Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2014-08-14

AUTHORS

Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra

ABSTRACT

Key PointsAs the number of environmental small subunit (SSU) ribosomal RNA gene sequences has greatly surpassed the number of cultured microorganisms, reconciliation of the established taxonomy and classification of the uncultured microorganisms are crucial.Rational taxonomic boundaries have been proposed for the high taxa (that is, genus and above) of the Bacteria and the Archaea on the basis of 16S rRNA gene sequence identities. These are : 94.5% for genus, 86.5% for family, 82.0% for order, 78.5% for class and 75.0% for phylum.The application of these thresholds to the clustering of the SILVA database confirms that the current number of formally described taxa at any rank (for example, ∼30 phyla) is negligible compared with the total number of detected taxa (for example, ∼1,300 phyla).In addition, the study of the annual rate of taxa discovery enables a new extrapolation of the total number of species (4 × 105) and high taxa on Earth (for example, 1 × 105 genera), which indicates that most common terrestrial and aquatic habitats will be exhaustively described within the next 5 years.Taxon recovery tests that were carried out using partial 16S rRNA gene sequences show that short reads are not suitable for accurate richness estimations and accurate classifications of high taxa.On the basis of the general taxonomic thresholds and phylogenetic considerations, we suggest a new biodiversity unit known as the candidate taxonomic unit (CTU), which is compatible with the hierarchy that was established in the Bacteriological Code. The ability to specify a taxonomic rank for particular clades is a major advance in understanding tree topologies and goes beyond the classic phylogenetic delineation.The usefulness of CTUs has been intensively tested in the reclassification of the phylum Spirochaetes and the classification of 15 candidate divisions and environmental clades that are presented in this Analysis article, which also provide new insights into the coherence of classes, phyla and superphyla.By providing explicit and well-documented guidelines, it is hoped that this work will facilitate the implementation of the many changes in the current taxonomy that are necessary to develop a common taxonomic classification of high taxa of bacteria and archaea on the basis of SSU rRNA gene sequences. More... »

PAGES

635-645

References to SciGraph publications

  • 2013-04-17. When should a DDH experiment be mandatory in microbial taxonomy? in ARCHIVES OF MICROBIOLOGY
  • 2011-08-18. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 1998-01. Santa Rosalia revisited: Why are there so many species of bacteria? in ANTONIE VAN LEEUWENHOEK
  • 2002-05. Challenges for taxonomy in NATURE
  • 2010-06-07. The ecological coherence of high bacterial taxonomic ranks in NATURE REVIEWS MICROBIOLOGY
  • 2010-07-01. Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2001. Overview: A Phylogenetic Backbone and Taxonomic Framework for Procaryotic Systematics in BERGEY’S MANUAL® OF SYSTEMATIC BACTERIOLOGY
  • 2013-07-30. Microbiome research goes without a home in NATURE
  • 2012-07-26. Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • Journal

