Patient Education3 min read

Faecal Microbiota Transplant

Overview

The gut is home to trillions of bacteria and other microbes, called the microbiota or microbiome, which help digestion and protect against harmful germs. Antibiotics and illness can disturb this balance. In a faecal microbiota transplant (FMT), stool from a healthy, screened donor is processed and delivered into your bowel so that healthy bacteria can re-establish themselves. It can be given through a colonoscope (a camera tube passed through the anus), through a tube passed through the nose into the stomach or small bowel, as an enema, or as capsules or a prepared preparation swallowed by mouth. The preparation depends on the centre and may use fresh or frozen material.

Who needs it

People who have had repeated C. difficile infections despite appropriate antibiotics

People with a severe C. difficile infection that is not responding to standard treatment, in selected cases

People who may join a research study for other conditions, where available and suitable

Risks

•

Short-term bloating, gas, cramps, nausea, constipation or loose stools (common)

•

Risks of the route used: sedation reactions, bleeding, or a tear in the bowel with colonoscopy (rare); gagging or nose irritation with a tube; vomiting and breathing in material into the lungs if given into the stomach (rare)

•

Infection passed from the donor, which is kept very low by careful screening but cannot be removed entirely; serious infections have been reported, especially in people with weakened immunity

•

Possible unknown long-term effects, since the microbiota are complex and research is still developing; for this reason FMT is used when the benefit is clear

•

The treatment does not always work, and C. difficile can return; a repeat procedure may be needed.

•

Seek urgent help if you develop fever, severe or worsening belly pain, a swollen hard belly, persistent vomiting, blood in the stool, severe diarrhoea with dehydration, or breathing difficulty.

Before the procedure

The donor is screened with blood and stool tests and a health questionnaire for infections, and the material is prepared by an approved service. Ask your team about how donors are checked and about the safety measures in place.

If the transplant is done by colonoscopy you will need bowel preparation (a strong laxative), fasting, and usually sedation, so arrange for an adult to take you home. If it is by capsules, enema or tube, the preparation differs, so follow the exact instructions.

You may be asked to stop certain medicines, such as acid-reducing tablets or anti-diarrhoea medicines, and to take a medicine that slows the bowel shortly before. Do not stop any medicine unless told to. Tell the team about your other medicines, including immune-suppressing ones, blood thinners and diabetes medicines.

Tell the team about allergies (including food allergies, since donor stool may carry traces of foods), pregnancy, weakened immunity, severe bowel disease, and previous reactions to sedation. If you fast for Ramadan, discuss the timing.

When to See a Doctor

Call your doctor or go to emergency if after the procedure you have severe or worsening abdominal pain, fever, repeated vomiting, heavy bleeding, black stools or fainting.

Why it is done

The main established use is for Clostridioides difficile (C. difficile) infection that keeps coming back after antibiotic treatment. C. difficile is a germ that can overgrow when normal gut bacteria are wiped out by antibiotics, causing severe watery diarrhoea and colitis (inflammation of the colon). Restoring a healthy bacterial community can stop repeated attacks in many people when antibiotics alone have failed. FMT is also being studied for other conditions, such as ulcerative colitis, but for these it is mostly done within research and is not routine care; talk to your doctor about the current evidence.

During the procedure

The steps depend on the route. By colonoscopy: you lie on your side, you are usually sedated, and the doctor passes the scope and releases the prepared material in the colon, usually the right side or small bowel; this takes a short time. By enema: you lie on your side and the liquid is placed in the lower bowel, and you try to hold it for as long as you can. By tube: a thin tube is passed through the nose and the material is delivered; you may feel pressure or gagging. By capsules: you swallow a number of capsules with water, with no procedure. You may be asked to lie still or rest for a while afterwards so the material stays in. The material may smell, and you may feel bloated.

After the procedure

Most people can go home the same day, once recovered from any sedation (do not drive, sign legal papers or make important decisions that day). Bloating, gas, cramping, mild nausea, loose stools or changes in bowel habit are common for a few days. Many people notice that diarrhoea improves within a few days, but it can take longer. You will be told when to eat and which medicines to restart. Try to avoid unnecessary antibiotics afterwards, since they can disturb the new balance, and tell every doctor you see that you have had C. difficile or an FMT. Follow-up may include a check for symptoms and sometimes stool tests, though these are not always needed if you are well.

When you get the results

Improvement in diarrhoea often starts within days to a couple of weeks, but the benefit is judged over the following weeks to months by whether the infection stays away. Your doctor will follow your symptoms and decide whether more tests or treatment are needed.

Alternatives

Standard treatment for C. difficile is a course of specific antibiotics, and for repeated infection, longer or tapering antibiotic courses and some newer medicines, including antibody treatments and approved microbiota-based products where available, can be used. FMT is usually offered after these options, or when they are not suitable. Stopping the antibiotic that triggered the infection when possible, and good hand washing with soap and water, help prevent spread. If you decline FMT, you can continue with other antibiotic strategies, though the infection may return. Your doctor will explain what is available in your centre.

Questions to ask your doctor

• Is FMT right for me, or are there other treatments to try first?

• Which route will be used, and what preparation do I need?

• How are donors screened, and how safe is it for me given my health?

• What should I do about antibiotics and other medicines afterwards?

• What should I do if the diarrhoea comes back?

Source and review

This guide comes from the Saudi Gastroenterology Association (SGA) patient library, prepared by the Approved for publication by SGA; individual clinician review is ongoing. Last reviewed: 2026-04-24. It is for education and does not replace your doctor's advice.

Frequently Asked Questions

What is Faecal Microbiota Transplant?

Why is Faecal Microbiota Transplant done?

What are the risks of Faecal Microbiota Transplant?

Short-term bloating, gas, cramps, nausea, constipation or loose stools (common); Risks of the route used: sedation reactions, bleeding, or a tear in the bowel with colonoscopy (rare); gagging or nose irritation with a tube; vomiting and breathing in material into the lungs if given into the stomach (rare); Infection passed from the donor, which is kept very low by careful screening but cannot be removed entirely; serious infections have been reported, especially in people with weakened immunity; Possible unknown long-term effects, since the microbiota are complex and research is still developing; for this reason FMT is used when the benefit is clear; The treatment does not always work, and C. difficile can return; a repeat procedure may be needed; Seek urgent help if you develop fever, severe or worsening belly pain, a swollen hard belly, persistent vomiting, blood in the stool, severe diarrhoea with dehydration, or breathing difficulty.

How do I prepare for Faecal Microbiota Transplant?

Your team will confirm that the diarrhoea is from C. difficile with a stool test and that you have finished or are finishing the antibiotic course they advise. Do not stop or change antibiotics yourself; The donor is screened with blood and stool tests and a health questionnaire for infections, and the material is prepared by an approved service. Ask your team about how donors are checked and about the safety measures in place; If the transplant is done by colonoscopy you will need bowel preparation (a strong laxative), fasting, and usually sedation, so arrange for an adult to take you home. If it is by capsules, enema or tube, the preparation differs, so follow the exact instructions; You may be asked to stop certain medicines, such as acid-reducing tablets or anti-diarrhoea medicines, and to take a medicine that slows the bowel shortly before. Do not stop any medicine unless told to. Tell the team about your other medicines, including immune-suppressing ones, blood thinners and diabetes medicines; Tell the team about allergies (including food allergies, since donor stool may carry traces of foods), pregnancy, weakened immunity, severe bowel disease, and previous reactions to sedation. If you fast for Ramadan, discuss the timing.