Seasonal dietary shifts are associated with significant alterations in the gut microbiome of herbivores, yet the specific impacts of these shifts on microbial metabolic functions have not been fully elucidated. To address this gap, we employed DNA metabarcoding of fecal samples and 16S rRNA gene sequencing to explore the relationship between seasonal diet and gut microbiome composition in a population of sika deer (Cervus nippon kopschi). Our findings indicate pronounced seasonal variations in both dietary composition and gut microbial community structure. Notably, during the winter months, the gut microbiome exhibited a significant enrichment of predicted pathways (predicted using PICRUSt2) related to fatty acid and lipid biosynthesis and degradation, amino acid degradation, and the TCA cycle. Conversely, the active growing seasons (spring and summer) were characterized by enhanced glycolysis and amino acid biosynthesis pathways. These functional shifts showed significant correlations with seasonal changes in dietary nutrients, such as crude protein and fiber, and climatic factors. Our results suggest that seasonal dietary changes are associated with a restructuring of the gut microbiome’s metabolic potential, which may assist sika deer in adapting to fluctuating physiological demands and environmental challenges across different seasons.

Seasonal environmental variations significantly affect the health and survival of wild ruminants such as sika deer (C. n. kopschi). This study characterized the adaptation of gut microbial communities to these seasonal shifts, supporting the host’s physiological needs. We employed high-throughput sequencing on sixty fecal samples collected throughout the four seasons to assess microbial diversity, composition, and potential functions. Our findings revealed significant seasonal fluctuations, with microbial diversity peaking in summer and reaching its nadir in winter. Taxonomic analysis showed that Firmicutes was the dominant phylum during spring (63.43%), summer (78.52%), and autumn (81.99%), whereas winter was dominated by Proteobacteria (50.60%), primarily due to the enrichment of Acinetobacter and Pseudomonas. Although the community structure formed three distinct seasonal enterotypes with dramatic shifts in bacterial taxa, functional profiling based on genomic databases indicated that core biological pathways remained remarkably stable throughout the year. These results demonstrate that sika deer maintain internal functional homeostasis by reorganizing their gut microbial composition to address harsh environmental stressors. This research provides a critical scientific basis for understanding the adaptive resilience of wild animals, offering valuable insights into the conservation and management of wildlife populations in dynamic ecosystems.