Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses

Authors: ABBAS, WASEEM - University Of Nebraska; Keel, Brittney; KACHMAN, STEPHAN - University Of Nebraska; FERNANDO, SAMODHA - University Of Nebraska; Wells, James - Jim; HALES, KRISTIN - Former ARS Employee; Lindholm-Perry, Amanda

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2020
Publication Date: 12/8/2020
Publication URL: https://handle.nal.usda.gov/10113/7365033
Citation: Abbas, W., Keel, B.N., Kachman, S.D., Fernando, S.C., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K. 2020. Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses. Journal of Animal Science. 98(12):1-13. https://doi.org/10.1093/jas/skaa359.
DOI: https://doi.org/10.1093/jas/skaa359

Interpretive Summary: Beef cattle liver abscesses are the highest cause of liver condemnation and costs the beef industry approximately $64 million annually. In addition to removing these livers from the food chain, abscesses reduce feed intake, body weight gain, carcass weight and may also affect cattle well-being. It is thought that liver abscess is caused by the release of bacteria from the rumen that is transported by the portal vein to the liver for colonization. The purpose of this study was to determine whether the expression of various ruminal genes and changes in the microbial populations in the rumen tissue were associated with animals with severe liver abscesses. Over 200 genes, enriched in inflammation and protein translation pathways in the rumen tissue, were differentially expressed between animals with and without liver abscesses. In addition, differences in bacterial populations between the rumen content and the bacteria strongly associated with the rumen tissue were identified. However, the rumen content populations were not associated with liver abscesses, but differences were identified in those bacterial communities associated with the rumen tissue and animals with and without liver abscesses. Moreover, there were also correlations between the genes differentially expressed and the amount of specific bacterial species. This study was a first step in evaluating the mechanisms in the rumen papillae that may be contributing to or were the result of damage to the rumen wall and the development of liver abscesses in cattle on a finishing diet. This study produced several genes and bacterial differences to pursue to gain more insight into the molecular mechanisms underlying liver abscess development in cattle.

Technical Abstract: Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry $64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Damage to the rumen wall could allow F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared to those with no liver abscesses. Rumen epithelial tissue and rumen content was collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared to animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain-enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were down-regulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also down-regulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals with and without liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.