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FMT: Faecal microbiota transplantation


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Faecal microbiota transplantation (FMT) is also called a stool transplantation. It transfers healthy bacteria from a donor into the intestines of the person needing the treatment (the recipient).

It is a treatment for people with diarrhoea caused by a type of bacteria called Clostridium difficile (C diff), or symptoms caused by ulcerative colitis.

FMT is only used if other treatments are not helping. 

What is faecal microbiota transplantation (FMT)?

FMT transfers healthy bacteria from a donor into the intestines of the person needing the treatment (the recipient). This is done through a processed mixture of liquid poo (stool). 

The idea is to balance of bacteria in the recipient’s intestine so that they can fight an infection.

Donors are usually healthy volunteers, but 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

A C diff infection can often come back after it has been treated. 

If you have one C diff infection, there is a 1 in 4 or 1 in 5 (20 to 25%) chance that it will come back. People who have had it more than once are more risk of having it again.

Treating recurrent C diff infections can be difficult, as the antibiotic treatment used becomes less helpful.

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.

FMT and ulcerative colitis

Research shows that FMT can be helpful for some people with ulcerative colitis. FMT will only be offered for ulcerative colitis after the inflammatory bowel disease team have decided that you are suitable.

In ulcerative colitis, FMT is done 4 times. The first 3 FMT's are given over 5 days, and the last 1 is given 4 weeks later. The first FMT will be done by a colonoscopy, and the next 3 will be given by enema.

Risks of an FMT

To date, there have not been any documented cases of infection through FMT. However, poo is a bodily fluid, so it is important that the donor is screened and tested.

Donors 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, 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 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 a you have a tear, you might need surgery to treat it.

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


  • Asking for your consent


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

    You will be asked to sign a consent form about the risks of undergoing a colonoscopy as well as a consent form for the FMT. If you would like more detailed information on colonoscopy, please ask your nurse or doctor.

    If you would like more information about our consent process, please ask a member of staff caring for you.

Other treatment options

Your doctors will already have tried different types or longer courses of antibiotics before they recommend an FMT. An FMT is only for people who have had the standard treatments, and these have not worked.

Preparing for an FMT

You will be asked to take an antibiotic called vancomycin for at least 4 days before the transplant. This should be stopped the evening before the procedure.

You will also be asked to take a laxative before the procedure, which is medicine that speeds up your bowel movements.

You will need to drink more fluids on the day before the procedure. You should try to drink a glass of water every hour.


You should have had the chance to talk about any medicines you are taking with your doctor or nurse before your procedure.

If you are taking antiplatelet or anticoagulants medicines to prevent blood clots (such as aspirin or clopidogrel, warfarin, rivaroxiban or dabigatran), tell your doctor or nurse before the date of your procedure. You should also tell them if you are taking sedatives, chronic pain medicines, or medicines for diabetes.

You should be able to take all of your medicines as usual, unless you have been told otherwise by the doctor or endoscopy nurse.

The day of your procedure

The procedure is performed either as an inpatient (if you are staying on a ward) or as a day case. It will be done on the Endoscopy Unit.

The procedure takes 30 to 40 minutes. An endoscopy nurse will be with you the whole time.

  1. When you arrive at the Endoscopy Unit, give your name to the receptionist or nurse.
  2. You will be asked to sit in the waiting area before being seen by an endoscopy nurse, who will ask you about your medical history. Tell the nurse if you have had any reactions or allergies to other tests or procedures in the past.
  3. You will be asked to remove all of your clothing and change into a gown. You might want to bring your dressing gown and slippers with you.
  4. Once you are ready, you will be taken to the second waiting area, called the ‘sub wait area’.
  5. In the procedure room, your doctor will explain more about the procedure and answer any questions you might have.
  6. You will be asked to lie down on your left-hand side on a couch, with your knees bent.
  7. A small, thin, tube called an endoscope will be put into your lower bowel through your bottom (anus).
  8. The transplant liquid will be passed down the endoscope during the procedure. 
  9. This might make you feel bloated, and you might feel like you need to go to the toilet, or pass wind. This is perfectly normal and is nothing to be embarrassed about.

An FMT is usually done with sedation or an injection of painkillers, but you can choose not to have sedation if you wish. Sedation is medicine that makes you sleepy and relaxed, but does not put you to sleep. Read more about having sedation for your FMT. 

If you do not have sedation, you might want to use Entonox (gas and air) for pain relief during your procedure.

Pain during an FMT

You should not feel pain during the procedure. Although you might have brief periods of discomfort, particularly when the endoscope is first put in.

Sometimes the doctor or nurse will press gently on your stomach or change your position to help the endoscope be put in.

After an FMT

After the procedure, you will be taken to the recovery area.

  • If you have had sedation, you will need to rest quietly until the sedative has worn off, which usually takes a couple of hours. The nurse will check your blood pressure and pulse, and offer you some tea and biscuits. Read more about having sedation for your FMT. 
  • If you have not had sedation you will be taken to the discharge area and you can leave the hospital straight after your procedure.

If you are not staying on a ward and do not have any other appointments on the day of your FMT, you can go home the same day. However, we do recommend that you wait until after you have opened your bowels.

You should rest at home after your procedure. You can eat and drink normally and should be able to carry out your usual activities 24 hours after the procedure.

After the procedure you are very likely to have loose bowel motions (diarrhoea), and feel a little bloated. The gut often takes a few days to begin to get better.

You should notice that how often you poo slows down, and that your poo is less runny. After a week, you should be having poo that is almost normal. During this time, you may have some stomach cramps or feel sick.

If you have sedation

If you have sedation, you must have someone to take you home and stay with you for 24 hours after your FMT. They should come with you to your appointment or be contactable by phone when you are ready to leave.

If you do not have someone to take you home, your procedure will be cancelled. If you cannot arrange for someone to collect you, contact your team to talk about other arrangements.

Even though you might feel well, the sedation lasts longer than you might think. In the first 24 hours after the procedure, you should not:

  • drive a car, or ride a bicycle
  • operate machinery
  • do anything that needs skill or judgement
  • drink alcohol
  • take sleeping tablets
  • go to work
  • make any important decisions, such as signing contracts or legal documents

When you go home

Talk to your GP, or go to your nearest Emergency Department (A&E), if you have:

  • severe tummy (abdominal) pain
  • a hight temperature (fever)
  • pass large amounts of blood after the procedure

Follow up appointment

About 1 in 5 people will need to have a second FMT procedure to treat their infection. The success rate for people having 1 or 2 faecal transplants is 94%.

You will be offered a follow up appointment to check whether or not the treatment has worked. At this appointment, you might be asked to give another poo sample.

Details of your follow up appointment will be given to you on the day of your procedure before you leave hospital.

Appointments at King's College Hospital

We work with King’s College Hospital in a partnership known as King’s Health Partners Academic Health Sciences Centre. We are working together to give people the best possible care.

We might invite you for appointments at King’s College Hospital. To make sure everyone you meet always has the most up-to-date information about your health, we might share information about you between the hospitals.


Resource number: 3975/VER2

Last reviewed: February 2019 | Next review: February 2022

A list of sources is available on request.

Where next?

 Contact us

If you have any questions or concerns about faecal microbiota transplantation (FMT), or you need to cancel or change your appointment, contact the Endoscopy Unit

Phone 020 7188 8887 

Monday to Friday, 9am to 5pm.

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