Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

• DOI: 10.1152/ajpregu.00387.2012
• Publication Date: 2012-11-15T03:37:14Z
• Authors: Hannah V. Carey; William A. Walters; Rob Knight
• Keywords: Verrucomicrobia; Hibernation; Ground squirrel; Omnivore; UniFrac

Many hibernating mammals suspend food intake during winter, relying solely on stored lipids to fuel metabolism. Winter fasting in these species eliminates a major source of degradable substrates support growth gut microbes, which may affect microbial community structure and host-microbial interactions. We explored the effect annual hibernation cycle microbiotas using deep sequencing 16S rRNA genes from ground squirrel cecal contents. Squirrel were dominated by members phyla Bacteroidetes, Firmicutes, Verrucomicrobia. UniFrac analysis showed that clustered strongly season, maternal influences, diet history, host age, body temperature had minimal effects. Phylogenetic diversity numbers operational taxonomic units lowest late winter highest spring after 2-wk period refeeding. Hibernation increased relative abundance Bacteroidetes Verrucomicrobia, contain capable surviving host-derived such as mucins, reduced many prefer dietary polysaccharides. short-chain fatty acid ammonia concentrations, decreased concentrations acetate butyrate, respectively. These results indicate microbiota is restructured each year manner reflects differences preferences for vs. substrates, thus competitive abilities different taxa survive altered environment hibernator gut.