Comprehensive detection of bacterial carbohydrate‐active enzyme coding genes expressed in cow rumen

Abstract To find the abundant and characteristic fibrolytic enzyme‐coding gene expressed in fiber‐associating microbiota, a metatranscriptomic data set was obtained from fiber‐associating microbiota, and it was compared with that of rumen fluid‐floating microbiota and two metagenomic data sets. Fibrolytic rumen bacteria associate with plant polysaccharide and hydrolyze it in the rumen. We obtained a metatranscriptomic assembly from fiber‐associating microbiota in three ruminally fistulated Holstein cows fed timothy ( Phleum pratense ) hay. Each metatranscriptomic data set involved over a thousand of the glycoside hydrolase (GH) gene transcripts that accounted for about 1% of total protein coding gene transcripts. Three‐quarters of the total GH gene transcripts were dominated by non‐structural oligosaccharide‐acting hydrolase gene transcripts. In the fiber‐associating microbiota, endo‐cellulase coding gene families, especially GHs 9 and 5, were abundantly detected, and GHs 9, 11, 30 and 43, carbohydrate esterase 8 and carbohydrate‐binding module 6 were characteristically detected. Most fibrolytic gene transcripts assigned to Fibrobacter succinogenes were detected in fiber‐associating sections, and GHs 45, 44, 74, 11, 30 and 16 were Fibrobacter ‐characteristically detected. The metatranscriptomic assembly highlighted the characteristic fibrolytic enzymes expressed in the fiber‐associated rumen microbiota and offered access to the fibrolytic activities in each fibrolytic bacteria.