Faecal microbiota transplantation (FMT)

Faecal microbiota transplantation (FMT) is also called a stool or poo transplantation. It can be an effective treatment for people with:

FMT is thought to work by helping to rebalance the bacteria and other organisms (the microbiota) in your intestines. The microbiota is transferred from a donor into your intestines either using a liquid or capsule preparation of FMT.  

Donors are usually healthy volunteers. They must:

  • be tested for a wide range of bacterial and parasitic infections
  • be free of health problems
  • lead a healthy lifestyle

FMT and a C diff infection (CDI)

CDI can come back after it has been treated. 

After treatment of a first infection, there is a 1 in 4 (25%) chance that it will come back. People who have had more than one episode of CDI are at even higher risk of it coming back again.

Treating recurrent CDI can be difficult, as the antibiotic treatment becomes less effective.

Your doctors might give you longer courses or different types of antibiotics, or other medicines. However, in a small number of cases this is not successful and your doctor might recommend FMT.

In most cases FMT only needs to be done once, but in patients who don't get better after the first dose it might be necessary to repeat it. 

FMT and ulcerative colitis (UC)

Research shows that FMT can be helpful for some people with UC. This is a long-term condition where your colon and rectum become inflamed.

You can read more about ulcerative colitis on the NHS website.

FMT will only be offered for UC after the inflammatory bowel disease team have decided that you are suitable.

In UC, FMT is done 4 times. The first FMT will be done by a colonoscopy, and the next 3 will be given by enema.

The first 3 transplants are given over 5 days. The last one is given 4 weeks later.

Risks of an FMT

As FMT is made from a bodily fluid (poo) there is a very small risk of the transfer of something harmful (a pathogen) from the donor to the recipient.

This risk is minimised by getting donors to complete a screening questionnaire similar to those used at blood banks and for organ or tissue transplants. 

  • Donors with risk factors for HIV and viral hepatitis cannot donate.
  • Donors with significant gastrointestinal or autoimmune disease, or with a history of cancer, also cannot donate.

Donors who meet the criteria have blood tests for a range of infectious diseases, such as HIV, hepatitis A, B, and C, and syphilis. They are also asked to give a poo sample to be tested for bacteria (such as salmonella and campylobacter), parasites, and C diff.

Serious complications from receiving FMT are very rare. The most serious risk is of the thin tube (endoscope) used during the procedure damaging your bowel. This happens in less than 1 in 1,000 procedures. If it does happen, it can cause an infection, bleeding or a tear in the lining of your bowel. If you have a tear, you might need surgery to treat it. FMT given by capsules avoids this risk, but is only safe if you don't have any swallowing problems.

Your doctor will talk to you about all of the potential risks in more detail, and you can ask them any questions you have.

Common side effects include:

  • reflux 
  • tummy bloating
  • a change in bowel habits (poo either become looser or harder to pass)
  • a changes in the smell of your poo

Occasionally patients will develop sickness or diarrhoea.

We want to involve you in decisions about your care and treatment. If you decide or are advised to have an FMT by colonoscopy and/or an enema, you will be asked to sign a consent form to say that you agree to have the treatment and you understand what it involves.

If you decide, or are advised, to have an FMT by capsules, we will ask for you to consent for the treatment, but you won't need to sign a consent form.

You can read more about giving your consent.

Other treatment options

Your doctors will already have tried other treatment options before they recommend an FMT. If you would like more information about other treatment options available, please ask a member of staff caring for you.

Follow up appointment

About 1 in 5 people will need to have a second FMT procedure to treat their CDI. The success rate for people having 1 or 2 FMT is more than 90 out of 100 cases (94%).

Not all people with UC will improve after FMT treatment. We will discuss further treatment options at your next appointment if required.

Resource number: 3975/VER3
Last reviewed: February 2023
Next review: February 2026

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