Microbial Functional Carriers and Metabolic Background Associated with Natural Musk Quality in Forest Musk Deer

Whether differences in natural musk quality are associated with identifiable microbial ecological and metabolic configurations remains unclear, as studies integrating phenotype, community composition, functional sources, and non-muscone metabolic background are lacking. In this study, integrated metagenomic and GC–MS/LC–MS analyses were conducted on six natural musk samples from forest musk deer on a single farm, categorized into low-quality-associated (S1, S2, and S6) and high-quality-associated (S3, S4, and S5) groups. The two groups exhibited phenotypic differentiation in muscone, moisture, and sensory characteristics. Genus-level composition revealed quality-associated consortia with individual heterogeneity. KEGG Level 3 pathway decomposition into taxonomic carriers showed that similar functional potential could be achieved across genera, particularly lipid, ketone-body, and terpenoid pathways. After excluding muscone, candidate features related to lipid/membrane components, sterols, macrocyclic ketones, and volatiles changed coordinately along the quality axis. These results outline a multi-omics evidence chain of “phenotypic differentiation–consortium reorganization–functional carrier redistribution–background metabolic remodeling”, in which the identity of the organisms carrying each function provides an additional explanatory layer beyond total pathway abundance. This exploratory cross-sectional study provides testable hypotheses on the quality-associated ecological–metabolic organization of natural musk and targets for subsequent mechanistic validation.