Fecal Matter Transplants – What You Need to Know

Nina Zeldes, PhD and Meg Seymour, PhD, National Center for Health Research

The gastrointestinal tract – the gut – of a healthy person contains thousands of microorganisms. These include many types of bacteria and yeast. All of these microorganisms make up the gut’s microbiome. We don’t yet fully understand exactly how important they are, but more and more research shows that the gut and its microbiome influence our overall health, and not just digestion. The results may surprise you. For example, recent studies suggest that the bacteria in our gut may have an impact on our mood.[1]

There are many different “good” bacteria in a healthy and balanced gut microbiome that are crucial for our health. They keep “bad” bacteria in check, for example by preventing an overgrowth of dangerous bacteria like E. coli. For more information about good and bad forms of bacteria, you can read this article.

When helpful bacteria are killed or get outnumbered by more dangerous types of bacteria, this can cause serious health problems. That can happen, for example, after taking antibiotics. For some patients, the unhealthy balance of bacteria can last for months or years, especially if the “bad” bacteria have become resistant to treatment.

For example, a Clostridium difficile infection (or c. diff) can cause frequent bowel movements and diarrhea, fever, stomach pain, and life-threatening colon inflammation.[2,3] To treat c. diff, doctors may try to restore the microbiome by adding or re-introducing good bacteria back to the gut. One way to do this is through a fecal matter transplant, a treatment that is not approved by the FDA, but that the FDA considers allowable as an investigative treatment for c. diff

What is a fecal matter transplant? 

Many of the bacteria in our guts are also in our stool (fecal matter). While this sounds unpleasant, a healthy person’s stool has many of the important beneficial bacteria that may be reduced or missing from the guts of people suffering from something like c. diff

Stool samples of a healthy person (a stool donor) could be used to reintroduce missing good bacteria into the gut of a sick patient to restore a healthy balance. Fecal matter transplant or fecal microbiota transplant (FMT) consists of placing stool samples from a healthy donor into the gut of another person for this purpose. The donor stool sample is usually placed in the colon during a colonoscopy or in the form of an enema in a doctor’s office. There are also capsules of freeze-dried stool donations that can be swallowed. The capsule dissolves in the gut to release the sample.

FMT treatments are still considered investigative.  None are approved by the FDA, but the FDA acknowledges that FMT doesn’t fit perfectly with FDA regulations because it isn’t exactly a manufactured product. After allowing the use of FMT without interference from the FDA, the agency issued a safety alert in June 2019 to warn that FMT can cause life-threatening infections.[4] 

Nevertheless, FDA continues to allow the use of FMT because there is evidence that it can help some patients recover from c.diff infections.[5,6] It is important to be careful with FMT because many patients who might get FMT are already sick, and could get sicker or even die if the FMT contains a dangerous bacteria that wasn’t identified before treatment. In one clinical trial, one patient died and several others became sick after receiving a stool transplant.[7] The stool sample had a rare form of E. coli that was not screened for and the donor had not shown symptoms.

Some physicians are also trying FMT for their patients with several other conditions such as Crohn’s disease and ulcerative colitis, despite these risks and despite the fact that these treatments have not yet been studied sufficiently for these conditions.[8,9] For this reason, Patients with conditions other than c. diff who are interested in FMT can only get access to FMT if they participate in a research study. Scientists have even done tests in animals in order to see if FMT might be a possible treatment for obesity, Alzheimer’s disease, Parkinson’s disease, and autism spectrum disorder.[10,11]

Unfortunately, some patients do not want to wait until FMT has been tested in clinical trials and become available at doctor’s offices. Instead, some people try these transplants themselves at home. 

How does a Fecal Matter Transplant work?

Regardless of the-method used to place the stool in the patient’s gut, the donor is tested for certain medical conditions and diseases, such as HIV and hepatitis. Stool donations are – excluded if the donor has a history of drug use, or has recently traveled to a country where parasitic infections are common. Donors who have recently taken antibiotics are also rejected, as research shows these medications can kill off some good bacteria, disrupting the natural gut biome. Some of the types of antibiotics that are shown to be especially disruptive to the gut bacteria are quinolones (such as Cipro and Levaquin), and sulfa drugs such as penicillin.[12] Stool banks such as OpenBiome try to carefully screen donors for things like obesity and diseases. The screening is strict; only 3% of people who apply to be donors are selected to donate samples, which is much lower that the 38% acceptance rate for people who attempt to donate blood.[13] Even so, some patients who have received stool donations from OpenBiome have died from getting an E.coli infection that was undetected in the donor.[14]

There is information online for “do it yourself” (DIY) fecal matter transplants that can be easily recreated at home, but they are risky. One major problem is that stool donations for DIY transplants are usually not screened as carefully as they would be in a medical setting.

DIY pills can also be dangerous. The capsules could disintegrate too soon in the stomach or the small-intestine. This can happen if they have not been designed to only dissolve in the gut. Here even healthy gut bacteria can cause serious health issues, such as SIBO (small-intestine bacterial overgrowth).

Bottom Line

Currently, FMT is not approved by the FDA but it isn’t rejected by the FDA either. That is why FMT can only be used in a medical setting as an investigational treatment for c. diff or in research studies for patients with other conditions. Although FMT treatments are promising, there are also several very serious risks, including death. Anyone considering FMT must be aware that they are taking a chance of harm because it has not been proven safe or effective. However, the risks are higher during the COVID-19 pandemic, due to the potential transmission of SARS-CoV-2 (the virus that causes COVID-19) through stool. The FDA has placed a warning on stool samples collected after December 1, 2019 and is urging that all stool samples be screened for SARS-CoV-2. [15]

It is too risky to do FMT at home. If you are considering FMT, talk to your doctor about whether it is a good option for your health issues and if it is possible to do in a medical setting. If so, health care professionals can help you get a stool sample that was adequately tested. For more information about c. diff and other antibiotic resistant bacterial infections, click here.  


All articles are reviewed and approved by Dr. Diana Zuckerman and other senior staff.

The National Center for Health Research is a nonprofit, nonpartisan research, education and advocacy organization that analyzes and explains the latest medical research and speaks out on policies and programs. We do not accept funding from pharmaceutical companies or medical device manufacturers. Find out how you can support us here.


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