Hibernation Shifts in Gut Microbiota Composition and Metabolic Function in the Chinese Horseshoe Bat ( Rhinolophus sinicus )

ABSTRACT The composition and function of animal gut microbiota are influenced by various intrinsic and extrinsic factors. Hibernation represents a significant physiological challenge for heterothermic mammals, yet the effects on gut microbiota in bats remain understudied. This study investigated seasonal variations in the gut microbiota of Rhinolophus sinicus between summer activity and winter hibernation using 16S rRNA gene sequencing ( n = 12 per group). Sequencing analysis identified 907 ASVs in the hibernation group and 555 ASVs in the summer group, with only 27 ASVs shared between groups, suggesting substantial seasonal turnover in microbial community membership. At the phylum level, Pseudomonadota (formerly Proteobacteria) dominated the gut microbiota, but no significant difference was found between seasons (77.52% during hibernation vs. 57.15% during summer). Bacillota (formerly Firmicutes) decreased significantly, while Actinomycetota (formerly Actinobacteriota) increased significantly in the hibernation group compared to the summer group. Genus‐level composition exhibited seasonal variation, with distinct microbial communities characterizing each period. Alpha diversity analysis revealed significant differences in Faith's phylogenetic diversity between seasons, suggesting shifts in phylogenetic composition, while Chao1, Shannon, and Simpson indices remained unchanged. Beta diversity analyses revealed significant structural divergence between seasonal groups. Functional prediction using PICRUSt2 suggested seasonal shifts in metabolism‐related pathways, with putative enrichment of lipid metabolism and xenobiotic biodegradation pathways during hibernation, while carbohydrate metabolism appeared more prominent during the active period. These findings suggest that winter fasting may alter intestinal microbial metabolic functions, potentially shifting the microbiota from carbohydrate‐oriented to lipid‐oriented metabolism. This study enhances our understanding of host‐microbiome crosstalk in hibernating mammals and highlights the potential adaptive role of gut microbes in facilitating survival under extreme physiological conditions.