Faecal microbiome transplantation (FMT) has generated huge recent interest, as it presents a potential solution to a significant clinical problem - the increasing incidence of Clostridium difficile infection. In the short term, however, there remain many practical questions regarding its use, including the optimal selection of donors, material preparation and the mechanics of delivery. In the longer term, enhanced understanding of the mechanisms of action of microbiome manipulation may potentiate novel therapies, such as targeted manipulation of the microbiome in C. difficile infection and beyond.