Abstract
BackgroundHerbivores 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 FindingsIn 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/SignificanceThe 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.
Highlights
Within the gastrointestinal tract of herbivores a complex group of anaerobic microorganisms, including bacteria, archaea and eukaryotes, produces a vast array of lignocellulolytic enzymes that in turn digest complex plant cell wall polysaccharides and ferment the released simple sugars
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
Cellulase activities are well known to be present in microbial communities found in soil, compost, and herbivore digestive tracts including the rumen
Summary
Within the gastrointestinal tract of herbivores a complex group of anaerobic microorganisms, including bacteria, archaea and eukaryotes, produces a vast array of lignocellulolytic enzymes that in turn digest complex plant cell wall polysaccharides and ferment the released simple sugars. The recent introduction of massively parallel sequencing technologies has enabled the sequencing of herbivore gut microbiomes, including foreguts of cattle and wallabies [10,11,12] and the hindgut of termites [13]. These studies have led to the identification of novel cellulolytic enzymes, many of which quite likely arise from the large majority of environmental microbes that are unculturable in the laboratory [4]. Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. The nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches
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