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Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.

Wang L, Hatem A, Catalyurek UV, Morrison M, Yu Z - PLoS ONE (2013)

Bottom Line: These subfamilies of GH5 proteins also showed significant phylum-dependent distribution.A number of polysaccharide utilization loci (PULs) were found, and two of them contained genes encoding Sus-like proteins and cellulases that have not been reported in previous metagenomic studies of samples from the rumens of cows or other herbivores.Future studies are needed to further explore how host genetics and diets affect the diversity and distribution of CAZymes and utilization of plant cell wall materials.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America.

ABSTRACT
The ruminal microbial community is a unique source of enzymes that underpin the conversion of cellulosic biomass. In this study, the microbial consortia adherent on solid digesta in the rumen of Jersey cattle were subjected to an activity-based metagenomic study to explore the genetic diversity of carbohydrolytic enzymes in Jersey cows, with a particular focus on cellulases and xylanases. Pyrosequencing and bioinformatic analyses of 120 carbohydrate-active fosmids identified genes encoding 575 putative Carbohydrate-Active Enzymes (CAZymes) and proteins putatively related to transcriptional regulation, transporters, and signal transduction coupled with polysaccharide degradation and metabolism. Most of these genes shared little similarity to sequences archived in databases. Genes that were predicted to encode glycoside hydrolases (GH) involved in xylan and cellulose hydrolysis (e.g., GH3, 5, 9, 10, 39 and 43) were well represented. A new subfamily (S-8) of GH5 was identified from contigs assigned to Firmicutes. These subfamilies of GH5 proteins also showed significant phylum-dependent distribution. A number of polysaccharide utilization loci (PULs) were found, and two of them contained genes encoding Sus-like proteins and cellulases that have not been reported in previous metagenomic studies of samples from the rumens of cows or other herbivores. Comparison with the large metagenomic datasets previously reported of other ruminant species (or cattle breeds) and wallabies showed that the rumen microbiome of Jersey cows might contain differing CAZymes. Future studies are needed to further explore how host genetics and diets affect the diversity and distribution of CAZymes and utilization of plant cell wall materials.

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A phylogenetic tree of the putative GH5 proteins from the available metagenomic datasets.The tree was drawn using the Neighbor-Joining method with bootstrap replication of 500. Branches with ≤ 50% bootstrap support were collapsed. The evolutionary distances were calculated using the p-distance method. Names of proteins (or predicted proteins) were presented by the source organisms and GenBank accession number. The predicted proteins identified in this study are bolded. The GH45 protein of Fibrobacter succinogenes S85 was used as an outgroup. S-1 to S-8 are subfamilies of GH5 proteins.
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pone-0078507-g003: A phylogenetic tree of the putative GH5 proteins from the available metagenomic datasets.The tree was drawn using the Neighbor-Joining method with bootstrap replication of 500. Branches with ≤ 50% bootstrap support were collapsed. The evolutionary distances were calculated using the p-distance method. Names of proteins (or predicted proteins) were presented by the source organisms and GenBank accession number. The predicted proteins identified in this study are bolded. The GH45 protein of Fibrobacter succinogenes S85 was used as an outgroup. S-1 to S-8 are subfamilies of GH5 proteins.

Mentions: In the large metagenomes reported previously [3]–[5], [7], [9] and the present study, GH5 is the most diverse and predominant family of cellulases (Table 1). The GH5 genes have been clustered into seven subfamilies (S-1 to S-7) [7]. GH5 genes belonging to these subfamilies were also identified in the present study (Figure 3). Besides those clustered with the previously identified GH5 subfamilies, seven new GH5 genes formed a new subfamily (referred to as S-8), which consisted of genes assigned to Firmicutes. Based on all available data of the GH5 family shown in Figure 3, it is intriguing that the distribution of the GH5 subfamilies showed significant taxonomic bias: Subfamilies S-1 to S-4 and S-8 were mainly assigned to Firmicutes, while subfamilies S-6 and S-7 were primarily assigned to Bacteroidetes.


Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.

