Metatranscriptome sequencing reveals insights into the gene expression of the bovine rumen wall microbial community during subacute ruminal acidosis. Bovine rumen wall metatranscriptome

The exploration of the bovine epimural microbiota residing on the rumen wall is relevant for basic and applied research for explaining the effect of subacute ruminal acidosis (SARA) on epimural microbiota community structure and host-microbe interactions. Comparatively little is known about the metabolic function and in situ gene expression of the epimural microbiota and whether or how they might be affected by a diet-induced SARA challenge. This study aimed to investigate differences in the gene expression of the epimural microbiota during a diet-induced SARA challenge. Three ruminally cannulated Holstein dairy cows were fed forage only during the baseline period followed by a four-week SARA challenge induced by a 60% concentrate diet. Cows were slowly adapted to the high-concentrate diet within the first six challenge days. Rumen papillae biopsies were taken at the baseline period and after four weeks SARA challenge. Bacterial and eukaryotic rRNA was depleted using the Illumina/Epicentre Ribo-Zero Gold rRNA Removal Kit (Epidemiology) and the metatranscriptome of the epimural microbiota of six samples in total at the baseline period and after four weeks SARA challenge was obtained using Illumina HiSeq 2500 sequencing.