All metazoans enter into complex and life-long interactions with bacterial communities that profoundly influence the hosts’ development, physiology, emotional and cognitive states, and the development and progression of disease. The overall prevalence of these interactions suggests a long coevolutionary history between host and beneficial symbiont and implies that a comprehensive understanding of any organism must also include an understanding of its microbiome. Therefore, my ongoing research aims are to (1) identify evolutionary conserved mechanisms that both promote host-microbe specificity during colonization and the establishment of symbiosis, and underlay continued symbiosis throughout the life of the organism, (2) understand how these mechanisms shape the microbiome, and (3) understand how that ecology shapes host biology.