Supplemental materials.docx

This research identifies distinct rumen microbial enterotypes in lactating dairy goats and explores their profound implications for rumen fermentation, microbial interactions, and milk production performance. Through comprehensive analysis of 141 lactating dairy goats, two rumen enterotypes were identified: RE1 (n = 31) and RE2 (n = 110). The RE1 enterotype, characterized by a dominance of Firmicutes taxa (e.g., Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, and Ruminococcus), was associated with significantly higher milk yield, milk protein content, milk amino acid (AA) concentrations, and elevated ruminal concentrations of total volatile fatty acids (VFA), propionate, butyrate, and AAs. In contrast, the RE2 enterotype was enriched with Bacteroidetes-affiliated genera (e.g., Prevotella, Rikenellaceae RC9 gut group, and Prevotellaceae UCG-003) and exhibited a higher acetate percentage and acetate-to-propionate ratio.Co-occurrence network analysis revealed distinct microbial interactions and keystone taxa between enterotypes, with multiple negative correlations between RE1- and RE2-enriched taxa. Notably, propionate, butyrate, and AA concentrations were positively correlated with the abundance of RE1-dominant taxa and their microbial modules. Structural equation modeling further demonstrated that specific microbial genera were directly linked to milk protein yield via ruminal AA concentrations.These findings underscore the strong relationship between rumen enterotype, fermentation efficiency, and lactational performance in dairy goats. Enterotypes may serve as microbial markers for identifying high-performance animals and open new avenues for improving lactation performance through precision feeding and microbiome-informed management strategies.