The goal of our study is to understand the interplay between host diet, the gut microbiota, and host biology. We utilize hibernation as a model system to measure the extreme shifts in nutrition from summer to winter, where there is an absence of food for a long period of time during seasonal hibernation in mammals, on abundance and diversity of gut microbiota. In addition, our aim is focused on the functional significance of these changes for microbiota and the host animal. We are utilizing novel technologies that will characterize and quantify microbiota function over the hibernation cycle through stable isotope-assisted labeling technology and metabolomic analysis of microbiota and ground squirrel breath and tissues. We will use bioinformatic tools to construct a systems-based analysis that integrates metagenome and metabolome features of the hibernator-microbiota symbiosis.