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.

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.

Tannins are plant-derived polyphenolic anti-nutritional factors that impair nutrient absorption, damage the intestinal barrier, and disrupt metabolic homeostasis. Some animals, however, have an innate resistance to the effects of tannins. Sika deer (Cervus nippon) exhibit strong tolerance to long-term consumption of tannin-rich oak plants, and Akkermansia muciniphila is considered a key functional bacterium, yet the underlying mechanism of this remains unclear. In this study, we transplanted fecal microbiota from tannin-acclimated sika deer into antibiotic-pretreated C57BL/6J mice, followed by tannin gavage to establish a stress model. Growth performance, serum glycolipid indices, and hepatic metabolic gene and protein expression were detected. Results showed no significant differences in body weight, fat deposition, or serum biochemical parameters between groups. In the transplantation group, key genes involved in glycolysis, detoxification, and lipid metabolism were significantly upregulated, while CYP7A1, a bile acid synthesis rate-limiting gene, was significantly downregulated at both transcriptional and protein levels. Akkermansia was specifically enriched in the gut of transplanted mice. In conclusion, the microbiota of the sika deer gut alleviates tannin toxicity and enhances host tolerance by regulating hepatic glycolipid and bile acid metabolism pathways. The results of our study provide new insights into the adaptation mechanisms of herbivores to high-tannin diets.

The gut microbiota is closely linked to nutrient metabolism and host health in birds, but whether variation in plant-derived diet composition is accompanied by corresponding gut microbiota variation during winter remains unclear. In this exploratory study, we analyzed 150 fecal samples from five groups of wintering Common Cranes (Grus grus) in the Yellow River Estuary during the 2025/2026 wintering season. Plant DNA metabarcoding and 16S rRNA sequencing were used to characterize the plant-derived diet composition, fecal microbiota, and predicted microbial functions. Both plant-derived diet composition and fecal microbiota structure differed significantly among groups. Groups J1 and J2, sampled concurrently in January, differed markedly in plant-derived diet composition, whereas overall fecal microbiota separation and differences in most predicted functions were relatively limited. Five plant family–bacterial genus associations passed FDR correction without sampling-group adjustment, but none remained significant after adjustment. Overall, plant-derived diet composition and fecal microbiota both varied across the sampled groups, but their patterns of differentiation were not fully concordant. Because sampling time and site were not fully crossed, these patterns cannot be attributed to diet alone. These findings support considering farmland foraging habitats in the management of wintering Common Cranes, with attention to food resource availability throughout winter.