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.

本研究明确了泌乳奶山羊的瘤胃微生物肠型，并探讨了其对瘤胃发酵、微生物互作以及泌乳生产性能的深远影响。通过对141头泌乳奶山羊的全面分析，本研究鉴定出两种瘤胃肠型：RE1（n = 31）与RE2（n = 110）。RE1肠型以厚壁菌门（Firmicutes）类群占优，例如颤螺菌科NK4A214群、克里斯滕森菌科R-7群以及瘤胃球菌属，其与更高的产奶量、乳蛋白含量、乳氨基酸（AA）浓度，以及瘤胃内总挥发性脂肪酸（VFA）、丙酸、丁酸与氨基酸浓度的显著升高密切相关。与之相对，RE2肠型富含拟杆菌门（Bacteroidetes）相关菌属，例如普雷沃氏菌属、理研菌科RC9肠道群以及普雷沃氏菌科UCG-003，其表现出更高的乙酸占比与乙酸/丙酸比值。共现网络分析揭示了不同肠型间独特的微生物互作模式与关键分类单元，RE1与RE2富集类群间存在多条负相关关联。值得注意的是，丙酸、丁酸与氨基酸浓度与RE1优势类群及其微生物模块的丰度呈正相关。结构方程模型进一步证实，特定微生物菌属可通过瘤胃氨基酸浓度直接影响乳蛋白产量。本研究结果凸显了奶山羊瘤胃肠型、发酵效率与泌乳性能之间的紧密关联。肠型可作为筛选高产个体的微生物标志物，同时为通过精准饲喂与微生物组导向的管理策略提升泌乳性能开辟了新途径。