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Faecal Microbiota Transplantation (FMT)

Patient information A-Z

What is faecal microbiota transplantation?

Faecal microbiota transplantation (FMT) is a treatment used for Clostridium difficile infection that is either recurring or is not responsive to standard treatments. FMT involves transfer of healthy bacteria in a mixture of prepared processed stool from a healthy donor to the intestine of the patient. The aim is to restore a healthy balance of bacteria in the gut. The donors have been screened in advance to ensure the stool provided is healthy and tested for a wide array of viral, bacterial and parasitic infections. This also includes screening for Covid19.

Why have FMT?

Clostridium difficile infection can recur after initial successful treatment (1 in 5 times) and in those with recurring Clostridium difficile infection the chance of further episodes is even greater (up to 1 in 2 times). Some patients with Clostridium difficile infection do not respond to standard treatments with different types of antibiotics. For people with recurring Clostridium difficile and those not responding to standard treatments faecal transplantation has been shown to be effective in curing the infection and with low rates of subsequent recurrent infection. Some patients may require two treatments with faecal transplantation to achieve cure.

What does FMT involve?

FMT can be performed in one of two ways. For most cases the stool mixture is infused via a tube inserted into the stomach via the nose. In rare cases the stool mixture is inserted into the large bowel via Colonoscopy. The choice of procedure will be decided between your Consultant and yourself. For further information regarding the latter procedure please find the accompanying leaflets on ‘Having a Colonoscopy’. This is performed in an inpatient setting, and can take up to three hours.


Before both procedures you will have been asked to take an antibiotic for at least four days prior to the procedure. This should be stopped the evening before the procedure. You will have an antiacid medication prior to the treatment and if you are having a colonoscopy you may require bowel preparation. Full details will be given to you by your Doctor. You should have had the chance to discuss any medications you are taking with one of our Nurses or Doctors prior to the procedure.


We want to involve you in decisions about your care and treatment. If you want to go ahead, you will be asked to sign a consent form. This states that you have agreed to have the treatment and understand what it involves and the associated risks of the procedure.


To date there are no cases of transmission of significant infection through FMT and it is considered a safe procedure.

Some patients may experience minor side effects including fever, bloating, nausea vomiting and constipation. These normally only last for one or two days. Please see the accompanying leaflets regarding the risks of the endoscopy procedure itself if having a colonoscopy.


Your Doctors will have already tried different types or longer courses of antibiotics. This treatment is only available to patients where these standard therapies have been tried and have been unsuccessful.

Follow Up / Results

You will be offered a follow up appointment to assess whether or not the treatment has been successful, and you may be asked to provide further stool samples. You will also be asked for information at Day 7 and Day 90 post FMT. Details will be given to you on the day of your procedure.

Contacts / Further information

Kim Lewis- Gastroenterology Medical Secretary 01223 348718

We are smoke-free

Smoking is not allowed anywhere on the hospital campus. For advice and support in quitting, contact your GP or the free NHS stop smoking helpline on 0800 169 0 169.

Other formats

Help accessing this information in other formats is available. To find out more about the services we provide, please visit our patient information help page (see link below) or telephone 01223 256998.

Contact us

Cambridge University Hospitals
NHS Foundation Trust
Hills Road, Cambridge

Telephone +44 (0)1223 245151