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

The transition from normal forage to a highly fermentable diet in beef cattle industry to achieve rapid weight gain can induce ruminal acidosis. The molecular host mechanisms occur in acidosis and as a response to acidosis are largely unknown. Therefore, we assayed histology and transcriptome profiling of rumen epithelium 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 were obtained using RNA-sequencing. The average of clean reads was 70,975,460 ± 984,046 reads in the normal sample and 71,142,189 ± 834,526 reads in the acidosis samples. We identified 1,074 differentially expressed genes between the two groups (p < 0.05), of which 624 were up- regulated and 450 down-regulated in the acidosis samples. Functional analysis indicated most of the up-regulated genes have a function in filament organization, positive regulation of epithelial and muscle fibre concentration, biomineral tissue development, negative regulation of fat cell differential, regulation of ion transmembrane transport, regulation of cell adhesion and butyrate and short-chain fatty acids absorption that are 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. Our results furthermore show differential expression of genes involved in the Map Kinase and Toll-like receptor signalling pathways: IL1B, CXCL5, IL36A and IL36B were significantly downregulated in acidosis rumen tissue samples. Our results suggest rapid shifts to rich fermentable carbohydrates diets cause an increase concentration of ruminal volatile fatty acids and tissue damage and significant changes in transcriptome profiles of rumen epithelial.