    TITLE

    Nature Reviews Microbiology

    ISSUE

    9

    VOLUME

    12

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nrmicro3330

    DOI

    http://dx.doi.org/10.1038/nrmicro3330

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1018109693

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25118885


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Microbiology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Archaea", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacteria", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computational Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Archaeal", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Bacterial", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Ribosomal", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Databases, Nucleic Acid", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Ribosomal, 16S", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Ribotyping", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, DNA", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Ribocon GmbH, Fahrenheitstrasse 1, D-28359, Bremen, Germany", 
              "id": "http://www.grid.ac/institutes/grid.437298.3", 
              "name": [
                "Department of Ecology and Marine Resources, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190, Esporles, Balearic Islands, Spain", 
                "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany", 
                "Ribocon GmbH, Fahrenheitstrasse 1, D-28359, Bremen, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yarza", 
            "givenName": "Pablo", 
            "id": "sg:person.01142757113.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01142757113.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany", 
              "id": "http://www.grid.ac/institutes/grid.419529.2", 
              "name": [
                "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yilmaz", 
            "givenName": "Pelin", 
            "id": "sg:person.01274774737.70", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01274774737.70"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany", 
              "id": "http://www.grid.ac/institutes/grid.419529.2", 
              "name": [
                "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pruesse", 
            "givenName": "Elmar", 
            "id": "sg:person.01100647363.23", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01100647363.23"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany", 
              "id": "http://www.grid.ac/institutes/grid.15078.3b", 
              "name": [
                "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany", 
                "Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gl\u00f6ckner", 
            "givenName": "Frank Oliver", 
            "id": "sg:person.0764345020.82", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764345020.82"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Lehrstuhl f\u00fcr Mikrobiologie, Technische Universit\u00e4t M\u00fcnchen, D-85350, Freising, Germany", 
              "id": "http://www.grid.ac/institutes/grid.6936.a", 
              "name": [
                "Lehrstuhl f\u00fcr Mikrobiologie, Technische Universit\u00e4t M\u00fcnchen, D-85350, Freising, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ludwig", 
            "givenName": "Wolfgang", 
            "id": "sg:person.01130261667.49", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01130261667.49"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Lehrstuhl f\u00fcr Mikrobiologie, Technische Universit\u00e4t M\u00fcnchen, D-85350, Freising, Germany", 
              "id": "http://www.grid.ac/institutes/grid.6936.a", 
              "name": [
                "Lehrstuhl f\u00fcr Mikrobiologie, Technische Universit\u00e4t M\u00fcnchen, D-85350, Freising, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Schleifer", 
            "givenName": "Karl-Heinz", 
            "id": "sg:person.01301526365.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01301526365.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Microbiology, University of Georgia, 527 Biological Sciences Building, 30605\u20132605, Athens, Georgia, USA", 
              "id": "http://www.grid.ac/institutes/grid.213876.9", 
              "name": [
                "Department of Microbiology, University of Georgia, 527 Biological Sciences Building, 30605\u20132605, Athens, Georgia, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Whitman", 
            "givenName": "William B.", 
            "id": "sg:person.01351157720.95", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351157720.95"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Soci\u00e9t\u00e9 de Bact\u00e9riologie Syst\u00e9matique et V\u00e9t\u00e9rinaire (SBSV) and \u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse (ENVT), F-31076, Toulouse cedex 03, France", 
              "id": "http://www.grid.ac/institutes/grid.418686.5", 
              "name": [
