We examined the seasonal changes of the cecal microbiota of captive arctic ground squirrels (Urocitellus parryii) by measuring microbial diversity and composition, total bacterial density and viability, and short-chain fatty acid concentrations at four sample periods (summer, torpor, interbout arousal, and posthibernation). Abundance of Firmicutes was lower, whereas abundances of Bacteroidetes, Verrucomicrobia, and Proteobacteria were higher during torpor and interbout arousal than in summer. Bacterial densities and percentages of live bacteria were significantly higher in summer than during torpor and interbout arousal. Likewise, total short-chain fatty acid concentrations were significantly greater during summer than during torpor and interbout arousal. Concentrations of individual short-chain fatty acids varied across sample periods, with butyrate concentrations higher and acetate concentrations lower during summer than at all other sample periods. Characteristics of the gut community posthibernation were more similar to those during torpor and interbout arousal than to those during summer. However, higher abundances of the genera Bacteroides and Akkermansia occurred during posthibernation than during interbout arousal and torpor. Collectively, our results clearly demonstrate that seasonal changes in physiology associated with hibernation and activity affect the gut microbial community in the arctic ground squirrel. Importantly, similarities between the gut microbiota of arctic ground squirrels and thirteen-lined ground squirrels suggest the potential for a core microbiota during hibernation.A lthough gut microbes share a mutualistic relationship with their mammalian hosts in which they benefit from access to fermentable substrates and a suitable living environment (1), the gut microbiota may be exposed to periods of little or no available dietary polysaccharides when the host is fasting. Extended periods of host fasting likely select for microbes that are able to degrade and subsist on host-derived substrates such as mucins and other glycoproteins (2-4). Indeed, several studies have revealed a profound effect of fasting on the gut microbiota. For example, fasting Burmese pythons (Python molurus) have higher relative abundances of Bacteroidetes, a phylum with species able to utilize hostderived substrates (1), whereas greater relative abundances of Firmicutes, which rely upon diet-derived substrates (5), were observed after the ingestion of a meal (6). Similarly, fasted Syrian hamsters (Mesocricetus auratus) exhibit decreased bacterial densities, relative abundance of Firmicutes, and microbial metabolic activity compared to those of fed hamsters (7).Many obligate seasonal hibernators (e.g., ground squirrels) naturally exhibit an endogenous circannual rhythm of hibernation and activity (reviewed in reference 8). During hibernation, animals voluntarily fast, and they conserve endogenous energy reserves by entering a state of torpor characterized by days to weeks of profoundly reduced metabolic rate, body temper...