Transcriptomic Changes in the Rumen Epithelium of Cattle after the Induction of Acidosis

Abstract

The transition from normal forage to a highly fermentable diet to achieve rapid weight gain in the cattle industry can induce ruminal acidosis. The molecular host mechanisms that occur in acidosis are largely unknown. Therefore, the histology and transcriptome profiling of rumen epithelium was investigated in normal and acidosis animals to understand the molecular mechanisms involved in the disease. The rumen epithelial transcriptome from acidosis (n=3) and control (n=3) Holstein steers was obtained using RNA-sequencing. The mean values of clean reads were 70,975,460±984,046 and 71,142,189±834,526 in normal and acidosis samples, respectively. In total, 1,074 differentially expressed genes were identified in the two groups (P<0.05), of which 624 and 450 genes were up- and down-regulated in the acidosis samples, respectively. Functional analysis indicated that the majority of the up-regulated genes had a function in filament organization, positive regulation of epithelial and muscle fiber concentration, biomineral tissue development, negative regulation of fat cell differential, regulation of ion transmembrane transport, regulation of cell adhesion and butyrate, as well as short-chain fatty acid absorption that was metabolized as an energy source. Functional analysis of the down-regulated genes revealed effects in immune response, positive regulation of T-cell migration, regulation of metabolic processes, and localization. Furthermore, the results showed a differential expression of genes involved in the Map Kinase and Toll-like receptor signaling pathways. The IL1B, CXCL5, IL36A, and IL36B were significantly down-regulated in acidosis rumen tissue samples. The results suggest that rapid shifts to rich fermentable carbohydrates diets cause an increase in the concentration of ruminal volatile fatty acids, tissue damage, and significant changes in transcriptome profiles of rumen epithelial.

Keywords: Acidosis; Cattle; Ruminal epithelial tissue; Transcriptome.

Figure 1

Biological process of the most significantly DE genes as identified by PANTHER A. Down-regulated genes B. Up-regulated genes

Figure 2

KEGG pathway for MAPK signaling pathway. The output of DAVID analysis showing the MAPK signaling pathway significantly enriched for DE genes. Genes within the significant differential expression in acidosis rumen tissue are shown in red.

Figure 3

A. Boxplot showing range and distribution of the gene expression level (log10 FPKM) in each sample, B. Density plot displaying distributions of FPKM scores across samples, C. Dendrogram of hierarchical clustering analysis of gene expression levels (FPKM) for each sample, D. M-A-plot, E. Volcano plot representing the relationship between fold-change and significance. Red points identifying differentially expressed genes between control and acidosis samples.

Figure 4

Comparison of the control and acidosis groups regarding the ruminal papillae count, length, and width (P<0.05).

Figure 5

A light micrograph of papillae to compare the histology results between the control group (C_0, C_1, C_2) and acidosis group (A_0, A_1, A_2) (scale bar = 200 µm).