Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI). The Firmicutes to Bacteroidetes ratio was significantly higher (P < 0.05) in positive-RFI steers (p-RFI, low feed efficiency) than in negative-RFI (n-RFI, high feed efficiency) steers. The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae, Ruminococcaceae and Christensenellaceae, as well as the genus Prevotella. Archaeal community richness was lower (P < 0.05) in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers. The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers (P < 0.05) and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of high-efficiency steers. However, analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups. Our results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial, archaeal and fungal communities. Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency, whereas among archaea, Methanobrevibacter was associated with steers classified as p-RFI. The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.

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评估内洛尔阉牛瘤胃微生物群与饲料效率之间的关系

反刍动物依靠瘤胃中复杂的微生物群落将宿主难以消化的饲料转化为营养物质。然而，人们对内洛尔（Bos indicus）牛的瘤胃微生物群与饲料效率性状之间的关系知之甚少，内洛尔牛是对全球牛肉市场具有重要经济意义的品种。在这里，我们通过剩余采食量 (RFI) 测量，比较了具有高和低饲料效率 (FE) 表型的内洛尔阉牛瘤胃中细菌、古菌和真菌群落的组成。正 RFI 阉牛（p-RFI，低饲料效率）中厚壁菌门与拟杆菌门的比例显着高于负 RFI（n-RFI，高饲料效率）阉牛（P < 0.05）。高 FE 和低 FE 阉牛的细菌组成差异主要与 Lachnospiraceae、Ruminococcaceae 和 Christensenellaceae 科以及 Prevotella 属的成员有关。p-RFI 中的古菌群落丰富度低于 n-RFI 中的古菌群落丰富度（P < 0.05），并且 Methanobrevibacter 属在 p-RFI 中增加或排除。n-RFI 阉牛的瘤胃固体部分中真菌属 Buwchfawromyces 的含量更高（P < 0.05），高效阉牛瘤胃微生物群中属于 Piromyces 属的高丰度 OTU 也有所增加。然而，对瘤胃发酵变量和功能预测的分析表明，不同 FE 组的微生物群具有相似的代谢输出。我们的结果表明，高 FE 和低 FE Nellore 阉牛瘤胃微生物群的差异包括来自细菌、古菌和真菌群落的特定分类群。在表现出高饲料效率的动物中鉴定出属于 Piromyces 属的生物标志物 OTU，而在古细菌中，Methanobrevibacter 与分类为 p-RFI 的阉牛相关。内洛尔阉牛中特定 RFI 相关微生物的鉴定可以指导针对瘤胃微生物的分离和功能表征的进一步研究，这些微生物对反刍动物的能量收集效率可能很重要。