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About FMT

What is FMT?

Faecal microbiota transplantation (FMT) is a medical treatment
where intestinal microbiota is transplanted to the intestines of a patient,
using faeces from a healthy donor.

FMT in Denmark

FMT is considered for patients with recurrent C difficile infection in all Danish hospitals.

The use of FMT in Denmark is described in a National Danish clinical guideline, published in 2021 following joint consensus between four scientific societies:

FMT in Europe

FMT is used in routine clinical care and in experimental studies throughout Europe.

At present, the use of FMT in Europe is unevenly distributed, demonstrated in a Europe-wide survey conducted in 2020.

Tissues and cells

The Council of Europe issues the technical guide for the safety and quality of tissues and cells for human application. The guide was thoroughly revised in 2022, including the adaptation of a thoroughly revised chapter on intestinal microbiota.

EU regulation: SoHO

Substance of human origin (SoHO) is a term applied by the European Commission to embrace blood, tissues, cells, organs and human-derived material such as breast milk and intestinal microbiota.

The EU legislation on blood, tissues and cells is under revision to include all SoHOs. The EU Commission issued the new regulation in 2024.

Microbiota modulation

Intestinal microbiota is a key determinant of human health. The synergy between host and microbiome affects diseases in all tissues of the human organism. Development of diseases such as Crohn’s disease, multiple sclerosis, diabetes mellitus, and obesity is linked to disturbances in the intestinal microbiome, termed dysbiosis. It is not clear if dysbiosis causes disease or rather develops as a consequence of disease.

Since two multicenter studies in Europe and USA (MetaHIT and Human Microbiome Project) provided in-depth analyses of the human intestinal microbiota, using next-generation sequencing methods, our understanding of “our other genome” has increased massively. We now know multiple ways to modulate the intestinal microbiome, using either diet, medications such as antibiotics, cultured microorganisms (probiotics), or faecal microbiota transplantation.

Our microbiomes are under constant development, and attempts to conserve microbiota for the future include the microbiota vault.


Clinical trials

Use of medical treatments is best investigated by clinical trials. ClinicalTrials.gov is a public registry of ongoing clinical trials, currently including more than 100 trials investigating the use of FMT in humans.

Results from clinical trials are published in scientific journals following peer review. Findings from different trials may be combined and analysed in systematic reviews and meta-analyses. Find CEFTA publications of clinical trials, systematic reviews, and meta-analyses under “Publications”.

  • FMT for C difficile infection
    A meta-analysis documented the effect of FMT for recurrent C difficile infection – 81% following one FMT and 91% following repeat FMT. The number needed to treat, i.e. the number of patients needed to treat in order to achieve week 8 resolution of disease, is 1.5.
    (Open access via EClinicalMedicine)
  • Early FMT in patients with C difficile infection
    In a double-blinded, placebo-controlled clinical trial, we planned to randomise 84 patients with their first or second episode of C. difficile to receiving either encapsulated FMT or encapsulated placebo following standard therapy with oral vancomycin. The primary outcome was resolution of C difficile-associated disease 8 weeks after treatment. The study was stopped after an interim analysis of the first 42randomised patients due to a marked effect difference between patients who had received active FMT and those who had received placebo. The study was published in September 2022 in Lancet Gastroenterology and Hepatology.

  • FMT for diabetes mellitus type 1 with chronic diarrhea
    Chronic diarrhea in patients with diabetes mellitus type 1 may result from a colonic dysbiosis. In this double-blinded, placebo-controlled clinical trial, we randomise patients with diabetes mellitus type 1 and chronic diarrhea to either FMT week 0 and FMT week 4 or placebo week 0 and FMT week 4, with safety as the main outcome and symptom scores week 8 as secondary outcome measures.
    Study protocol
  • FMT for irritable bowel syndrome
    Several clinical studies have been conducted, yelding different results, ranging from a marked difference between FMT and placebo in favour of placebo, via studies finding no difference, to studies finding a discrete, but statistically significant difference in favour of FMT. This Danish study found placebo treatment superior to FMT. 
    (Open access via Gut, a BMJ journal)
  • FMT for decompensated liver cirrhosis
    Liver cirrhosis is associated with marked dysbiosis, i.a. an altered microbiota composition. Pilot trials indicate that patients with hepatic encephalopathy, a life-threatening complication to liver cirrhosis, may benefit from FMT.