Gut microbiome enterotypes drive divergent lactation performance in dairy goats through host-microbe metabolic cross-talk

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 <i>Turicibacter</i>, <i>Romboutsia</i>, and <i>Clostridium sensu stricto 1</i> 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.