Stage-Specific Dynamic of Gut Microbiota Across the Musk-Secretion Cycle in Forest Musk Deer (Moschus berezovskii)

Musk secretion in forest musk deer (Moschus berezovskii) involves unique physiological processes, yet the paradox of heightened energy expenditure concurrent with voluntary fasting during this period remains poorly understood. Given the role of gut microbiota in host energy metabolism and health, we characterized its compositional and functional dynamics across the musk-secretion cycle. Fecal samples were collected from male forest musk deer at three stages—before (BMS), during (DMS), and after musk secretion (AMS)—and analyzed via full-length 16S rRNA gene sequencing. Results showed that alpha diversity differed significantly among groups (Simpson index: p = 0.027). Beta diversity analysis revealed significant community restructuring across stages (Adonis, R2 = 0.173, p < 0.01), while LEfSe analysis (LDA > 4.0) identified a series of stage-specific taxa, further corroborating the existence of inter-group differences. In terms of species composition, Firmicutes and Bacteroidetes dominated across all stages. Significant inter-stage differences were observed in Verrucomicrobiota (highest in DMS), Patescibacteria (lowest in DMS), Proteobacteria (progressively declining), and Actinobacteria (progressively declining). At the genus level, Akkermansia, Candidatus Saccharimonas, Roseburia, and Butyricicoccus showed significant variation across the musk-secretion cycle. Notably, Akkermansia muciniphila varied significantly across stages despite high inter-individual variability. Functional prediction revealed the enrichment of hydrocarbon degradation and nitrogen fixation in BMS, and anaerobic respiration and reductive acetogenesis in DMS. This study provides foundational insights into the gut microecological mechanisms underlying musk secretion in forest musk deer.