Host associated microbiomes are starting to be recognized as crucial communities that shape the health and ecology of everything from crops to humans. Microbial communities’ interactions with their host have been shown to affect health, behavior, growth, and reproduction in myriad ways. We are only beginning to understand the importance of these interactions that span from mutualism to pathogenicity. At the same time, these are complex communities often consisting of hundreds of species, interacting amongst themselves and with the environment much like any other free-living community. Due to the dazzling diversity of host-associated microbial communities and the fact that they have only recently been objects of study, much of the research has been focused on simply quantifying and identifying the members of such communities. The field is just beginning to go beyond its natural history phase, from describing community composition and dynamics to understanding its functioning and species interactions. In order to apply our knowledge of these systems to improve host fitness and functioning, we must improve our mechanistic understanding of how host-associated microbial communities are assembled and maintained. This is where the application of ecological theory and concepts can be of great importance. Community ecology has developed tools over the past century to understand what factors drive community composition and function. It remains to be seen, however, how well the insights from free-living communities apply to those that are host-associated. Multiple levels of feedbacks and selection might come into play and profoundly alter our expectations. In this session, we invite researchers who are using the tools of macro-scale community ecology to deepen our understanding of these microbial communities. The talks will cover a broad range of host-associated microbial communities, from plants, to animals to humans and include speakers at different stages of their careers.