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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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Distribution of CAZy families at the lowest taxon assigned by MEGAN.The taxa were based on the NCBI taxonomy. The numbers of CAZy genes identified in each taxon were shown in pie chart. CBM, carbohydrate binding module, GH, glycoside hydrolase, GT, glycosyl transferase, CE, carbohydrate esterase, PL, polysaccharide lyase. Environmental samples (Bacteria), bacteria recovered from environment that could not be assigned to existing phyla; Unclassified bacteria, bacteria that could not be classified to existing phyla.
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pone-0078507-g001: Distribution of CAZy families at the lowest taxon assigned by MEGAN.The taxa were based on the NCBI taxonomy. The numbers of CAZy genes identified in each taxon were shown in pie chart. CBM, carbohydrate binding module, GH, glycoside hydrolase, GT, glycosyl transferase, CE, carbohydrate esterase, PL, polysaccharide lyase. Environmental samples (Bacteria), bacteria recovered from environment that could not be assigned to existing phyla; Unclassified bacteria, bacteria that could not be classified to existing phyla.

Mentions: The host organisms of all the ORFs were also inferred using MEGAN. Overall, 1256 of the 3553 predicted ORFs were assigned to the phylum Firmicutes. Of all the 3553 predicted ORFs, only 622 were assigned to 21 genera or other sub-phylum taxa (Figure 1). The Major genera included Clostridium (2.2% of total ORFs), Ruminococcus (2.2%), Butyrivibrio (2.2%), Prevotella (1.4%), and unclassified Lachnospiraceae (1.2%). A greater number of GH genes (17 in total) were assigned to Ruminococcus than to other genera. The other major genera were also represented with multiple CAZy genes. Given the high abundance of Prevotella in the rumen microbiome [19]–[21], it is intriguing that it was not well represented by the identified CAZy genes. It should be noted that although many CAZy genes (67 CAZy genes including 39 GHs) were assigned to known fibrolytic genera (e.g., Clostridium, Ruminococcus, Butyrivibrio, and Prevotella), none of them appeared to be derived from the type species or type strains of these genera, indicating a greater diversity of cellulolytic bacteria than that represented by those type species. The assignment of many CAZy genes to the above genera may reflect the presence of conserved functional domains shared among fibrolytic bacteria.


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)

Distribution of CAZy families at the lowest taxon assigned by MEGAN.The taxa were based on the NCBI taxonomy. The numbers of CAZy genes identified in each taxon were shown in pie chart. CBM, carbohydrate binding module, GH, glycoside hydrolase, GT, glycosyl transferase, CE, carbohydrate esterase, PL, polysaccharide lyase. Environmental samples (Bacteria), bacteria recovered from environment that could not be assigned to existing phyla; Unclassified bacteria, bacteria that could not be classified to existing phyla.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0078507-g001: Distribution of CAZy families at the lowest taxon assigned by MEGAN.The taxa were based on the NCBI taxonomy. The numbers of CAZy genes identified in each taxon were shown in pie chart. CBM, carbohydrate binding module, GH, glycoside hydrolase, GT, glycosyl transferase, CE, carbohydrate esterase, PL, polysaccharide lyase. Environmental samples (Bacteria), bacteria recovered from environment that could not be assigned to existing phyla; Unclassified bacteria, bacteria that could not be classified to existing phyla.
Mentions: The host organisms of all the ORFs were also inferred using MEGAN. Overall, 1256 of the 3553 predicted ORFs were assigned to the phylum Firmicutes. Of all the 3553 predicted ORFs, only 622 were assigned to 21 genera or other sub-phylum taxa (Figure 1). The Major genera included Clostridium (2.2% of total ORFs), Ruminococcus (2.2%), Butyrivibrio (2.2%), Prevotella (1.4%), and unclassified Lachnospiraceae (1.2%). A greater number of GH genes (17 in total) were assigned to Ruminococcus than to other genera. The other major genera were also represented with multiple CAZy genes. Given the high abundance of Prevotella in the rumen microbiome [19]–[21], it is intriguing that it was not well represented by the identified CAZy genes. It should be noted that although many CAZy genes (67 CAZy genes including 39 GHs) were assigned to known fibrolytic genera (e.g., Clostridium, Ruminococcus, Butyrivibrio, and Prevotella), none of them appeared to be derived from the type species or type strains of these genera, indicating a greater diversity of cellulolytic bacteria than that represented by those type species. The assignment of many CAZy genes to the above genera may reflect the presence of conserved functional domains shared among fibrolytic bacteria.

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