Faecal microbiota transfer (FMT) aims at restoring a disturbed gut microbiotaby introducing faecal material from a healthy donor into a patient’s intestine. This approach is known as a safe and effective treatment in patients with recurrent Clostridioides difficile infection. This thesis describes the outcomes of two clinical studies in which FMT was investigated as a therapy for irritable bowel syndrome (IBS) patients andin collagenous colitis (CC) patients. Paper I showed that there were no significant differences in IBS symptom scores between patients receiving faecal material from a healthy donor (allogenic FMT) and patients receiving their own faecal material back (autologous FMT). However, unlike autologous FMT, allogenic FMT significantly decreased symptom scores compared to baseline. Additionally, allogenic FMT wasshown to alter the faecal as well as the mucosal microbiota of the IBSpatients. However, also the autologous FMT had an effect on the faecal and mucosal microbiota indicating that the bowel cleansing and/or theprocessing of the autologous faecal material affected the gut microbiota. Paper II showed that the allogenic FMT evoked a clearly different host response in IBS patients than the autologous FMT. Paper III showedthat allogenic FMT did not result in altered faecal metabolite profilesbut in disturbed interactions between the gut microbiota and its metabolites compared to autologous FMT. Paper IV describes the outcomes of the second clinical study in which repeated FMTs resulted inless diarrhoea in a subset of the treated CC patients.

Although symptoms improved in both clinical studies, the introduction of a new microbiota by FMT did not seem to be the miracle curefor IBS and CC. However, a subset of patients could benefit from FMT, and a future challenge is to identify this subset. The findings of this thesis are essential for designing further studies aimed at increasing FMT efficacy.