Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen
Publication Date
November 07, 2012
Journal
PLOS ONE
Authors
Derrick E. Fouts, Sebastian Szpakowski, Janaki Purushe, Manolito Torralba, et al
Volume
7
Issue
11
Pages
e48289
DOI
https://dx.plos.org/10.1371/journal.pone.0048289
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0048289
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23144861
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492333
Europe PMC
http://europepmc.org/abstract/MED/23144861
Web of Science
000311935800043
Scopus
84868708445
Mendeley
http://www.mendeley.com/research/next-generation-sequencing-define-prokaryotic-fungal-diversity-bovine-rumen
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Mendeley | Further Information

{"title"=>"Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen", "type"=>"journal", "authors"=>[{"first_name"=>"Derrick E.", "last_name"=>"Fouts", "scopus_author_id"=>"7004101734"}, {"first_name"=>"Sebastian", "last_name"=>"Szpakowski", "scopus_author_id"=>"34873655700"}, {"first_name"=>"Janaki", "last_name"=>"Purushe", "scopus_author_id"=>"36136288100"}, {"first_name"=>"Manolito", "last_name"=>"Torralba", "scopus_author_id"=>"35747428100"}, {"first_name"=>"Richard C.", "last_name"=>"Waterman", "scopus_author_id"=>"22935902100"}, {"first_name"=>"Michael D.", "last_name"=>"MacNeil", "scopus_author_id"=>"7006732687"}, {"first_name"=>"Leeson J.", "last_name"=>"Alexander", "scopus_author_id"=>"55423675000"}, {"first_name"=>"Karen E.", "last_name"=>"Nelson", "scopus_author_id"=>"7403227781"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84868708445", "pui"=>"366024945", "doi"=>"10.1371/journal.pone.0048289", "isbn"=>"1932-6203", "sgr"=>"84868708445", "pmid"=>"23144861"}, "id"=>"20067c44-cac8-30d5-844b-c33887ae9ca8", "abstract"=>"A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1-V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4-99.9% of OTUs represented by more than one read, using Good's coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.", "link"=>"http://www.mendeley.com/research/next-generation-sequencing-define-prokaryotic-fungal-diversity-bovine-rumen", "reader_count"=>135, "reader_count_by_academic_status"=>{"Unspecified"=>9, "Professor > Associate Professor"=>4, "Researcher"=>43, "Student > Doctoral Student"=>11, "Student > Ph. D. 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Student"=>29, "Student > Postgraduate"=>7, "Student > Master"=>17, "Other"=>2, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>12, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>89, "Medicine and Dentistry"=>4, "Veterinary Science and Veterinary Medicine"=>5, "Chemistry"=>1, "Social Sciences"=>2, "Computer Science"=>3, "Immunology and Microbiology"=>2, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>89}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>12}, "Environmental Science"=>{"Environmental Science"=>6}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>5}}, "reader_count_by_country"=>{"United States"=>3, "Japan"=>1, "Philippines"=>1, "China"=>1, "Brazil"=>3, "United Kingdom"=>2, "Slovakia"=>1, "Chile"=>1, "Kenya"=>1, "France"=>1, "Germany"=>2}, "group_count"=>5}

