Roles of the gut virome and mycobiome in faecal microbiota transplantation

Faecal microbiota transplantation (FMT) is an innovative approach to treat diseases associated with a gut dysbiosis, by transferring a healthy stool microbiota to a diseased recipient.Beyond the bacteriome, the human gut also harbours diverse communities of viruses and fungi, collectively known as the virome and the mycobiome.The impact of these latter two microbiome components on success of FMT therapy has not been appreciated until very recently.We herein review the current literature on the effects of the gut virome and mycobiome in the FMT treatment of various diseases.We discuss both the beneficial effects and health concerns of the viral and fungal transfer during FMT.We particularly highlight the roles of bacteriophages (bacterial viruses) and Candida species (fungi) in FMT efficacy.We also summarise the intricate relationships between the gut virome, mycobiome, bacteriome, and host immunity, underlying FMT.Future efforts should be devoted to understanding the versatile roles as well as the therapeutic mechanisms of specific and/or combination of viral and fungal lineages in different diseases.Harnessing the gut virome, mycobiome, and bacteriome in combination and precision hold a promising prospect in future FMT-and microbiota-based therapies.