Microbiomes are a core component of plant and animal health, including as a result of their role in shaping disease susceptibility and extending host adaptability. In this talk I will explore the selective forces that shape the plant microbiome, including how this microbiome assembles, is shaped by phage-mediated selection, and how it impacts plant health. First, I will discuss recent results in which we explore the relative importance of dispersal, host plant ‘filtering,’ and competition on microbial community composition. I will then emphasize how these effects might differ across plant tissues/microbial habitats, and highlight ways in which these processes can be explored. I will then expand from microbiome assembly to microbiome function; including how both can be directly impacted by the presence of bacteriophage viruses in and on leaves. Finally, I will explore how this knowledge might be leveraged for human health and sustainable agriculture.