The vertebrate gut is home to trillions of microbes that have evolved complex, mutualistic relationships with their hosts. The microbiota has profound and diverse effects on animal development and physiology (McFall-Ngai et al., 2013), perhaps best exemplified in the gastrointestinal tract which has been shaped through evolution to achieve a tolerant, cooperative relationship with gut symbionts. Host diet is a major factor that influences the diversity and abundance of the microbiota. To meet their metabolic needs, most gut microbes (in non-ruminant animals) utilize dietary components that have escaped small intestinal digestion and absorption. Certain host-derived substrates, such mucin glycans and nutrients in shed epithelial cells, can also be metabolized. Our recent studies have focused on the role of gut microbiota in shaping seasonal flexibility in gastrointestinal structure and function in hibernating mammals. As in other seasonal hibernators, 13-lined ground squirrels undergo a distinct annual cycle that prepares them for the physiological extremes that occur during the winter months. After emergence in spring when body mass is at a nadir, ground squirrels fatten through summer and fall, and then gradually reduce food intake and activity until emergence into burrows. Food intake ceases once hibernation begins and metabolism shifts to a primary reliance on lipids for fuel. Although periods of extended fasting are a normal and necessary component of the annual hibernation cycle, they have the potential to compromise gastrointestinal integrity. The absence of enteral nutrients, particularly in species that do not fast on a regular basis, can reduce expression of brush border enzymes and nutrient transporters and increase intestinal permeability, which elevates the risk of bacterial translocation. In contrast, species that hibernate display a remarkable degree of adaptive flexibility in gut structure and function that minimizes adverse changes during winter fasting. Seasonal cycles of feeding and fasting can also impact the relationship between hibernators and their resident gut microbes. In 13-lined ground squirrels, the microbiota associated with luminal contents undergoes seasonal restructuring during the hibernation season that reflects shifts in taxonomic groups that rely to varying degrees on dietary vs. host-derived substrates (Carey et al., 2013). Although microbial metabolism is largely suppressed during the low body temperatures of winter torpor, periodic arousals to euthermia provide sufficient time for microbial degradation of endogenous substrates, resulting in production of short-chain fatty acids that can be utilized by the host. Seasonal flexibility in host characteristics likely contributes to maintenance of a mutually beneficial, tolerant state. For example, several features of the intestinal immune system, which is the primary sensor of gut microbes and their metabolites, are modified during hibernation in a manner indicative of altered host-microbe signaling in the absence of inflammation or pathologic immune cell infiltration (Kurtz and Carey, 2007). Enterocytes in hibernating squirrels increase expression of the tight junction protein occludin, which may help to restrict paracellular movement of bacterial metabolites in the setting of a “leakier” gut (Carey et al., 2012). Mucin protein expression also rises shortly after hibernation begins, which is important because the mucus layer both protects the host epithelium from microbial invasion and provides metabolizable substrates for microbial proliferation. Mucus production in the hibernator gut may be particularly important for the mucosa-associated microbiota, a population that resides adjacent to the epithelium in the mucus layer. Our recent studies indicate that the mucosal microbiota undergoes some of the same seasonal trends as seen in the luminal population, e.g., reductions in relative abundance of Firmicutes taxa and increases in abundance of Bacteroidetes and Betaproteobacteria. Phylogenetic diversity across the annual cycle is highest and lowest in microbiotas of spring and late winter squirrels, respectively. Together, these studies emphasize that investigation of gastrointestinal flexibility in animals should incorporate the potential contributions of gut microbes, which can have profound effects on their hosts beginning at birth and extending into adulthood through recurring seasonal events that affect the host-microbial symbiosis.