Dietary Changes Are Associated with Seasonal Restructuring of the Gut Microbiome in Cervus nippon kopschi

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.