The emerging world of the fungal microbiome

•The study of the fungal microbiome lags behind our understanding of the bacterial microbiome.•All humans and laboratory animals carry indigenous fungal communities when healthy.•The fungal microbiome is significantly smaller than the bacterial microbiome.•The role of the fungal microbiome as a cofactor in disease has likely been underestimated.

The study of the fungal microbiota (‘mycobiome’) is a new and rapidly emerging field that lags behind our understanding of the bacterial microbiome. Every human has fungi as part of their microbiota, but the total number of fungal cells is orders of magnitude smaller than that of the bacterial microbiota. However, the impact of the mycobiome on human health is significant, especially as a reservoir for blooms of pathogenic microbes when the host is compromised and as a potential cofactor in inflammatory diseases and metabolic disorders.