Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows
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{"title"=>"Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows", "type"=>"journal", "authors"=>[{"first_name"=>"Lingling", "last_name"=>"Wang", "scopus_author_id"=>"44661970000"}, {"first_name"=>"Ayat", "last_name"=>"Hatem", "scopus_author_id"=>"36144237600"}, {"first_name"=>"Umit V.", "last_name"=>"Catalyurek", "scopus_author_id"=>"13807295300"}, {"first_name"=>"Mark", "last_name"=>"Morrison", "scopus_author_id"=>"7201675268"}, {"first_name"=>"Zhongtang", "last_name"=>"Yu", "scopus_author_id"=>"7404346378"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24223817", "sgr"=>"84892399148", "doi"=>"10.1371/journal.pone.0078507", "scopus"=>"2-s2.0-84892399148", "pui"=>"372116942", "issn"=>"19326203"}, "id"=>"4d0fba52-36ed-353d-8160-e37332b10c5c", "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.", "link"=>"http://www.mendeley.com/research/metagenomic-insights-carbohydrateactive-enzymes-carried-microorganisms-adhering-solid-digesta-rumen", "reader_count"=>64, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>16, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>3, "Student > Master"=>8, "Student > Bachelor"=>7, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>16, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>3, "Student > Master"=>8, "Student > Bachelor"=>7, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>9, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>39, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>39}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>9}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Hong Kong"=>1, "Philippines"=>1, "Brazil"=>2, "Italy"=>2, "Slovakia"=>1, "France"=>2, "Germany"=>1, "India"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1268236"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["cazy", "lowest", "taxon", "assigned"], "article_id"=>841807, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078507.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_CAZy_families_at_the_lowest_taxon_assigned_by_MEGAN_/841807", "title"=>"Distribution of CAZy families at the lowest taxon assigned by MEGAN.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-05 02:47:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1268238"], "description"=>"<p>GH  =  glycoside hydrolase, GT  =  glycoside transferase, CE  =  carbohydrate esterase, CBM  =  carbohydrate binding module, PL  =  polysaccharide lyase. Taxa: <i>F</i>  =  <i>Firmicutes</i>, <i>B/C  =  Bacteroidetes/Chlroobi</i>, <i>B</i>  =  Bacteria, <i>A  =  Actinobacteria</i>. Substrate: C  =  cellulose, X  =  xylan/hemicellulose, G =  Glucosides, S  =  starch or sucrose, M  =  Mannan. T (black)  =  transporter. H (green)  =  sensor histidine kinase. Transcriptional regulators (red capital letters): R  =  transcriptional regulator, L  =  LacI family, X  =  XRE family, M  =  MerR family, A  =  AraC family, Y  =  LysR family, D  =  DeoR family, C  =  Cro/CI family, N  =  TetR, V  =  VicR, G  =  GntR family, P  =  PadR family. Mobile elements (blue): I  =  integrase, Q  =  transposase. Sigma factor and related genes (pink): E  =  ECFσ, F  =  anti-sigma factor antagonist, J  =  anti-YlaC sigma factor, σ  =  sigma-70 factor. Sugar related regulatory factors (italic brown): B  =  sugar fermentation stimulation protein SfsA, O  =  sucrose operon repressor ScrR, K  =  trehalose operon repressor. Sus-like system genes (underlined): S  =  SusC/SusD, S*  =  SusC. Z (grey)  =  zinc finger domain protein of LSD1 subclass.</p>", "links"=>[], "tags"=>["cazy", "contigs", "degradative", "substrates"], "article_id"=>841808, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078507.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_CAZy_families_and_genetic_features_in_the_contigs_that_contain_gt_2_degradative_CAZy_families_with_clear_substrates_designated_/841808", "title"=>"Distribution of CAZy families and genetic features in the contigs that contain > 2 degradative CAZy families with clear substrates designated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-05 02:47:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1268250", "https://ndownloader.figshare.com/files/1268251", "https://ndownloader.figshare.com/files/1268252", "https://ndownloader.figshare.com/files/1268253", "https://ndownloader.figshare.com/files/1268254", "https://ndownloader.figshare.com/files/1268255", "https://ndownloader.figshare.com/files/1268256", "https://ndownloader.figshare.com/files/1268257"], "description"=>"<div><p>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 <i>Firmicutes</i>. 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.</p></div>", "links"=>[], "tags"=>["insights", "carbohydrate-active", "enzymes", "carried", "microorganisms", "adhering", "digesta", "rumen"], "article_id"=>841820, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078507.s001", "https://dx.doi.org/10.1371/journal.pone.0078507.s002", "https://dx.doi.org/10.1371/journal.pone.0078507.s003", "https://dx.doi.org/10.1371/journal.pone.0078507.s004", "https://dx.doi.org/10.1371/journal.pone.0078507.s005", "https://dx.doi.org/10.1371/journal.pone.0078507.s006", "https://dx.doi.org/10.1371/journal.pone.0078507.s007", "https://dx.doi.org/10.1371/journal.pone.0078507.s008"], "stats"=>{"downloads"=>20, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metagenomic_Insights_into_the_Carbohydrate_Active_Enzymes_Carried_by_the_Microorganisms_Adhering_to_Solid_Digesta_in_the_Rumen_of_Cows_/841820", "title"=>"Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-05 02:47:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1268247"], "description"=>"<p>Data are presented using the format described in reference <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Pope1\" target=\"_blank\">[5]</a>. GHs were grouped based on their major activity in plant fiber degradation.</p><p>NR, not reported.