title: Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.
authors.forename: Meng
authors.initials: M
authors.lastname: Qi
authors.forename: Pan
authors.initials: P
authors.lastname: Wang
authors.forename: Nicholas
authors.initials: N
authors.lastname: O'Toole
authors.forename: Perry S
authors.initials: PS
authors.lastname: Barboza
authors.forename: Emilio
authors.initials: E
authors.lastname: Ungerfeld
authors.forename: Mary Beth
authors.initials: MB
authors.lastname: Leigh
authors.forename: L Brent
authors.initials: LB
authors.lastname: Selinger
authors.forename: Greg
authors.initials: G
authors.lastname: Butler
authors.forename: Adrian
authors.initials: A
authors.lastname: Tsang
authors.forename: Tim A
authors.initials: TA
authors.lastname: McAllister
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Forster
mesh_terms: D000818:Animals; D004950:Esterases / Q000235:genetics; D056890:Eukaryota / Q000378:metabolism*; D006026:Glycoside Hydrolases / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D011133:Polysaccharide-Lyases / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012417:Rumen / Q000378:metabolism*; D012418:Ruminants / Q000378:metabolism*
chemical_list: D004950:Esterases; D006026:Glycoside Hydrolases; D011133:Polysaccharide-Lyases