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Fecal microbiota transplantation (FMT) is effective in treating recurrent
Clostridium difficile
infection (CDI). Bacterial colonization in recipients after FMT has been studied, but little is known about the role of the gut fungal community, or mycobiota. Here, we show evidence of gut fungal dysbiosis in CDI, and that donor-derived fungal colonization in recipients is associated with FMT response. CDI is accompanied by over-representation of
Candida albicans
and decreased fungal diversity, richness, and evenness. Cure after FMT is associated with increased colonization of donor-derived fungal taxa in recipients. Recipients of successful FMT (“responders”) display, after FMT, a high relative abundance of
Saccharomyces
and
Aspergillus
, whereas “nonresponders” and individuals treated with antibiotics display a dominant presence of
Candida
. High abundance of
C. albicans
in donor stool also correlates with reduced FMT efficacy. Furthermore,
C. albicans
reduces FMT efficacy in a mouse model of CDI, while antifungal treatment reestablishes its efficacy, supporting a potential causal relationship between gut fungal dysbiosis and FMT outcome.
Fecal microbiota transplantation (FMT) is effective in treating recurrent
Clostridium difficile
infection (CDI). Here, the authors show that the composition of the gut fungal microbiota of donors and recipients, and especially the abundance of
Candida
, correlates with FMT outcome in CDI patients.