Abstract
Diet is a major factor that influences the structure of gut microbiota. Hibernating mammals that fast for several months each winter provide an extreme example of natural dietary change that can impact the microbiome. We explored this relationship using 16S rRNA pyrosequencing of DNA extracted from cecal contents of 13‐lined ground squirrel litters over one year. In all seasons dominant phyla were Bacteroidetes and Firmicutes. Principal component analysis of UniFrac distances showed that samples clustered strongly by season, with summer communities distinct from winter, and spring (2 wk after feeding resumed) intermediate. For hibernators, time since start of torpor (i.e., length of fast) influenced community diversity but torpor/arousal state did not. Bacterial taxa that distinguished hibernator microbiotas from summer included greater representation of mucin degraders (i.e., Verrucomicrobiaceae and Bacteroidales), reduced occurrence of Clostridiales and the absence of Lactobacilliaceae. The diversity of maternal microbiotas had little influence on seasonal clustering of their young. The results from this natural system underscore the profound impact of host diet on the structure of gut microbial communities. Supported by funds from UW‐Madison School of Veterinary Medicine (HVC), the Bill and Melinda Gates Foundation (RK) and the Howard Hughes Medical Institute (RK).
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