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Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.

Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VG - PLoS ONE (2012)

Bottom Line: Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1).Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation.Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. phil.pope@umb.no

ABSTRACT
Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus). Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1). Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.

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Microbial community analysis of the Svalbard reindeer rumen microbiome and comparison with microbiomes from other selected gut environments.(A) Diversity and relative abundance of the most abundant bacterial taxa identified in the rumen of the Svalbard reindeer based on phylogenetic analysis of 16S rRNA genes. (B) OTU network map showing OTU interactions between all rarefied samples from the Svalbard reindeer, Norwegian reindeer feeding on a commercial feed, Tammar wallaby, rumen and termite. OTUs are represented by dots and dot sizes reflect sequence counts within the OTU. Dot colour indicates the number of microbiomes in which the OTU was found (1 =  white, 2 =  yellow, 3 =  orange, 4 =  red). The lines radiating from each of the five grey dots link the OTUs to their source microbiomes: Svalbard reindeer, dark blue (this study); Norwegian reindeer, light blue (this study; dataset included for comparative purposes only); Termite_PL3, yellow [4]; bovine, green [6]; Tammar wallaby, orange [5]. (C) Principal coordinate axes (PCoA) for the unweighted UniFrac analyses are coloured by host animal; Svalbard reindeer (2 samples: ▸▴) dark-blue; Norwegian reindeer (2 samples: ♦♦) light-blue; bovine rumen (•) green; Tammar wallaby (◂) red; termite (▪) orange. (D) Composition of the Svalbard reindeer rumen metagenome sequence dataset, based on sequence composition-based binning of 1394 assembled scaffolds (∼5.4 Mb) using PhyloPythiaS. For a complete rrs inventory and comparisons between the two Svalbard reindeer samples at an OTU definition of 97% ID see Table S1.
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pone-0038571-g001: Microbial community analysis of the Svalbard reindeer rumen microbiome and comparison with microbiomes from other selected gut environments.(A) Diversity and relative abundance of the most abundant bacterial taxa identified in the rumen of the Svalbard reindeer based on phylogenetic analysis of 16S rRNA genes. (B) OTU network map showing OTU interactions between all rarefied samples from the Svalbard reindeer, Norwegian reindeer feeding on a commercial feed, Tammar wallaby, rumen and termite. OTUs are represented by dots and dot sizes reflect sequence counts within the OTU. Dot colour indicates the number of microbiomes in which the OTU was found (1 =  white, 2 =  yellow, 3 =  orange, 4 =  red). The lines radiating from each of the five grey dots link the OTUs to their source microbiomes: Svalbard reindeer, dark blue (this study); Norwegian reindeer, light blue (this study; dataset included for comparative purposes only); Termite_PL3, yellow [4]; bovine, green [6]; Tammar wallaby, orange [5]. (C) Principal coordinate axes (PCoA) for the unweighted UniFrac analyses are coloured by host animal; Svalbard reindeer (2 samples: ▸▴) dark-blue; Norwegian reindeer (2 samples: ♦♦) light-blue; bovine rumen (•) green; Tammar wallaby (◂) red; termite (▪) orange. (D) Composition of the Svalbard reindeer rumen metagenome sequence dataset, based on sequence composition-based binning of 1394 assembled scaffolds (∼5.4 Mb) using PhyloPythiaS. For a complete rrs inventory and comparisons between the two Svalbard reindeer samples at an OTU definition of 97% ID see Table S1.

Mentions: The microbial community structure was determined using both 16S rRNA gene amplicon pyrosequencing and sequence-composition binning (PhyloPythiaS) of scaffolds assembled from metagenomic sequences (Figure 1). Using 16S rRNA gene analysis we determined there was little variation between the two animals used for this study: 90.4% and 91.5% of OTUs found in the rumen communities of animals SR1 and SR2, respectively, were shared between the two samples (Figure 1, Table S1). There were only a few instances of large differences in OTU relative abundance between the two samples (Table S1).


Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.

Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VG - PLoS ONE (2012)

Microbial community analysis of the Svalbard reindeer rumen microbiome and comparison with microbiomes from other selected gut environments.(A) Diversity and relative abundance of the most abundant bacterial taxa identified in the rumen of the Svalbard reindeer based on phylogenetic analysis of 16S rRNA genes. (B) OTU network map showing OTU interactions between all rarefied samples from the Svalbard reindeer, Norwegian reindeer feeding on a commercial feed, Tammar wallaby, rumen and termite. OTUs are represented by dots and dot sizes reflect sequence counts within the OTU. Dot colour indicates the number of microbiomes in which the OTU was found (1 =  white, 2 =  yellow, 3 =  orange, 4 =  red). The lines radiating from each of the five grey dots link the OTUs to their source microbiomes: Svalbard reindeer, dark blue (this study); Norwegian reindeer, light blue (this study; dataset included for comparative purposes only); Termite_PL3, yellow [4]; bovine, green [6]; Tammar wallaby, orange [5]. (C) Principal coordinate axes (PCoA) for the unweighted UniFrac analyses are coloured by host animal; Svalbard reindeer (2 samples: ▸▴) dark-blue; Norwegian reindeer (2 samples: ♦♦) light-blue; bovine rumen (•) green; Tammar wallaby (◂) red; termite (▪) orange. (D) Composition of the Svalbard reindeer rumen metagenome sequence dataset, based on sequence composition-based binning of 1394 assembled scaffolds (∼5.4 Mb) using PhyloPythiaS. For a complete rrs inventory and comparisons between the two Svalbard reindeer samples at an OTU definition of 97% ID see Table S1.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3368933&req=5

pone-0038571-g001: Microbial community analysis of the Svalbard reindeer rumen microbiome and comparison with microbiomes from other selected gut environments.(A) Diversity and relative abundance of the most abundant bacterial taxa identified in the rumen of the Svalbard reindeer based on phylogenetic analysis of 16S rRNA genes. (B) OTU network map showing OTU interactions between all rarefied samples from the Svalbard reindeer, Norwegian reindeer feeding on a commercial feed, Tammar wallaby, rumen and termite. OTUs are represented by dots and dot sizes reflect sequence counts within the OTU. Dot colour indicates the number of microbiomes in which the OTU was found (1 =  white, 2 =  yellow, 3 =  orange, 4 =  red). The lines radiating from each of the five grey dots link the OTUs to their source microbiomes: Svalbard reindeer, dark blue (this study); Norwegian reindeer, light blue (this study; dataset included for comparative purposes only); Termite_PL3, yellow [4]; bovine, green [6]; Tammar wallaby, orange [5]. (C) Principal coordinate axes (PCoA) for the unweighted UniFrac analyses are coloured by host animal; Svalbard reindeer (2 samples: ▸▴) dark-blue; Norwegian reindeer (2 samples: ♦♦) light-blue; bovine rumen (•) green; Tammar wallaby (◂) red; termite (▪) orange. (D) Composition of the Svalbard reindeer rumen metagenome sequence dataset, based on sequence composition-based binning of 1394 assembled scaffolds (∼5.4 Mb) using PhyloPythiaS. For a complete rrs inventory and comparisons between the two Svalbard reindeer samples at an OTU definition of 97% ID see Table S1.
Mentions: The microbial community structure was determined using both 16S rRNA gene amplicon pyrosequencing and sequence-composition binning (PhyloPythiaS) of scaffolds assembled from metagenomic sequences (Figure 1). Using 16S rRNA gene analysis we determined there was little variation between the two animals used for this study: 90.4% and 91.5% of OTUs found in the rumen communities of animals SR1 and SR2, respectively, were shared between the two samples (Figure 1, Table S1). There were only a few instances of large differences in OTU relative abundance between the two samples (Table S1).

Bottom Line: Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1).Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation.Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. phil.pope@umb.no

ABSTRACT
Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus). Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1). Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.

Show MeSH