Gut microbiota is known to play a main role in human health and disease. Reconstitution of the physiologic gut microbiota represents a primary target in the treatment of diseases related to the impairment of gut microbiota composition. Fecal microbiota transplantation (FMT) is the infusion of feces from a healthy donor to a patient to cure a specific disease. Fecal microbiota transplantation has demonstrated undoubted efficacy in the management of recurrent C. difficile infection, and it is also considered a promising therapeutic avenue for other diseases associated with gut microbiota imbalance.

Over time, different procedural protocols of fecal microbiota transplantation have been experienced, and methodology has not yet been standardized up to now. Future efforts for the improvement of the therapeutic performance of the fecal microbiota transplantation will include, respectively, the definition of specific protocols for each disease, the application of brand new technique for the assessment of gut microbiota composition (e.g. metagenomics) to clinical practice, and the development of larger, well-designed, randomized controlled trials on this topic.