Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

<h4>Background</h4>Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the ba...

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Autores principales:	Meng Qi, Pan Wang, Nicholas O'Toole, Perry S Barboza, Emilio Ungerfeld, Mary Beth Leigh, L Brent Selinger, Greg Butler, Adrian Tsang, Tim A McAllister, Robert J Forster
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3541feb152d6403db50473e6cd28b9b0
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spelling	oai:doaj.org-article:3541feb152d6403db50473e6cd28b9b02021-11-18T06:52:55ZSnapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.1932-620310.1371/journal.pone.0020521https://doaj.org/article/3541feb152d6403db50473e6cd28b9b02011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21655220/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.<h4>Methodology/principal findings</h4>In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.<h4>Conclusions/significance</h4>The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.Meng QiPan WangNicholas O'ToolePerry S BarbozaEmilio UngerfeldMary Beth LeighL Brent SelingerGreg ButlerAdrian TsangTim A McAllisterRobert J ForsterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 5, p e20521 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Meng Qi Pan Wang Nicholas O'Toole Perry S Barboza Emilio Ungerfeld Mary Beth Leigh L Brent Selinger Greg Butler Adrian Tsang Tim A McAllister Robert J Forster Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
description	<h4>Background</h4>Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.<h4>Methodology/principal findings</h4>In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.<h4>Conclusions/significance</h4>The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.
format	article
author	Meng Qi Pan Wang Nicholas O'Toole Perry S Barboza Emilio Ungerfeld Mary Beth Leigh L Brent Selinger Greg Butler Adrian Tsang Tim A McAllister Robert J Forster
author_facet	Meng Qi Pan Wang Nicholas O'Toole Perry S Barboza Emilio Ungerfeld Mary Beth Leigh L Brent Selinger Greg Butler Adrian Tsang Tim A McAllister Robert J Forster
author_sort	Meng Qi
title	Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
title_short	Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
title_full	Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
title_fullStr	Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
title_full_unstemmed	Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
title_sort	snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/3541feb152d6403db50473e6cd28b9b0
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Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

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