Distinct rumen enterotypes in lactating dairy goats: Implications for rumen fermentation, microbial interactions, and milk production performance

The rumen microbiome plays a pivotal role in nutrient metabolism and host health, ultimately influencing production performance in ruminants, including dairy goats. Although enterotypes-distinct clusters of gut microbiota-have been identified, their effect on rumen fermentation and milk production in dairy goats remains poorly understood. This study aimed to characterize rumen microbial enterotypes and investigate their associations with fermentation characteristics and milk production traits in lactating dairy goats. A comprehensive analysis of 141 lactating dairy goats identified 2 rumen enterotypes: RE1 (n = 31) and RE2 (n = 110). Goats with the RE1 enterotype exhibited significantly higher milk yield, milk protein content, milk AA concentrations, and elevated concentrations of rumen total VFA, propionate, butyrate, and AA compared with the RE2 microbiota. The RE1 microbiota was dominated by Firmicutes taxa, including Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, and Ruminococcus, and was characterized by a lower acetate percentage and acetate-to-propionate ratio. In contrast, the RE2 microbiota was enriched with Bacteroidetes-affiliated genera, such as Prevotella, Rikenellaceae RC9 gut group, and Prevotellaceae UCG-003. Co-occurrence network analysis uncovered distinct interactions and keystone taxa between the 2 enterotypes, revealing multiple negative correlations between taxa enriched in the RE1 microbiota and those enriched in the RE2 microbiota. Notably, concentrations of propionate, butyrate, and AA were positively correlated with the abundance of RE1-dominant taxa and their corresponding microbial modules. Furthermore, structural equation modeling revealed that specific genera were directly linked with milk protein yield through their correlations with ruminal AA concentrations. These findings demonstrate a strong linkage between rumen enterotype, fermentation efficiency, and lactational performance in dairy goats. Enterotypes may serve as microbial markers for identifying high-performance animals and offer new opportunities to enhance lactation performance through precision feeding and microbiome-informed management strategies in dairy goats.