Background/Question/Methods The microbiome and pathobiome are increasingly recognized as key determinants of how wildlife responds to global change and habitat loss, but it is unknown why microbial associations vary depending on species traits and their other species interactions. We examine if host traits and diet interaction shape microbial associations. We analyze the microbiomes and parasites of 1,686 wild bees and managed honey bees across 34 species that vary widely in phenotypic traits.
Results/Conclusions We found that bees with more distinct traits host more distinct pathobiomes. For the microbiome, the number of plants a bee interacted with was a stronger predictor of microbial distinctness and diversity than trait distinctness or the fundamental, species-level diet breadth. We also found that microbiome and pathobiome community composition were correlated and that microbiome composition was further shaped by the community composition of the pollen collected by individual bees. Our findings demonstrate that both species-level and individual-level variation in host traits act as filters affecting the assembly of microbes in free-living organisms.