Abstract
The gut microbiome plays a pivotal role in modulating nutrient metabolism and lactation efficiency in ruminants, yet its functional stratification into enterotypes and implications for dairy goats remain unexplored. Here, we identified two distinct gut microbiome enterotypes in 134 lactating dairy goats: TR-cluster (n = 43) was enriched in Turicibacter, Romboutsia, and Clostridium sensu stricto 1, while CO-cluster (n = 91) exhibited higher abundance of Christensenellaceae R-7 and Oscillospiraceae UCG-005. Goats in the TR-cluster exhibited higher milk yield, fat-corrected milk yield, and milk fat yield, along with increased concentrations of total volatile fatty acids (VFA), including acetate, propionate, and butyrate in the gut, as well as elevated serum glucose and total bile acids levels. Despite lower microbial diversity, the TR-cluster was functionally enriched in metabolic pathways related to energy metabolism, amino acid metabolism, and lipid biosynthesis, whereas the CO-cluster showed enrichment in membrane transport and genetic information processing. Co-occurrence network analysis revealed distinct microbial interaction patterns and keystone taxa, with the TR-cluster displaying more complex inter-module connectivity. Moreover, correlation analyses demonstrated that TR-cluster-enriched genera, such as Turicibacter and Romboutsia, were positively associated with enhanced gut fermentation and improved lactation traits. Overall, these findings reveal that gut microbial enterotypes are strongly linked to gut fermentation and lactation traits in dairy goats, offering novel insights for microbiota-targeted strategies to improve ruminant productivity. IMPORTANCE: Dairy goats are critical for global milk production, yet the gut microbiome-driven mechanisms that underlie individual differences in lactation performance remain largely unknown. To our knowledge, this is the largest cohort study to date that comprehensively characterizes gut microbiome enterotypes in lactating dairy goats and establishes their impact on gut fermentation, host metabolism, and milk production. We identified two distinct enterotypes with different microbial signatures, functional capacities, and ecological structures. Notably, the enterotype dominated by Turicibacter, Romboutsia, and Clostridium sensu stricto 1 was associated with improved lactation performance, enhanced VFA production, and beneficial metabolic profiles. The identification of keystone taxa and enterotype-specific microbial interactions offers a new perspective on host-microbiome relationships in ruminants. Our findings lay the foundation for precision microbiome management and targeted interventions to enhance the health and productivity of dairy animals.