                "Soci\u00e9t\u00e9 de Bact\u00e9riologie Syst\u00e9matique et V\u00e9t\u00e9rinaire (SBSV) and \u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse (ENVT), F-31076, Toulouse cedex 03, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Euz\u00e9by", 
            "givenName": "Jean", 
            "id": "sg:person.0601714613.51", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601714613.51"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany", 
              "id": "http://www.grid.ac/institutes/grid.419529.2", 
              "name": [
                "Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Amann", 
            "givenName": "Rudolf", 
            "id": "sg:person.01167734006.82", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167734006.82"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Ecology and Marine Resources, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190, Esporles, Balearic Islands, Spain", 
              "id": "http://www.grid.ac/institutes/grid.466857.e", 
              "name": [
                "Department of Ecology and Marine Resources, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190, Esporles, Balearic Islands, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rossell\u00f3-M\u00f3ra", 
            "givenName": "Ramon", 
            "id": "sg:person.0664234342.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0664234342.14"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/417017a", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028561703", 
              "https://doi.org/10.1038/417017a"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1000665216662", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043457281", 
              "https://doi.org/10.1023/a:1000665216662"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/500016a", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017195767", 
              "https://doi.org/10.1038/500016a"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro2367", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052470816", 
              "https://doi.org/10.1038/nrmicro2367"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2010.87", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035301217", 
              "https://doi.org/10.1038/ismej.2010.87"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-0-387-21609-6_8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015420409", 
              "https://doi.org/10.1007/978-0-387-21609-6_8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2012.82", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015690230", 
              "https://doi.org/10.1038/ismej.2012.82"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2011.109", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010316628", 
              "https://doi.org/10.1038/ismej.2011.109"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00203-013-0888-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043406325", 
              "https://doi.org/10.1007/s00203-013-0888-4"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2014-08-14", 
        "datePublishedReg": "2014-08-14", 
        "description": "Key PointsAs the number of environmental small subunit (SSU) ribosomal RNA gene sequences has greatly surpassed the number of cultured microorganisms, reconciliation of the established taxonomy and classification of the uncultured microorganisms are crucial.Rational taxonomic boundaries have been proposed for the high taxa (that is, genus and above) of the Bacteria and the Archaea on the basis of 16S rRNA gene sequence identities. These are : 94.5% for genus, 86.5% for family, 82.0% for order, 78.5% for class and 75.0% for phylum.The application of these thresholds to the clustering of the SILVA database confirms that the current number of formally described taxa at any rank (for example, \u223c30 phyla) is negligible compared with the total number of detected taxa (for example, \u223c1,300 phyla).In addition, the study of the annual rate of taxa discovery enables a new extrapolation of the total number of species (4 \u00d7 105) and high taxa on Earth (for example, 1 \u00d7 105 genera), which indicates that most common terrestrial and aquatic habitats will be exhaustively described within the next 5 years.Taxon recovery tests that were carried out using partial 16S rRNA gene sequences show that short reads are not suitable for accurate richness estimations and accurate classifications of high taxa.On the basis of the general taxonomic thresholds and phylogenetic considerations, we suggest a new biodiversity unit known as the candidate taxonomic unit (CTU), which is compatible with the hierarchy that was established in the Bacteriological Code. The ability to specify a taxonomic rank for particular clades is a major advance in understanding tree topologies and goes beyond the classic phylogenetic delineation.The usefulness of CTUs has been intensively tested in the reclassification of the phylum Spirochaetes and the classification of 15 candidate divisions and environmental clades that are presented in this Analysis article, which also provide new insights into the coherence of classes, phyla and superphyla.By providing explicit and well-documented guidelines, it is hoped that this work will facilitate the implementation of the many changes in the current taxonomy that are necessary to develop a common taxonomic classification of high taxa of bacteria and archaea on the basis of SSU rRNA gene sequences.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/nrmicro3330", 
