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Metacommunity theory provides a framework for how community patterns arise from processes across scales, which is relevant for understanding patterns in host-associated microbial assemblages. Microbial metacommunities may have important roles in host health through interactions with pathogens; however, it is unclear how pathogens affect host microbial metacommunities. Here, we studied relationships between a fungal pathogen and a host-associated microbial metacommunity. We hypothesized that a fungal pathogen of bats,  Pseudogymnoascus destructans,  correlates with a shift in metacommunity structure and changes in relationships between community composition, and factors shaping these assemblages, such as ecoregion. We sampled bat cutaneous microbial assemblages in the presence/absence of  P. destructans  and analyzed microbial metacommunity composition and relationships with structuring variables. Absence of  P. destructans  correlated with a metacommunity characterized by a common core microbial group that was lacking in disease positive bats. Additionally,  P. destructans  presence correlated with a change in the relationship between community structure and ecoregion. Our results suggest that the fungal pathogen intensifies local processes influencing a microbial metacommunity and highlights the importance of cutaneous microbial assemblages in host–pathogen interactions.

The presence of Pseudogymnoascus destructans, a fungal pathogen of bats, correlates with changes in microbial metacommunity structure