Clostridium difficile-associated diarrhea is the most common bacteria-associated diarrhea in Sweden. C. difficile infection (CDI) affects predominantly elderly patients who have received antibiotics. The first line treatment is antibiotics against the CDI, usually metronidazole, or vancomycin if the symptoms are more severe. However, since almost all CDI are caused by antibiotic treatment and thereby disruption of normal flora, the continued antibiotic treatment may wipe out the CD but doesn't help restoring the normal flora, rather keep it away. The lack of normal flora is likely the major reasons for the recurrences of CDI in around 30% of the patients treated with vancomycin or metronidazole. The risk of recurrence doubles after two or more occurrences, and the high recurrence rate demands increased healthcare cost in Sweden (€30 million per year). Preservation or restoration of a normal gut flora is obviously crucial for recovery from CDI. Fecal microbiota transplantation (FMT), first published in 1958, represents one treatment that allows fast and easy reconstitution of a normal gut microbiota. In recent years the interest for FMT has increased enormously and it is now a common treatment of recurrent CDI. Although FMT has been used in Swedish hospitals and demonstrated high efficacy in treating CDI patients, the research in monitoring the microbiome change is lacking. We have performed shotgun metagenomics analysis on patient and donor pairs to investigate the alteration in the microbiome functions.