Wang L, Hatem A, Catalyurek UV, Morrison M, Yu Z - PLoS ONE (2013)

A phylogenetic tree of the putative GH5 proteins from the available metagenomic datasets.The tree was drawn using the Neighbor-Joining method with bootstrap replication of 500. Branches with ≤ 50% bootstrap support were collapsed. The evolutionary distances were calculated using the p-distance method. Names of proteins (or predicted proteins) were presented by the source organisms and GenBank accession number. The predicted proteins identified in this study are bolded. The GH45 protein of Fibrobacter succinogenes S85 was used as an outgroup. S-1 to S-8 are subfamilies of GH5 proteins.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3818352&req=5

pone-0078507-g003: A phylogenetic tree of the putative GH5 proteins from the available metagenomic datasets.The tree was drawn using the Neighbor-Joining method with bootstrap replication of 500. Branches with ≤ 50% bootstrap support were collapsed. The evolutionary distances were calculated using the p-distance method. Names of proteins (or predicted proteins) were presented by the source organisms and GenBank accession number. The predicted proteins identified in this study are bolded. The GH45 protein of Fibrobacter succinogenes S85 was used as an outgroup. S-1 to S-8 are subfamilies of GH5 proteins.
Mentions: In the large metagenomes reported previously [3]–[5], [7], [9] and the present study, GH5 is the most diverse and predominant family of cellulases (Table 1). The GH5 genes have been clustered into seven subfamilies (S-1 to S-7) [7]. GH5 genes belonging to these subfamilies were also identified in the present study (Figure 3). Besides those clustered with the previously identified GH5 subfamilies, seven new GH5 genes formed a new subfamily (referred to as S-8), which consisted of genes assigned to Firmicutes. Based on all available data of the GH5 family shown in Figure 3, it is intriguing that the distribution of the GH5 subfamilies showed significant taxonomic bias: Subfamilies S-1 to S-4 and S-8 were mainly assigned to Firmicutes, while subfamilies S-6 and S-7 were primarily assigned to Bacteroidetes.

Bottom Line: These subfamilies of GH5 proteins also showed significant phylum-dependent distribution.A number of polysaccharide utilization loci (PULs) were found, and two of them contained genes encoding Sus-like proteins and cellulases that have not been reported in previous metagenomic studies of samples from the rumens of cows or other herbivores.Future studies are needed to further explore how host genetics and diets affect the diversity and distribution of CAZymes and utilization of plant cell wall materials.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America.

ABSTRACT
The ruminal microbial community is a unique source of enzymes that underpin the conversion of cellulosic biomass. In this study, the microbial consortia adherent on solid digesta in the rumen of Jersey cattle were subjected to an activity-based metagenomic study to explore the genetic diversity of carbohydrolytic enzymes in Jersey cows, with a particular focus on cellulases and xylanases. Pyrosequencing and bioinformatic analyses of 120 carbohydrate-active fosmids identified genes encoding 575 putative Carbohydrate-Active Enzymes (CAZymes) and proteins putatively related to transcriptional regulation, transporters, and signal transduction coupled with polysaccharide degradation and metabolism. Most of these genes shared little similarity to sequences archived in databases. Genes that were predicted to encode glycoside hydrolases (GH) involved in xylan and cellulose hydrolysis (e.g., GH3, 5, 9, 10, 39 and 43) were well represented. A new subfamily (S-8) of GH5 was identified from contigs assigned to Firmicutes. These subfamilies of GH5 proteins also showed significant phylum-dependent distribution. A number of polysaccharide utilization loci (PULs) were found, and two of them contained genes encoding Sus-like proteins and cellulases that have not been reported in previous metagenomic studies of samples from the rumens of cows or other herbivores. Comparison with the large metagenomic datasets previously reported of other ruminant species (or cattle breeds) and wallabies showed that the rumen microbiome of Jersey cows might contain differing CAZymes. Future studies are needed to further explore how host genetics and diets affect the diversity and distribution of CAZymes and utilization of plant cell wall materials.

Show MeSH