recovered after treatment.

The FDA (Food and Drug Administration) has issued new guidelines for fecal transplantation. The organization says that the organism that killed the stool recipient plus some other multidrug-resistant microbes should be screened for in future fecal transplants. "Screened for" means that specific tests are performed to identify the particular species of bacterium in a sample. Though this sounds like an excellent step to take, it may not be enough to guarantee safety. Different bacteria may require different tests to prove that they are present. A doctor familiar with the cases described above made the comment shown below.

It’s important to remember that there may be other such organisms out there that aren’t being screened for.

— Dr. Elizabeth Hohmann, Harvard Medical School (with respect to a stool donation), via NBC News

Fecal Medicine

Though much of the research into the effectiveness of fecal transplants has been related to intestinal problems, some scientists are exploring its effects on other diseases. In Canada, medical researchers are investigating whether the transplants can be beneficial for some types of depression and for improving immunotherapy treatment for cancer, for example. A few researchers are using the term "fetal medicine" to describe their investigations.

Some researchers are warning us about getting carried away with the idea that fecal transplants can help anything that ails us. Others point out we sometimes don’t know whether bad intestinal bacteria are causing a health problem or whether the health problem is favouring the existence of bad bacteria in the gut. Still, the research is fascinating and could be very important.

The Acceptibility of Fecal Transplantation

At the moment, fecal transplantation is usually considered to be a “last resort” treatment for patients suffering from debilitating or very dangerous intestinal problems who have tried all other treatments without success. This is because there hasn’t been much scientific research concerning fecal transplantation (although this situation is currently changing) and also because of the difficulty in ensuring that the donated feces is prepared properly and is free of pathogens.

As the effectiveness of the treatment is being demonstrated—especially in the case of serious C. diff infections—its use is spreading. Where I live, the procedure is becoming more acceptable and more common. Fecal transplants still have limited availability at the moment, however.

Receiving someone else’s feces may sound repulsive to a healthy person. For someone who is experiencing debilitating intestinal symptoms, though, the process mIgor sound like it could be a godsend. Hopefully, researchers will discover ways to make fecal transplants effective and safe for even more people and diseases.


  • C. difficile infections could be treated with fecal transplants from the CBC (Canadian Broadcasting Corporation)
  • A link between the transplant and the immune system has been discovered from the Medical Xpress news service
  • Donor microbes persist for up to two years after a fecal transplant to treat recurrent C. difficile infection from the University of Alabama at Birmingham
  • Fecal study shows promise for Crohn's Disease from WebMD
  • Fecal microbiota transplant is effective for patients with ulcerative colitis from the Medical Xpress news service
  • Drugmakers tackle 'ick' factor with fecal transplant therapies from Reuters
  • Why fecal medicine could be the next buzz from the CBC
  • A fecal transplant led to a patient's death from NBC News

This content is accurate and true to the best of the author’s knowledge and does not substitute for diagnosis, prognosis, treatment, prescription, and/or dietary advice from a licensed health professional. Drugs, supplements, and natural remedies may have dangerous side effects. If pregnant or nursing, consult with a qualified provider on an individual basis. Seek immediate help if you are experiencing a medical emergency.

Questions & Answers

Question: How is the fecal donor screened and specimen collected?

Answer: The collection process depends on the agency involved. One agency here in Canada gives donors a special attachment that is placed over a toilet seat. The attachment contains a plastic container for stool collection. Once the stool has been deposited, the container must be packaged according to instructions and taken to the agency.

Based on the agency’s requirements, before becoming a donor, a person must complete a questionnaire and undergo blood and stool tests. The blood and stool are checked for pathogens. Some examples of pathogens tested for by different agencies are Clostridium difficile, Giardia, Cryptosporidium, Isospora, Helicobacter pylori, and Rotavirus.

Question: Does the donor in a fecal transplant have to have blood or histocompatibility?

Answer: No, not as far as I know. It's very important that someone visits a doctor in order to get a donation, however. The most serious risk is the transfer of pathogens (microbes that cause disease) from the donor to the recipient. A doctor will be able to provide a safe source of feces that has been medically tested for specific pathogens. He or she will also be able to provide an effective transfer of the material.

