Contribution of the Rumen Epithelial Transcriptome and Microbial Community to Variation in Beef Cattle Feed Efficiency

  • Author / Creator
    Kong, Rebecca
  • Feed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency. However, it is unknown how the rumen epithelium and its associated microorganisms influence the feed efficiency of cattle. Our study aimed to understand how host gene expression in the rumen epithelium and the activity of rumen epithelial attached microbes contribute to differences in feed efficiency. Residual feed intake (RFI) of 175 Hereford x Angus steers was measured using a GrowSafe system. The rumen epithelial transcriptome from 9 of the most efficient (low (L-) RFI) and 9 of the most inefficient (high (H-) RFI) steers was obtained using RNA-seq. Differential gene expression analysis was conducted using DESeq2 software and Weighted Gene Co-expression Network Analysis (WGCNA) was performed to identify gene modules that are correlated with RFI. Additionally, we identified and quantified the relative abundance of bacterial and archaeal 16S rRNA transcripts as an indication of their activity. Within the rumen epithelium there were 122 genes that were differentially expressed between L- and H- RFI steers (p<0.05). Also, WGCNA identified a significant module of 764 genes that negatively correlated with RFI (r=-0.5, p=0.03). Functional analysis revealed up-regulation of genes in the L-RFI epithelium involved in modulation of intercellular adhesion, cell migration, cytoskeletal organization, protein and cell turnover, oxidative phosphorylation, and acetylation. Our results suggest the increased tissue morphogenesis in the L-RFI epithelium may increase epithelial paracellular permeability for the absorption of nutrients. Up-regulation of oxidative phosphorylation and acetylation in the L-RFI epithelium indicate potential increased energy production to support the energetic demands of increased tissue morphogenesis in feed efficient animals. There was no significant difference between RFI groups in the activity of archaeal phylotypes on the epithelium. However, the bacterial families Campylobacteraceae and Neisseriaceae had significantly greater activity on the L-RFI epithelium (p<0.05) and they play a role in oxygen scavenging. Overall, L-RFI (efficient) steers may have increased rumen tissue morphogenesis that possibly increase paracellular permeability for the absorption of nutrients, thereby providing a greater substrate supply for whole-body energy production. They also have greater activity of rumen epithelial attached oxygen scavenging bacteria that may provide more optimal feed fermentation conditions, which contributes to high feed efficiency.

  • Subjects / Keywords
  • Graduation date
    Spring 2016
  • Type of Item
  • Degree
    Master of Science
  • DOI
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.