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Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/292423", "https://ndownloader.figshare.com/files/292491", "https://ndownloader.figshare.com/files/292558", "https://ndownloader.figshare.com/files/292623", "https://ndownloader.figshare.com/files/292670", "https://ndownloader.figshare.com/files/292725", "https://ndownloader.figshare.com/files/292760", "https://ndownloader.figshare.com/files/292921", "https://ndownloader.figshare.com/files/292965"], "description"=>"<div><p>A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1–V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order <em>Clostridiales</em>, <em>Bacteroidales</em>, <em>Erysipelotrichales</em> and unclassified TM7. Abundance of <em>Prevotella</em> species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4–99.9% of OTUs represented by more than one read, using Good’s coverage. Examination of the fungal community identified numerous novel groups. <em>Prevotella</em> and <em>Tannerella</em> were overrepresented in the liquid fraction of the rumen while <em>Butyrivibrio</em> and <em>Blautia</em> were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.</p> </div>", "links"=>[], "tags"=>["sequencing", "prokaryotic", "fungal", "bovine", "rumen"], "article_id"=>117560, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.s001", "https://dx.doi.org/10.1371/journal.pone.0048289.s002", "https://dx.doi.org/10.1371/journal.pone.0048289.s003", "https://dx.doi.org/10.1371/journal.pone.0048289.s004", "https://dx.doi.org/10.1371/journal.pone.0048289.s005", "https://dx.doi.org/10.1371/journal.pone.0048289.s006", "https://dx.doi.org/10.1371/journal.pone.0048289.s007", "https://dx.doi.org/10.1371/journal.pone.0048289.s008", "https://dx.doi.org/10.1371/journal.pone.0048289.s009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Next_Generation_Sequencing_to_Define_Prokaryotic_and_Fungal_Diversity_in_the_Bovine_Rumen__/117560", "title"=>"Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-07 02:06:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/545978"], "description"=>"<p>The Venn diagram depicts OTUs that were unique to the 12 cows used in this study (COWS), unique to the public repositories (REF) or shared.</p>", "links"=>[], "tags"=>["rumen", "ssu", "microbial", "sequences"], "article_id"=>216465, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_rumen_SSU_microbial_sequences_to_data_in_public_repositories_/216465", "title"=>"Comparison of rumen SSU microbial sequences to data in public repositories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:47:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/546083"], "description"=>"<p>Bar-charts display the taxonomic profiles for <i>Bacteria</i> (A), <i>Archaea</i> (B), and <i>Fungi</i> (C) of OTUs counted at the genus level.</p>", "links"=>[], "tags"=>["rumen", "microbial", "12"], "article_id"=>216569, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bovine_rumen_microbial_diversity_among_12_cows_/216569", "title"=>"Bovine rumen microbial diversity among 12 cows.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:49:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/546218"], "description"=>"<p>Bar-charts (left panels) and PCA scatter plots (right panels) display the OTU-based taxonomic profiles and similarity among profiles, respectively for <i>Bacteria</i> (A), <i>Archaea</i> (B), and <i>Fungi</i> (C). The relative abundance of seven bacteria with significant differences in liquid and solid fractions of the rumen was plotted (D).</p>", "links"=>[], "tags"=>["microbial", "bovine", "rumen", "fractions", "12"], "article_id"=>216705, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_microbial_diversity_in_bovine_rumen_solid_S_and_liquid_L_fractions_in_12_cows_/216705", "title"=>"Comparison of microbial diversity in bovine rumen solid (S) and liquid (L) fractions in 12 cows.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:51:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/546325"], "description"=>"<p>Taxonomic classes of <i>Bacteria</i> (gray italics), Fungi (black) and <i>Archaea</i> (black italics) are listed on the right side of the plot. The key denotes log10 transformed abundance patterns. The taxa are clustered based on abundance pattern correlation using a distance metric defined as 1-|r|. The dendrogram on the left side of the plot summarizes the clustering of taxa. Asterisks on nodes denote statistically significant correlations (P<0.05). The names of significantly significant correlated classes are indicated by bold face font.</p>", "links"=>[], "tags"=>["otu", "abundance"], "article_id"=>216814, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cross_domain_OTU_comparison_based_on_abundance_pattern_correlations_/216814", "title"=>"Cross domain OTU comparison based on abundance pattern correlations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:53:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/546451"], "description"=>"<p>NJ tree clustering of OTU representatives labeled based on similarity to known sequences. The color of the branch indicates bootstrapping value: blue when bootstrapping was <50%, red when bootstrapping was >50%. The width of the branch is proportional to the number of animals (1–12) that exhibited a given OTU. This number of animals is also indicated in the last part of the OTU label. Gray- and black-labeled OTUs were classified using BLAST and at least 97% identity to a target sequence. Black labels highlight a subset of these OTUs with vague annotation. OTUs labeled in blue did not match a target using BLAST, but were subsequently classified using LCA based on 90% identity to a SILVA database match. OTUs in red failed both BLAST and LCA and are presumably novel taxa.</p>", "links"=>[], "tags"=>["fungal", "18s", "rrna", "sequences", "bovine"], "article_id"=>216933, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_diversity_of_fungal_18S_rRNA_sequences_in_bovine_rumen_/216933", "title"=>"Phylogenetic diversity of fungal 18S rRNA sequences in bovine rumen.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:55:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/546584"], "description"=>"<p>Diversity among 12 cows and public repositories.</p>", "links"=>[], "tags"=>["12", "cows"], "article_id"=>217073, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_among_12_cows_and_public_repositories_/217073", "title"=>"Diversity among 12 cows and public repositories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 01:57:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/546623"], "description"=>"<p>Sampling microbial diversity across 12 cows.</p>", "links"=>[], "tags"=>["microbial", "12"], "article_id"=>217111, "categories"=>["Medicine", "Microbiology", "Physiology", "Biotechnology", "Genetics", "Evolutionary Biology"], "users"=>["Derrick E. Fouts", "Sebastian Szpakowski", "Janaki Purushe", "Manolito Torralba", "Richard C. Waterman", "Michael D. MacNeil", "Leeson J. Alexander", "Karen E. Nelson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048289.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_microbial_diversity_across_12_cows_/217111", "title"=>"Sampling microbial diversity across 12 cows.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 01:58:31"}

PMC Usage Stats | Further Information

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Relative Metric

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