title: 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.
authors.affiliation: NARO Institute of Livestock and Grassland Science. tshinkai@affrc.go.jp.
authors.forename: Takumi
authors.initials: T
authors.lastname: Shinkai
authors.affiliation: NARO Institute of Livestock and Grassland Science.|Graduate School of Life and Environmental Sciences, University of Tsukuba.
authors.forename: Makoto
authors.initials: M
authors.lastname: Mitsumori
authors.affiliation: Graduate School of Life and Environmental Sciences, University of Tsukuba.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Sofyan
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Harumi
authors.initials: H
authors.lastname: Sasaki
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Katayose
authors.affiliation: NARO Institute of Livestock and Grassland Science.|National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Akio
authors.initials: A
authors.lastname: Takenaka
mesh_terms: D000821:Animal Feed; D000818:Animals; D002417:Cattle; D044602:Cellulases / Q000235:genetics*; D005260:Female; D045848:Fibrobacter / Q000201:enzymology*; D006026:Glycoside Hydrolases / Q000235:genetics*; D006868:Hydrolysis; D064307:Microbiota; D031784:Phleum / Q000737:chemistry; D011134:Polysaccharides / Q000378:metabolism*; D012417:Rumen / Q000382:microbiology*
chemical_list: D011134:Polysaccharides; D044602:Cellulases; D006026:Glycoside Hydrolases
keywords: Fibrobacter succinogenes; cellulase; metatranscriptomic analysis; plant polysaccharide; rumen