Animals are in constant association with diverse and abundant microbial communities, collectively referred to as the microbiome. These interactions have important roles in animal development and physiology. Research in the Broderick Lab uses the invertebrate model Drosophila melanogaster to study interactions that occur between an animal, its microbiome, and pathogens. How does the microbiome establish and maintain itself? What are the host and microbiota factors that mediate their interactions? How stable are these microbiome-dependent effects in response to perturbation by pathogens and time? Understanding the molecular basis of these interactions will inform our understanding of the evolution of host-microbe associations and define mechanisms that promote animal health.