Dynamics of the cecal microbial communities of arctic ground squirrels

Arctic ground squirrels exhibit an endogenous annual cycle characterized by extreme changes in metabolism, feeding, gut morphology and body temperature, all of which may impact, or be impacted by, their gut microbial community. The objectives of my thesis were to determine the effects of 1) hibernation, 2) development and 3) relatedness on the gut microbial community of arctic ground squirrels. I characterized the diversity, density and metabolic activity of the cecal microbial community of the arctic ground squirrel at key physiological time points across the annual cycle. During hibernation, the cecal microbiota of squirrels were lower in microbial diversity, density and viability, and differed in relative abundance of dominant community members as compared to the active season. Analysis of cecal short chain fatty acid (SCFA) concentrations revealed functional changes in the gut microbiota; during hibernation the microbiome had lower metabolic activity and their dominant fermentation pathway differed from that of the active season. Characteristics of the gut microbial community more closely resembled the hibernation community three days after ending hibernation. Across the active season, variance in gut microbial diversity among squirrels was high but was most similar among littermates, indicating a strong maternal effect at all sampling periods, except weaning. Bacterial density, viability and metabolic activity were highest during the pre-hibernation fattening phase, suggesting a possible facilitative role of the gut microbiota in fattening. Lower bacterial density, viability and SCFA concentrations at the end of the active season suggest that anticipatory alterations in the gut microbial community precede hibernation, though the mechanism remains unclear. My results indicate diversity, density and activity of the gut microbiome can reflect the physiological state of the host, but also that maternal influences on the gut microbial community supersedes seasonal changes in host physiology throughout development during the first active season.