41 Differential Gene Expression of the Bovine Rumen Epithelial Microbiota During a Sub-acute Ruminal Acidosis (SARA) Challenge Free

Sub-Acute Ruminal Acidosis (SARA) is a metabolic disorder in dairy cattle characterized by a lowered ruminal pH, as a result of high grain diets. Dairy cows experiencing SARA show decreased milk production and impaired health; thus, SARA has major economic impacts. SARA has been associated with changes in the rumen epithelial microbiota. Previously, we performed meta-transcriptome sequencing on rumen epithelial biopsy samples from 3 fistulated Holstein cows before (baseline) and after switching to high concentrate feed to induce SARA to analyze the gene expression of the rumen epithelial microbiota. In this previous analysis, 1,607 features were detected using the KEGG Ontology reference database, including a wide variety of metabolic genes, as well as stress response, motility, and other functions. However, only 3 features were differentially expressed between baseline and SARA conditions using this approach. Here, we present a re-analysis of the meta-transcriptomics data using an improved bioinformatics pipeline to reveal additional genetic diversity and differentially expressed genes. We performed a de novo transcriptome co-assembly with Trinity, mapped reads to the assembled contigs, used RSEM to determine read counts, and DESEQ2 for detection of differentially expressed genes (Q < 0.05). Features were annotated using EggNOG, providing taxonomic predictions and GO, COG, and KEGG-based functional prediction. Using this method, a total of 76,861 transcripts were assembled, and 4,935 genes were differentially expressed between baseline and SARA conditions, representing a substantial improvement over the previous analysis. Our preliminary analysis indicates high expression levels of central metabolism and housekeeping genes, as well as oxidative stress response genes, and outer membrane proteins among rumen epithelial bacteria. Differentially expressed archaeal genes were primarily upregulated under SARA conditions and included genes involved in methanogenesis. Further analyses are ongoing and will provide insight into gene expression of the rumen epithelial microbiota, and their association with SARA.