title: Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet.
abstract: Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studiedin vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymesin vivo. The present study used RNA-sequencing to reveal both the expression of genes encoding carbohydrate-active enzymes (CAZymes) by the rumen microbiota of a lactating dairy cow and the microorganisms forming the fiber-degrading community. Functional analysis identified 12,237 CAZymes, accounting for 1% of the transcripts. The CAZyme profile was dominated by families GH94 (cellobiose-phosphorylase), GH13 (amylase), GH43 and GH10 (hemicellulases), GH9 and GH48 (cellulases), PL11 (pectinase) as well as GH2 and GH3 (oligosaccharidases). Our data support the pivotal role of the most characterized fibrolytic bacteria (Prevotella, RuminocccusandFibrobacter), and highlight a substantial, although most probably underestimated, contribution of fungi and ciliate protozoa to polysaccharide degradation. Particularly these results may motivate further exploration of the role and the functions of protozoa in the rumen. Moreover, an important part of the fibrolytic bacterial community remains to be characterized since one third of the CAZyme transcripts originated from distantly related strains. These findings are used to highlight limitations of current metatranscriptomics approaches to understand the functional rumen microbial community and opportunities to circumvent them.
authors.affiliation: UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Comtet-Marre
authors.affiliation: EA4678 CIDAM, Clermont Université, Université d'Auvergne Clermont-Ferrand, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Parisot
authors.affiliation: UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Lepercq
authors.affiliation: UR454 Unité de Microbiologie, INRASaint-Genès-Champanelle, France; Lallemand Animal NutritionBlagnac, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Chaucheyras-Durand
authors.affiliation: UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Mosoni
authors.affiliation: EA4678 CIDAM, Clermont Université, Université d'Auvergne Clermont-Ferrand, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
authors.affiliation: Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke) Jokioinen, Finland.
authors.forename: Ali R
authors.initials: AR
authors.lastname: Bayat
authors.affiliation: Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke)Jokioinen, Finland; Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Shingfield
authors.affiliation: EA4678 CIDAM, Clermont Université, Université d'Auvergne Clermont-Ferrand, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
authors.affiliation: UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Forano
keywords: carbohydrate esterases; fiber degradation; glycoside hydrolases; metatranscriptomics; polysaccharide lyases; rumen