Metatranscriptomic Analysis of Sub-Acute Ruminal Acidosis in Beef Cattle

SIMPLE SUMMARY: This study evaluated the functional activity of rumen microbiota during sub-acute ruminal acidosis, a metabolic disease of ruminants characterized by low pH caused by feeding highly fermentable carbohydrate feeds. The abundance of rumen bacteria that degrade cellulose (Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans) were reduced by induced acidotic challenge. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study enhances our understanding of the response of rumen microbiota to sub-acute ruminal acidosis by revealing transcriptionally active taxa and metabolic pathways of rumen microbiota. ABSTRACT: Subacute ruminal acidosis (SARA) is a metabolic disease of ruminants characterized by low pH, with significant impacts on rumen microbial activity, and animal productivity and health. Microbial changes during subacute ruminal acidosis have previously been analyzed using quantitative PCR and 16S rRNA sequencing, which do not reveal the actual activity of the rumen microbial population. Here, we report the functional activity of the rumen microbiota during subacute ruminal acidosis. Eight rumen-cannulated Holstein steers were assigned randomly to acidosis-inducing or control diet. Rumen fluid samples were taken at 0, 3, 6, and 9 h relative to feeding from both treatments on the challenge day. A metatranscriptome library was prepared from RNA extracted from the samples and the sequencing of the metatranscriptome library was performed on Illumina HiSeq4000 following a 2 × 150 bp index run. Cellulolytic ruminal bacteria including Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans were reduced by an induced acidotic challenge. Up to 68 functional genes were differentially expressed between the two treatments. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study reveals transcriptionally active taxa and metabolic pathways of rumen microbiota during induced acidotic challenge.