</p>a<p>Pope <i>et al</i>, 2010 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Pope2\" target=\"_blank\">[9]</a> (sequencing of activity-screened fosmids using 454 GS FLX).</p>b<p>Brulc, <i>et al</i>, 2009 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Brulc1\" target=\"_blank\">[4]</a>. The number of fiber-adherent samples was the average of three fiber adherent samples (shotgun metagenomic sequencing using 454 GS20).</p>c<p>Hess <i>et al</i>, 2011 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Hess1\" target=\"_blank\">[3]</a> (shotgun metagenomic sequencing using Illumina GAII and HiSeq2000).</p>d<p>Pope <i>et al</i>, 2012 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Pope1\" target=\"_blank\">[5]</a> (shotgun metagenomic sequencing and sequencing of activity-screened BAC clones using 454 GS FLX Titanium).</p>e<p>Dai <i>et al</i>, 2012 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Dai1\" target=\"_blank\">[7]</a> (sequencing of activity-screened BAC clones using 454 GS FLX Titanium).</p>*<p>Percentage of each group relative to the total number of GH’s identified in each metagenomic dataset.</p>#<p>Numbers inside and outside parentheses are those retrieved from the BAC library and shotgun sequencing, respectively. The data inside the parentheses showed the dereplicated GHs.</p>", "links"=>[], "tags"=>["gh", "metagenomes"], "article_id"=>841817, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078507.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_major_GH_families_identified_in_large_metagenomes_of_herbivores_/841817", "title"=>"Comparison of the major GH families identified in large metagenomes of herbivores.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-05 02:47:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1268245"], "description"=>"<p>The genes of the two PULs identified in this study were listed in Table S4. The figure was partly adapted from the paper by Pope <i>et al </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507-Pope1\" target=\"_blank\">[5]</a>. Consistent with that paper, black genes represent putative response-regulators. SusE/SusF-like genes encode outer-membrane proteins. Trans: putative transporter. BACON: a carbohydrate binding domain. TonB: TonB-dependent receptor family, which functions to transport solutes and macromolecules with a membrane spanning β-barrel proteins. TW-64 and TW-33 are sample IDs for the GH9 and GH5 genes (respectively) identified within the AC2a PUL. GenBank accession numbers and/or IMG Gene Object ID numbers are provided for each cluster/scaffold when available, and details for each gene were listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078507#pone.0078507.s007\" target=\"_blank\">Table S6</a>. A: hypothetical lipoprotein; B, E, G, J: putative polygalacturonase; C: sialic acid acetylesterase; D, H, I, hypothetical protein; F: SusC homolog. Both F and the first SusC in contig 196-PUL19 are located at the end of the contigs.</p>", "links"=>[], "tags"=>["cellulolytic", "puls", "metagenomes"], "article_id"=>841815, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078507.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_organization_of_representative_cellulolytic_PULs_identified_in_available_metagenomes_and_the_present_study_shown_in_bold_/841815", "title"=>"Gene organization of representative cellulolytic PULs identified in available metagenomes and the present study (shown in bold).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-05 02:47:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1268246"], "description"=>"<p>Notes: <sup>a</sup> total ORFs in the present metagenomic dataset that were found to be similar to the genes of each sequenced genome; <sup>b</sup> total ORFs in the metagenomic dataset that exhibited similarity to the CAZy genes of each sequenced genome; <sup>c-k</sup> ORFs in the metagenomic dataset that were found similar to the carbohydrate binding module (CBM), glycoside hydrolase (GH); glycosyl transferase (GT), carbohydrate esterase (CE), polysaccharide lyase (PL), signal peptide (SP), transmembrane domain (TM), and both SP and TM.</p>*<p>One GH3 in the metagenomic dataset exhibited 91% amino acid similarity with a GH3 in the genome of <i>P</i>. <i>ruminicola</i> 23.</p>", "links"=>[], "tags"=>["orfs", "metagenomic", "dataset", "exhibited", "similarities", "genes", "sequenced", "genomes", "rumen", "fibrolytic", "bacterial"], "article_id"=>841816, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078507.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_ORFs_in_the_present_metagenomic_dataset_that_exhibited_similarities_to_the_genes_in_the_sequenced_genomes_of_the_rumen_fibrolytic_bacterial_species_/841816", "title"=>"Number of ORFs in the present metagenomic dataset that exhibited similarities to the genes in the sequenced genomes of the rumen fibrolytic bacterial species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-05 02:47:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1268241"], "description"=>"<p>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 <i>Fibrobacter succinogenes</i> S85 was used as an outgroup. S-1 to S-8 are subfamilies of GH5 proteins.</p>", "links"=>[], "tags"=>["phylogenetic", "putative", "gh5", "proteins", "metagenomic"], "article_id"=>841811, "categories"=>["Biological Sciences"], "users"=>["Lingling Wang", "Ayat Hatem", "Umit V. Catalyurek", "Mark Morrison", "Zhongtang Yu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078507.g003", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_phylogenetic_tree_of_the_putative_GH5_proteins_from_the_available_metagenomic_datasets_/841811", "title"=>"A phylogenetic tree of the putative GH5 proteins from the available metagenomic datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-05 02:47:18"}

PMC Usage Stats | Further Information

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Relative Metric

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