Host-associated microbiomes play key roles in shaping the ecology and evolution of host populations, but we remain some way from predicting how they assemble, change over time, or are shaped by biotic interactions. Among the biotic selection pressures known to impact microbiome diversity are responses of the host organism, competitive and cooperative interactions within the microbiome, and the impact of bacteriophage viruses. Theoretical predictions of how these factors impact microbiome composition and stability are beginning to take shape, and it is clear that detecting the relative impacts of these selection pressures requires more than correlative study. In this talk I will introduce the variety of empirical and theoretical approaches that can be used to better understand the microbiome and its impact on host health. I will focus on the plant phyllosphere as an excellent model system for testing these ideas and describe recent data from both the field and laboratory that offer new insight to the relative roles of biotic interactions in shaping microbiome assembly and function. I will finish by highlighting the remaining open questions and the need for collaborative and interdisciplinary work in this field.