        "inLanguage": "en", 
        "isAccessibleForFree": false, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3781187", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3796246", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3782531", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1032854", 
            "issn": [
              "1740-1526", 
              "1740-1534"
            ], 
            "name": "Nature Reviews Microbiology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "9", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "12"
          }
        ], 
        "keywords": [
          "rRNA gene sequences", 
          "higher taxa", 
          "gene sequences", 
          "small subunit ribosomal RNA gene sequences", 
          "SSU rRNA gene sequences", 
          "rRNA gene sequence identity", 
          "ribosomal RNA gene sequences", 
          "gene sequence identity", 
          "RNA gene sequences", 
          "environmental clade", 
          "uncultured microorganisms", 
          "taxonomic boundaries", 
          "candidate divisions", 
          "phylogenetic delineation", 
          "phylum Spirochaetes", 
          "current taxonomy", 
          "uncultured bacteria", 
          "phylogenetic considerations", 
          "taxonomic ranks", 
          "aquatic habitats", 
          "particular clades", 
          "taxonomic units", 
          "biodiversity units", 
          "sequence identity", 
          "SILVA database", 
          "taxonomic classification", 
          "taxa", 
          "richness estimation", 
          "archaea", 
          "short reads", 
          "tree topology", 
          "cultured microorganisms", 
          "Bacteriological Code", 
          "clade", 
          "phyla", 
          "bacteria", 
          "sequence", 
          "new insights", 
          "microorganisms", 
          "taxonomy", 
          "superphyla", 
          "habitats", 
          "Key PointsAs", 
          "genus", 
          "species", 
          "spirochaetes", 
          "reads", 
          "major advances", 
          "total number", 
          "family", 
          "division", 
          "discovery", 
          "current number", 
          "basis", 
          "insights", 
          "number", 
          "reclassification", 
          "identity", 
          "ability", 
          "advances", 
          "class", 
          "clustering", 
          "delineation", 
          "addition", 
          "changes", 
          "new extrapolation", 
          "rank", 
          "study", 
          "classification", 
          "database", 
          "units", 
          "accurate classification", 
          "topology", 
          "Earth", 
          "annual rate", 
          "rate", 
          "hierarchy", 
          "analysis article", 
          "order", 
          "years", 
          "work", 
          "extrapolation", 
          "boundaries", 
          "applications", 
          "usefulness", 
          "threshold", 
          "test", 
          "code", 
          "consideration", 
          "reconciliation", 
          "estimation", 
          "article", 
          "guidelines", 
          "recovery tests", 
          "implementation", 
          "coherence", 
          "PointsAs", 
          "environmental small subunit (SSU) ribosomal RNA gene sequences", 
          "subunit (SSU) ribosomal RNA gene sequences", 
          "Rational taxonomic boundaries", 
          "taxa discovery", 
          "Taxon recovery tests", 
          "accurate richness estimations", 
          "general taxonomic thresholds", 
          "taxonomic thresholds", 
          "new biodiversity unit", 
          "candidate taxonomic unit", 
          "classic phylogenetic delineation", 
          "usefulness of CTUs", 
          "coherence of classes", 
          "common taxonomic classification"
        ], 
        "name": "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences", 
        "pagination": "635-645", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1018109693"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/nrmicro3330"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "25118885"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/nrmicro3330", 
          "https://app.dimensions.ai/details/publication/pub.1018109693"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-01-01T18:33", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/article/article_635.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/nrmicro3330"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nrmicro3330'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nrmicro3330'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nrmicro3330'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nrmicro3330'


