Comprehensive Sampling Across Seasons and Habitats Revealed the Composition and Functional Attributes of Gut...

Several rodent species are considered global pests owing to their broad dietary habits, with stable gut microbiota enterotypes playing a vital role in host digestion. This study examined the Gansu zokor, a subterranean pest rodent endemic to the Loess Plateau. By extensive sampling across seasons and habitats, we characterized the gut microbiota enterotypes and clarified the mechanisms underlying their adaptation to diverse dietary resources. The gut microbiota of the Gansu zokor was categorized into two distinct enterotypes (E1 and E2), whose distribution varied markedly by season and habitat. The α and β diversity differed notably between the two enterotypes. Although Bacillota (formerly Firmicutes) and Bacteroidota dominated both enterotypes, the Bacillota/Bacteroidota ratio was markedly higher in E2, and this higher ratio was correlated with greater host body weight and BMI. Probiotic biomarkers such as Muribaculum and Alistipes were enriched in E1, whereas E2 was enriched in the Lachnospiraceae NK4A136 group, Butyribacter, and Roseburia. Potential pathogens such as Bordetella, Acinetobacter, and Desulfovibrio also serve as key biomarkers. E1 was enriched with genes involved in lipid metabolism, transport, and catabolism, while E2 was characterized by genes related to terpenoid and polyketide metabolism. Co-occurrence networks revealed more interconnected interactions in E1, but higher modularity in E2. Stochastic processes (e.g., drift) governed microbial assembly in E1, whereas deterministic processes (e.g., homogeneous selection) dominated in E2. Enterotype stratification was closely correlated with host body size parameters and microbial α diversity. Research identifies two distinct enterotypes of zokors, clarifying their traits and links to food resource utilization. These findings illuminate the ecological adaptations of subterranean rodents and offer a theoretical basis for developing microbe-based pest control strategies.