PSIX-4 Metatranscriptomic analysis of sub-acute ruminal acidosis in beef cattle

Abstract This study evaluated the functional activity of the rumen microbiota during subacute ruminal acidosis (SARA) using metatranscriptomics. Eight rumen-cannulated Holstein steers were assigned randomly to control diet (CON) or acidosis-inducing diet (CHA) for 20 d. Sub-acute ruminal acidosis was induced on d 18; feed was restricted to 50% of ad libitum intake for CHA group on day 17. On day 18, ground corn grain, equivalent to 25% of the mean dry matter intake (DMI) of each steer in CHA treatment was administered directly in the rumen prior to feeding. Thereafter, rumen fluid samples were taken at 0, 3, 6, and 9 h relative to feeding from both treatments. Metatranscriptome library was prepared from RNA extracted from the samples and sequencing of metatranscriptome library was done on Illumina HiSeq4000 following a 2 x 150bp index run. Linear discriminant analysis (LDA) effect size comparisons were made between CON and CHA groups. Alpha level of 0.05 was used for both the Kruskal–Wallis and pairwise Wilcoxon tests. Linear discriminant analysis scores greater than 2.0 were used for taxonomy and 1.0 for functional genes. Additionally, functional genes enriched in both treatments were mapped to the KEGG reference metabolism pathway. Cellulolytic rumen bacteria including Fibriobacter succinogenes, Ruminococcus albus, and R. bicirculans were reduced (LDA > 2.0, P < 0.05) during SARA. Up to 68 functional genes were differentially expressed between the two treatments (LDA > 1.0, P < 0.05). Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways (Pseudomonas aeruginosa, Escherichia coli and Vibrio cholera) were enriched in acidotic-challenged beef cattle. This study explains the pathogenicity of SARA and enhances our understanding of the response of rumen microbiome to SARA by revealing transcriptionally active taxa and metabolic pathways of rumen microbiota.