The present invention resides in the discovery that altered abundance of fungal species in the gut and feces of both fecal microbiota transplantation (FMT) donors and recipients may influence the outcome of FMT treatment. Thus, novel methods are provided for identifying subjects as suitable donor or recipients for FMT, for assessing the likelihood of FMT treatment success, and for enhancing FMT treatment efficacy. Also provided are kits and compositions for FMT with enhanced efficacy.