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Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet

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 studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The pr...

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Autores principales: Comtet-Marre, Sophie, Parisot, Nicolas, Lepercq, Pascale, Chaucheyras-Durand, Frédérique, Mosoni, Pascale, Peyretaillade, Eric, Bayat, Ali R., Shingfield, Kevin J., Peyret, Pierre, Forano, Evelyne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5281551/
https://www.ncbi.nlm.nih.gov/pubmed/28197133
http://dx.doi.org/10.3389/fmicb.2017.00067
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author Comtet-Marre, Sophie
Parisot, Nicolas
Lepercq, Pascale
Chaucheyras-Durand, Frédérique
Mosoni, Pascale
Peyretaillade, Eric
Bayat, Ali R.
Shingfield, Kevin J.
Peyret, Pierre
Forano, Evelyne
author_facet Comtet-Marre, Sophie
Parisot, Nicolas
Lepercq, Pascale
Chaucheyras-Durand, Frédérique
Mosoni, Pascale
Peyretaillade, Eric
Bayat, Ali R.
Shingfield, Kevin J.
Peyret, Pierre
Forano, Evelyne
author_sort Comtet-Marre, Sophie
collection PubMed
description 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 studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in 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, Ruminocccus and Fibrobacter), 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.
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spelling pubmed-52815512017-02-14 Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet Comtet-Marre, Sophie Parisot, Nicolas Lepercq, Pascale Chaucheyras-Durand, Frédérique Mosoni, Pascale Peyretaillade, Eric Bayat, Ali R. Shingfield, Kevin J. Peyret, Pierre Forano, Evelyne Front Microbiol Microbiology 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 studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in 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, Ruminocccus and Fibrobacter), 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. Frontiers Media S.A. 2017-01-31 /pmc/articles/PMC5281551/ /pubmed/28197133 http://dx.doi.org/10.3389/fmicb.2017.00067 Text en Copyright © 2017 Comtet-Marre, Parisot, Lepercq, Chaucheyras-Durand, Mosoni, Peyretaillade, Bayat, Shingfield, Peyret and Forano. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Comtet-Marre, Sophie
Parisot, Nicolas
Lepercq, Pascale
Chaucheyras-Durand, Frédérique
Mosoni, Pascale
Peyretaillade, Eric
Bayat, Ali R.
Shingfield, Kevin J.
Peyret, Pierre
Forano, Evelyne
Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
title Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
title_full Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
title_fullStr Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
title_full_unstemmed Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
title_short Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
title_sort metatranscriptomics reveals the active bacterial and eukaryotic fibrolytic communities in the rumen of dairy cow fed a mixed diet
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5281551/
https://www.ncbi.nlm.nih.gov/pubmed/28197133
http://dx.doi.org/10.3389/fmicb.2017.00067
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