© 2011 Linda Crampton


Linda Crampton (author) from British Columbia, Canada on December 31, 2015:

Thank you very much for the interesting comment and for sharing your experience and opinion, Aelbarsha. I appreciate your visit.

Abdelhakim Elbarsha from Benghazi/Libya on December 31, 2015:

Thanks for great hub.

The issue of fecal transplantation is hot. The evidence is growing regarding the effectiveness of fecal transplantation in curing many gut disorders, and probably systemic diseases like metabolic syndrome.

The future may bring more, and other diseases not related to the digestive tract may be targeted by restoring a normal colonic bacterial population.

I personally expect that many diseases labelled as "idiopathic" are caused by abnormally increased exposure to external toxins or antigens delivered to our system from an altered colonic medium.

Linda Crampton (author) from British Columbia, Canada on May 17, 2012:

Thanks for sharing a very interesting story, Toppin Martin. I'm glad that the fecal transplant worked so successfully for you!

Toppin Martin on May 17, 2012:

Had eleven months of C.Diff. Had colonoscopy during which the fecal matter from my best friend was deposited along the length of colon. I am now C.Diff free. The only thing that allowed me to be functional during those eleven months was a steady diet of Vancomycin at the cost of $196 per day day dose. It's a simple procedure with cure rates over 90%. Don't live with this. Get the transplant!

Linda Crampton (author) from British Columbia, Canada on April 09, 2011:

Thank you for the comment and the vote, kashmir56!

Thomas Silvia from Massachusetts on April 09, 2011:

Hi AliciaC, thanks for all this great information, i have not heard of this before so thanks for making me aware of it .

Useful and vote up !!!

Linda Crampton (author) from British Columbia, Canada on April 08, 2011:

H, prasetio30. Thank you for visiting my hub and for the rating!

prasetio30 from malang-indonesia on April 08, 2011:

I had never knew about this. I learn much from you. Thanks for writing this. Rated up! Have a nice weekend..


Linda Crampton (author) from British Columbia, Canada on April 07, 2011:

I'm glad that your friend found help for her colitis, Fossillady. It can be a horrible disorder. The more treatments discovered the better!

Kathi Mirto from Fennville on April 07, 2011:

I have a friend who suffers from colitis and it really messed up her daily life. She had surgery to remove a blockage and is doing great now! It's always good to know they are making more advances.

Linda Crampton (author) from British Columbia, Canada on April 06, 2011:

Hi, Chatkath. Thanks for the comment. You must have some interesting discussions with your sister!

Kathy from California on April 06, 2011:

Wow, this is really interesting stuff, I must say. My sister is a nurse/director at an endoscopy center so I hear a bit too much sometimes about the procedures but this is all stuff I did not know! Great and informative Hub!!!

Linda Crampton (author) from British Columbia, Canada on April 06, 2011:

Hi, A. A. Zavala. Yes, fecal transplantation is probably very unappealing for most people, and researchers don’t yet know if it will work for everyone who has Crohn’s disease or other severe intestinal problems. However, the people that I’ve read about who received a fecal transplant were having a miserable life, in pain and unable to move far from a bathroom. In this situation I guess they thought it was worth receiving the transplant.

Thank you very much, Simone!! At the moment a fecal transplant sounds very disagreeable to me too, but if I had a health problem that was serious enough, and if there there was evidence that a fecal transplant might help, I would consider it.

Simone Haruko Smith from San Francisco on April 06, 2011:

Whoah. Wow. Wow! You've offered an excellent discussion of the subject- and it sure is an interesting one! Voted up and useful... I just hope I never need a fecal transplant =_=

Augustine A Zavala from Texas on April 06, 2011:

Its a bizarre way of treating Crohn's, and patients may not like the idea. I'm just glad we're looking at all options in treating disease.

Linda Crampton (author) from British Columbia, Canada on April 06, 2011:

Yes, it is fascinating! I'm very interested in the research concerning the effects of fecal transplantation on other health problems in addition to intestinal disorders.

Augustine A Zavala from Texas on April 06, 2011:

I read about the fecal transplantation technique, and heard about it on NPR. Fascinating!