The microbiome is the community of bacteria and fungi associated with different environments, including the surface, digestive tract, or other organs of multicellular organisms. In organisms with highly specialized diets, like many herbivorous insects, the role of the gut microbiome is especially critical. Microbes living in the specialist organism can detoxify or digest plant tissues independently or in concert with proteins expressed by the host. Thus, microbiome differences could play an important role in the evolution of specialized diets, and ultimately the genetic divergence of populations feeding on different different resources. We want to understand the role of the microbiome in the ongoing split between two specialized lineages of the peacock fly, Tephritis conura. Here in Scandinavia, adult flies lay eggs on, and larvae develop inside, the buds of the melancholy thistle, Cirsium heterophyllum. To the south, however, they have shifted their host use to the cabbage thistle, C. oleraceum. These ecotypes are diverged enough that larvae have decreased survival and experience other fitness costs when developing on the wrong host plant. The ecotypes also exhibit divergent gene expression, suggesting that suggest different groups of genes are important for eating the different thistles. However, it is unclear whether these flies also rely on different microbial associations to specialize on their respective host plants. Using DNA and RNA sequencing data, we will test 1) whether the microbiome differs among populations of the two ecotypes, and 2) whether switching larvae onto the wrong host plant disrupts that microbiome in a way that affects larval survival.