Table_2_Multi-omics analysis reveals the effects of host-rumen microbiota interactions on growth performance in a goat model.docx

The growth rate of young ruminants has been associated with production performance in later life, with recent studies highlighting the importance of rumen microbes in supporting the health and growth of ruminants. However, the specific role of rumen epithelium bacteria and microbiota-host interactions in influencing the early life growth rate of ruminants remains poorly understood. In this study, we investigated the rumen fermentation pattern, microbiota characteristics, and global gene expression profiles of the rumen epithelium in 6-month-old goats with varying growth rates. Our results showed that goats with high average daily gain (HADG) exhibited higher rumen propionate concentrations. Goats with low average daily gain (LADG) had the higher relative abundances of rumen epithelium bacteria genera U29-B03 and Quinella, while exhibiting a lower relative abundance of Lachnospiraceae UCG-009. In the rumen fluid, the relative abundances of bacteria genus Alloprevotella were lower and Desulfovibrio were higher in LADG goats compared to HADG goats. Additionally, the relative abundance of fungal genus Symmetrospora was lower in LADG goats compared to HADG goats. Transcriptome analysis showed that 415 genes were differentially expressed between LADG and HADG goats, which were enriched in functions related to cell junction and cell adhesion, etc. Correlation analysis revealed that rumen epithelium bacteria genera UCG-005 and Candidatus Saccharimonas were negatively associated, while Lachnospiraceae NK3A20 group and Oscillospiraceae NK4A214 group were positively associated with average daily gain (ADG) and genes related to barrier function. The rumen fluid bacteria genus Alloprevotella was positively correlated, while Desulfovibrio was negatively correlated with rumen propionate and ammoniacal nitrogen (NH3-N) concentrations, as well as genes related to barrier function and short chain fatty acids (SCFAs) transport. In summary, our study reveals that the higher ruminal fermentation efficiency, improved rumen epithelial barrier functions, and enhanced SCFAs transport in HADG goats could be attributed to the rumen microbiota, particularly the rumen epithelium bacteria, such as Lachnospiraceae and Oscillospiraceae NK4A214 group.

幼龄反刍动物（ruminant）的生长速率与其后期生产性能密切相关，已有研究强调瘤胃（rumen）微生物对维持反刍动物健康与生长的重要作用。然而，瘤胃上皮（rumen epithelium）细菌以及微生物-宿主互作在调控反刍动物早期生长速率中的具体作用，目前仍有待阐明。本研究针对生长速率存在差异的6月龄山羊，对其瘤胃发酵模式、微生物群落特征以及瘤胃上皮的全局基因表达谱展开了探究。本研究结果显示，高平均日增重（high average daily gain, HADG）组山羊的瘤胃丙酸浓度更高。低平均日增重（low average daily gain, LADG）组山羊的瘤胃上皮细菌属U29-B03和Quinella的相对丰度更高，而Lachnospiraceae UCG-009的相对丰度更低。与HADG组山羊相比，LADG组山羊瘤胃液中细菌属Alloprevotella的相对丰度更低，而Desulfovibrio的相对丰度更高。此外，LADG组山羊瘤胃液中真菌属Symmetrospora的相对丰度亦低于HADG组山羊。转录组分析显示，LADG组与HADG组山羊间共有415个差异表达基因，这些基因显著富集于细胞连接、细胞黏附等功能通路。相关性分析结果表明，瘤胃上皮细菌属UCG-005与Candidatus Saccharimonas的相对丰度与平均日增重（average daily gain, ADG）及屏障功能相关基因呈负相关；而Lachnospiraceae NK3A20群和Oscillospiraceae NK4A214群的相对丰度则与上述指标呈正相关。瘤胃液细菌属Alloprevotella的相对丰度与瘤胃丙酸、氨态氮（ammoniacal nitrogen, NH3-N）浓度以及屏障功能和短链脂肪酸（short chain fatty acids, SCFAs）转运相关基因呈正相关；而Desulfovibrio的相对丰度则与上述指标呈负相关。综上，本研究表明，HADG组山羊更高的瘤胃发酵效率、更完善的瘤胃上皮屏障功能以及更强的SCFAs转运能力，可归因于其瘤胃微生物群落，尤其是瘤胃上皮细菌（如Lachnospiraceae和Oscillospiraceae NK4A214群）。