Comparison of microbiota in different intestinal regions between hibernating and active Daurian ground squirrels

The gut microbiota plays a crucial role in modulating host physiology and behaviour. While seasonal variations in gut microbiota have been extensively documented, microbial adaptations across distinct intestinal regions during hibernation and active periods remain poorly understood. Using the Daurian ground squirrel (Spermophilus dauricus), a typical hibernating rodent with seasonal feeding behaviours, we employed 16S rRNA gene sequencing to investigate spatiotemporal changes in the gut microbiota between winter (hibernation) and summer (active period). Our results revealed that microbial diversity was lower in the small intestine than in the caecum and large intestine during summer. Furthermore, the small intestine exhibited higher microbial diversity in winter compared to summer, while the caecum and large intestine showed the opposite trend. The phylum Bacteroidota was more abundant in the large intestine and caecum than in the small intestine. In winter, phylum Bacillota abundance displayed a pronounced spatial gradient, decreasing progressively from the small intestine to the caecum and large intestine. Genus-level analysis indicated distinct seasonal shifts in the relative abundances of Blautia, Hungatella, Weissella, and Alistipes across intestinal regions. Functional prediction further suggested an enrichment of region-specific microbial pathways involved in seasonal adaptation. These findings demonstrate that hibernation in ground squirrels entails a substantial restructuring of the gut microbiota, characterized by clear spatial heterogeneity in diversity and composition; the caecum and large intestine maintained higher microbial diversity and evenness than the small intestine and exhibited unique seasonal dynamics. This study advances our understanding of hibernation adaptation mechanisms from an ecological perspective of the gut microbiota.