Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
Livestock Gentec, Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6H 2P5, Canada.
Sci Rep. 2023 Sep 27;13(1):16209. doi: 10.1038/s41598-023-43097-8.
Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.
研究宿主-微生物在瘤胃中的相互作用及其对理想生产性状的影响，可能会导致潜在的微生物组操作或遗传选择，以提高牛的饲料效率。本研究调查了两个纯肉牛品种（安格斯牛和夏洛莱牛）和一个复合肉牛杂交品种（金赛拉牛）的宿主转录组及其与瘤胃古菌和细菌丰度差异的相关性，这些品种在残余饲料采食量（RFI；低 RFI 与高 RFI）方面存在差异。本研究使用瘤胃组织的 RNA 测序和 16S rRNA 基因扩增子测序，确定了差异表达基因（FDR ≤ 0.05，|log（Fold-change）|＞2）和差异丰度（p 值＜0.05）的古菌和细菌扩增子序列变异体（ASV）。使用 Spearman 相关性分析确定了基因表达与 ASV 之间的显著相关性（p 值＜0.05）。与细菌 ASV 相关的基因与肌肉收缩和免疫系统的调节有关。鉴定出了与 Angus 牛（CCL17、CCR3 和 CXCL10）、Charolais 牛（KCNK9、GGT1 和 IL6）和 Kinsella 牛（ESR2）的饲料效率状态相关的潜在功能候选基因。本研究结果为宿主和瘤胃微生物特性在选择和培育更高效饲料的肉牛方面的适用性提供了更多的见解。
