Fecal microbiota transplantation (FMT) is a rather straightforward therapy that manipulates the human gastrointestinal (GI) microbiota, by which a healthy donor microbiota is transferred into an existing but disturbed microbial ecosystem. This is a natural process that occurs already at birth; infants are rapidly colonized by a specific microbial community, the composition of which strongly depends on the mode of delivery and which therefore most likely originates from the mother (Palmer et al. 2007; Tannock et al. 1990). Since this early life microbial community already contains most, if not all, of the predominantly anaerobic microbes that are only found in the GI tract, it is reasonable to assume that early life colonization is the ultimate natural fecal transplantation.