This leaflet gives you information about faecal microbiota transplantation (FMT), including the benefits, risks and what to expect.

Treatment of Clostridioides difficile Infection (CDI)

Treatment of CDI with the antibiotics Vancomycin or Fidaxomicin kills the C. difficile bacteria. However, in some people diarrhoea returns a few days after stopping the antibiotics, this is called a recurrence.

Recurrence happens when the normal gut bacteria do not return to healthy levels, allowing any remaining C. difficile bacteria to increase in numbers and cause symptoms again.

After one episode of CDI there is a up to a 1 in 5 chance that it will come back. People who have had CDI more than once are at an even greater risk of recurrence.

Treatment of recurrent episodes of CDI can be difficult as the antibiotics can be less effective. Longer courses, different antibiotics or other medications can be used, however, in a small number of cases this is not successful and your doctor may recommend an alternative treatment called FMT or faecal microbiota transplant.

What is a faecal microbiota transplant?

A faecal microbiota transplant (FMT) is a filtered suspension of donated faeces (stool) prepared in the laboratory at the University of Birmingham.

The normal bacteria in the donated faeces replaces the missing bacteria in the gut of the person with recurrent CDI with the aim of restoring a healthy balance.

The symptoms of C. difficile infection are stopped in around 91% of people who receive FMT treatment, compared to only 30 to 40% of people who receive antibiotic treatment for recurrent CDI. People usually see improvement in their diarrhoea within 24 to 72 hours after the FMT.

Flatulence, belching and/or constipation may be experienced in the days following FMT.

What are the risks of treatment with FMT?

Faecal donors are screened for common infections spread by blood and faeces and stopped from donating if any are detected. Donors undergo a clinical, social and travel risk assessment and are only allowed to donate if there are no additional risks for infection found. However, there may be unrecognised pathogens in the FMT, which could cause infection in the recipient. So far there have not been any documented cases of infection through FMT from the donor to the recipient.

The FMT is given through a nasogastric tube (a fine tube that goes up the nose and then into the stomach) and there is a very small risk of perforation from placement of the nasogastric tube. There is also a risk of misplacement of the nasogastric tube into the lungs.

Delivery of FMT into the lungs would cause a serious infection. Steps are taken by staff to ensure correct placement of the tube into the stomach to minimise this risk.

What will happen when I have FMT?

You will be asked to take an antibiotic (Vancomycin) for 4 days before the transplant, which will stop the evening before the procedure.

You will need to be ‘Nil by mouth’, which means no food or drink for 6 hours before the FMT.

You will be asked to take a tablet of Omeprazole on the morning of treatment. This will reduce the amount of stomach acid which could kill the bacteria being given in the FMT.

A tablet of Domperidone will also be given to help the stomach to empty into the small intestine.

The nasogastric tube is placed into the stomach the morning of the procedure and a syringe containing the FMT is connected to the nasogastric tube. The FMT is administered down the tube. You should not be able to smell or taste the FMT. The nasogastric tube is then flushed with a saline solution and will be removed 1 hour after the procedure.

Once the nasogastric tube has been removed you will then be able to eat and drink as normal.

What should I expect after FMT treatment?

If you are not an inpatient (staying on a ward) you can go home the same day. If you are an inpatient the doctors and nurses will continue to monitor your stool each day you are in hospital.

The gut often takes a few days to begin to get better. You should notice that your stool frequency (number of times a day you pass a stool) gradually reduces and your stools are more formed (less runny). After 5 to 7 days, you should be passing a nearly normal stool.

If your stool frequency and firmness has not improved 5 to 7 days after FMT please contact your GP and the Infection Prevention and Control Nurses at the hospital. Sometimes a second stool transplant is needed (1 in 5 people may need to have a second FMT).

Follow-up after FMT

FMT is a new treatment so therefore it is important to understand if it works.

In addition to any routine clinical follow up you may have, your doctor will complete a FMT specific questionnaire about your progress 90 days after your FMT treatment. To complete this questionnaire your doctor will ask you questions about your health after FMT, any side effects of the treatment and how satisfied you were with the treatment. This data will be collected by your doctor and sent to the University of Birmingham Microbiome Treatment Centre. Your treatment outcome data will be anonymised in this questionnaire.


If you have any questions please do not hesitate to contact the Infection Prevention and Control Nurses at Gloucestershire Hospitals NHS Trust on:

Tel: 0300 422 6122

Monday to Friday, 9:00am to 4:00pm

Further information

For more information about C. difficile and CDI please see our patient information leaflet: Clostridioides difficile Infection (CDI) GHPI1073

Printable version of this page

Faecal Microbiota Transplant (FMT) GHPI1734_06_22 Department: Infection control Review due: June 2025 PDF, 179.3 KB, 4 pages
Reference number GHPI1734_06_22
Department Infection control
Review due June 2025