Microbiomes are complex communities of microorganisms that colonize many surfaces of an animal's body, especially those niches lined with carbohydrate-rich mucosal layers such as the eyes, male and female reproductive tracts, and the gastrointestinal tract. While a vast majority of data from microbiome studies has relied almost extensively on metagenomics-based approaches to identify individual species within these small complex communities, the contributions of these communities to host physiology remain poorly understood. We used a combination of culture- and non culture-based approaches to identify and begin functionally characterizing microbial inhabitants stably colonized in the midgut epithelium of the invertebrate model Manduca sexta (tobacco hornworm), an agriculture pest of Nicotiana attenuata (wild-tobacco) and many additional solanaceous plants.