Limits...
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.

Show MeSH
Comparison of the carbohydrate active enzymes identified from muskoxen rumen metatranscriptome (using all assembled contigs) with those of four other foregut metagenomes and five rumen/anaerobic microorganisms.The percentages of each enzyme family were shown in the cells. Refer to Table S4 for a complete comparison. Dendrogram on the top indicates the relationship of the GHs identified based on similar percentage distribution. Muskox MT: Muskoxen rumen metatranscriptome; Fibrobacter: Genome of Fibrobacter succinogenes S85; Ruminococcus: Genome of Ruminococcus flavefaciens; Clostridium: Genome of Clostridium thermocellum; Piromyces: EST sequence of Piromyces sp. E2; Macropod MG: Macropod foregut microbiome [11]; Termite MG: Termite hindgut microbiome [13]; Bovine MG-Hess: Bovine Rumen microbiome by Hess et al [12]; Bovine MG-Brulc: Bovine Rumen microbiome by Brulc et al [10]; and Prevotella: Genome of Prevotella ruminicola.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3105075&req=5

pone-0020521-g004: Comparison of the carbohydrate active enzymes identified from muskoxen rumen metatranscriptome (using all assembled contigs) with those of four other foregut metagenomes and five rumen/anaerobic microorganisms.The percentages of each enzyme family were shown in the cells. Refer to Table S4 for a complete comparison. Dendrogram on the top indicates the relationship of the GHs identified based on similar percentage distribution. Muskox MT: Muskoxen rumen metatranscriptome; Fibrobacter: Genome of Fibrobacter succinogenes S85; Ruminococcus: Genome of Ruminococcus flavefaciens; Clostridium: Genome of Clostridium thermocellum; Piromyces: EST sequence of Piromyces sp. E2; Macropod MG: Macropod foregut microbiome [11]; Termite MG: Termite hindgut microbiome [13]; Bovine MG-Hess: Bovine Rumen microbiome by Hess et al [12]; Bovine MG-Brulc: Bovine Rumen microbiome by Brulc et al [10]; and Prevotella: Genome of Prevotella ruminicola.

Mentions: Sequence homology based enzyme annotation was biased toward the identification of known enzymes that were already present in the database. To minimize this bias, we used a more sensitive Pfam-HMM search to identify Carbohydrate Active enZYme (CAZy) modules (Figure 4, Table 1, Table S4). In all, these analyses identified 400 k reads potentially encoding lignocellulolytic enzyme modules, spanning about 110 CAZy families. The read number in each family gives an indication of the expression status of that group. However, it needs to be pointed out that the number of reads that matched to lignocellulolytic enzymes was likely underestimated because the short reads (108 nt, translated into 36 amino acid residues maximum) resulted in a less robust database search score than that which would have been obtained using the full sequence of complete genes.


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)

Comparison of the carbohydrate active enzymes identified from muskoxen rumen metatranscriptome (using all assembled contigs) with those of four other foregut metagenomes and five rumen/anaerobic microorganisms.The percentages of each enzyme family were shown in the cells. Refer to Table S4 for a complete comparison. Dendrogram on the top indicates the relationship of the GHs identified based on similar percentage distribution. Muskox MT: Muskoxen rumen metatranscriptome; Fibrobacter: Genome of Fibrobacter succinogenes S85; Ruminococcus: Genome of Ruminococcus flavefaciens; Clostridium: Genome of Clostridium thermocellum; Piromyces: EST sequence of Piromyces sp. E2; Macropod MG: Macropod foregut microbiome [11]; Termite MG: Termite hindgut microbiome [13]; Bovine MG-Hess: Bovine Rumen microbiome by Hess et al [12]; Bovine MG-Brulc: Bovine Rumen microbiome by Brulc et al [10]; and Prevotella: Genome of Prevotella ruminicola.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020521-g004: Comparison of the carbohydrate active enzymes identified from muskoxen rumen metatranscriptome (using all assembled contigs) with those of four other foregut metagenomes and five rumen/anaerobic microorganisms.The percentages of each enzyme family were shown in the cells. Refer to Table S4 for a complete comparison. Dendrogram on the top indicates the relationship of the GHs identified based on similar percentage distribution. Muskox MT: Muskoxen rumen metatranscriptome; Fibrobacter: Genome of Fibrobacter succinogenes S85; Ruminococcus: Genome of Ruminococcus flavefaciens; Clostridium: Genome of Clostridium thermocellum; Piromyces: EST sequence of Piromyces sp. E2; Macropod MG: Macropod foregut microbiome [11]; Termite MG: Termite hindgut microbiome [13]; Bovine MG-Hess: Bovine Rumen microbiome by Hess et al [12]; Bovine MG-Brulc: Bovine Rumen microbiome by Brulc et al [10]; and Prevotella: Genome of Prevotella ruminicola.
Mentions: Sequence homology based enzyme annotation was biased toward the identification of known enzymes that were already present in the database. To minimize this bias, we used a more sensitive Pfam-HMM search to identify Carbohydrate Active enZYme (CAZy) modules (Figure 4, Table 1, Table S4). In all, these analyses identified 400 k reads potentially encoding lignocellulolytic enzyme modules, spanning about 110 CAZy families. The read number in each family gives an indication of the expression status of that group. However, it needs to be pointed out that the number of reads that matched to lignocellulolytic enzymes was likely underestimated because the short reads (108 nt, translated into 36 amino acid residues maximum) resulted in a less robust database search score than that which would have been obtained using the full sequence of complete genes.

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