Microorganisms are intricately involved in the ecology of many insects, often contributing to host fitness and forming evolutionarily stable associations. The interactions between hosts and microbes can significantly alter their evolutionary trajectories, enabling them to adapt to novel environmental conditions. In this thesis I have examined how host ecology can shape the interactions of bacteria with insects of agricultural and epidemiological importance. I have described the bacterial communities associated with Bactrocera oleae (the olive fruit fly) and generated draft genome sequences for several members of the gut microbiota, including the symbiotic bacterium “Candidatus Erwinia dacicola”. Comparative genomic analyses indicate that Ca. E. dacicola and a novel facultative bacterium Tatumella TA1 may perform key nutritional functions for the host, including the synthesis of essential amino acids and ammonia assimilation from host nitrogenous waste products. Tatumella TA1 is consistently associated with all life stages of populations collected in Israel and Crete at low relative abundance, and encodes large adhesion proteins that may assist in attachment to the host epithelium or other members of the microbiota in the B. oleae gut. I have also examined the variation in frequency and relative abundance of facultative microbes that infect several Glossina spp. (the tsetse fly): the sole vector of African trypanosomes in Sub-Saharan Africa. In addition to three vertically transmitted endosymbionts (Wigglesworthia, Sodalis, and Wolbachia), tsetse flies are infected with two additional potential reproductive manipulators: Spiroplasma and Rickettsia, and a novel strain of Klebsiella. The draft genomes generated for these taxa over the course of this thesis provide the opportunity for future studies in to their role in host biology and how community interactions can shape the transmission and evolutionary dynamics of host-associated microbes
