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

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ - PLoS ONE (2011)

Bottom Line: These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.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.

View Article: PubMed Central - PubMed

Affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.

ABSTRACT

Background: 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.

Methodology/principal findings: 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.

Conclusions/significance: 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.

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Summary statistics for muskoxen rumen eukaryotes metatranscriptome analysis.
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pone-0020521-g001: Summary statistics for muskoxen rumen eukaryotes metatranscriptome analysis.

Mentions: In the present study, we adopted a metatranscriptomic approach to identify enzymes from the muskoxen rumen microbial community. We used samples from muskoxen fed on triticale straw and brome hay for deep sequencing with the goal to obtain transcripts encoding carbohydrate-active enzymes. Total RNA was extracted from rumen solids to ensure isolation of the cellulolytic microbial biofilm as well as RNA from microbes deeply embedded in the plant fiber. After purification, the eukaryotic mRNA was sequenced using the Illumina Genome Analyzer II platform. This approach resulted in a total of 25,900,806 reads, with an average read length of 108 nt, generating a total of 2.8 gigabases of sequence data (Figure 1).


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

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ - PLoS ONE (2011)

Summary statistics for muskoxen rumen eukaryotes metatranscriptome analysis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105075&req=5

pone-0020521-g001: Summary statistics for muskoxen rumen eukaryotes metatranscriptome analysis.
Mentions: In the present study, we adopted a metatranscriptomic approach to identify enzymes from the muskoxen rumen microbial community. We used samples from muskoxen fed on triticale straw and brome hay for deep sequencing with the goal to obtain transcripts encoding carbohydrate-active enzymes. Total RNA was extracted from rumen solids to ensure isolation of the cellulolytic microbial biofilm as well as RNA from microbes deeply embedded in the plant fiber. After purification, the eukaryotic mRNA was sequenced using the Illumina Genome Analyzer II platform. This approach resulted in a total of 25,900,806 reads, with an average read length of 108 nt, generating a total of 2.8 gigabases of sequence data (Figure 1).

Bottom Line: These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.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.

View Article: PubMed Central - PubMed

Affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.

ABSTRACT

Background: 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.

Methodology/principal findings: 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.

Conclusions/significance: 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.

Show MeSH