     

    This table displays all metadata directly associated to this object as RDF triples.

    343 TRIPLES      22 PREDICATES      156 URIs      139 LITERALS      18 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/nrmicro3330 schema:about N291234e812c4472cb349f992ef1fae34
    2 N466e769814014411a84b063be2b382b1
    3 N5e0ec513c5734442b2b4d47a4eaec0f5
    4 N86aed387884b4852a443d82a9013a2d3
    5 N88176636015d4b3790bb191e9df2dbaa
    6 N93d7f3d7e5b14a48947035a5c297e505
    7 N95481242bf4c47588ff5d48109e75744
    8 Nb87e4c0e38f14e14925ed30dd5d1a562
    9 Nc59998ee282c4d5db7dec0971a8ae16b
    10 Nf01e408e366e4d3ca7fbe12898665cf0
    11 Nf2a59843d7e4461ea8b4da691127a430
    12 anzsrc-for:06
    13 anzsrc-for:0605
    14 schema:author N4240fc33cb854196a78d9040e9b9d377
    15 schema:citation sg:pub.10.1007/978-0-387-21609-6_8
    16 sg:pub.10.1007/s00203-013-0888-4
    17 sg:pub.10.1023/a:1000665216662
    18 sg:pub.10.1038/417017a
    19 sg:pub.10.1038/500016a
    20 sg:pub.10.1038/ismej.2010.87
    21 sg:pub.10.1038/ismej.2011.109
    22 sg:pub.10.1038/ismej.2012.82
    23 sg:pub.10.1038/nrmicro2367
    24 schema:datePublished 2014-08-14
    25 schema:datePublishedReg 2014-08-14
    26 schema:description Key PointsAs the number of environmental small subunit (SSU) ribosomal RNA gene sequences has greatly surpassed the number of cultured microorganisms, reconciliation of the established taxonomy and classification of the uncultured microorganisms are crucial.Rational taxonomic boundaries have been proposed for the high taxa (that is, genus and above) of the Bacteria and the Archaea on the basis of 16S rRNA gene sequence identities. These are : 94.5% for genus, 86.5% for family, 82.0% for order, 78.5% for class and 75.0% for phylum.The application of these thresholds to the clustering of the SILVA database confirms that the current number of formally described taxa at any rank (for example, ∼30 phyla) is negligible compared with the total number of detected taxa (for example, ∼1,300 phyla).In addition, the study of the annual rate of taxa discovery enables a new extrapolation of the total number of species (4 × 105) and high taxa on Earth (for example, 1 × 105 genera), which indicates that most common terrestrial and aquatic habitats will be exhaustively described within the next 5 years.Taxon recovery tests that were carried out using partial 16S rRNA gene sequences show that short reads are not suitable for accurate richness estimations and accurate classifications of high taxa.On the basis of the general taxonomic thresholds and phylogenetic considerations, we suggest a new biodiversity unit known as the candidate taxonomic unit (CTU), which is compatible with the hierarchy that was established in the Bacteriological Code. The ability to specify a taxonomic rank for particular clades is a major advance in understanding tree topologies and goes beyond the classic phylogenetic delineation.The usefulness of CTUs has been intensively tested in the reclassification of the phylum Spirochaetes and the classification of 15 candidate divisions and environmental clades that are presented in this Analysis article, which also provide new insights into the coherence of classes, phyla and superphyla.By providing explicit and well-documented guidelines, it is hoped that this work will facilitate the implementation of the many changes in the current taxonomy that are necessary to develop a common taxonomic classification of high taxa of bacteria and archaea on the basis of SSU rRNA gene sequences.
    27 schema:genre article
    28 schema:inLanguage en
    29 schema:isAccessibleForFree false
    30 schema:isPartOf N4c2e0a4656644f1c808bb67b1f3333ad
    31 N6fa49afd05384447829d59c8ec8122bc
    32 sg:journal.1032854
    33 schema:keywords Bacteriological Code
    34 Earth
    35 Key PointsAs
    36 PointsAs
    37 RNA gene sequences
    38 Rational taxonomic boundaries
    39 SILVA database
    40 SSU rRNA gene sequences
    41 Taxon recovery tests
    42 ability
    43 accurate classification
    44 accurate richness estimations
    45 addition
    46 advances
    47 analysis article
    48 annual rate
    49 applications
    50 aquatic habitats
    51 archaea
    52 article
    53 bacteria
    54 basis
    55 biodiversity units
    56 boundaries
    57 candidate divisions
    58 candidate taxonomic unit
    59 changes
    60 clade
    61 class
    62 classic phylogenetic delineation
    63 classification
    64 clustering
    65 code
    66 coherence
    67 coherence of classes
    68 common taxonomic classification
    69 consideration
    70 cultured microorganisms
    71 current number
    72 current taxonomy
    73 database
    74 delineation
    75 discovery
    76 division
    77 environmental clade
    78 environmental small subunit (SSU) ribosomal RNA gene sequences
    79 estimation
    80 extrapolation
    81 family
    82 gene sequence identity
    83 gene sequences
    84 general taxonomic thresholds
    85 genus
    86 guidelines
    87 habitats
    88 hierarchy
    89 higher taxa
    90 identity
    91 implementation
    92 insights
    93 major advances
    94 microorganisms
    95 new biodiversity unit
    96 new extrapolation
    97 new insights
    98 number
    99 order
    100 particular clades
    101 phyla
    102 phylogenetic considerations
    103 phylogenetic delineation
    104 phylum Spirochaetes
    105 rRNA gene sequence identity
    106 rRNA gene sequences
    107 rank
    108 rate
    109 reads
    110 reclassification
    111 reconciliation
    112 recovery tests
    113 ribosomal RNA gene sequences
    114 richness estimation
    115 sequence
    116 sequence identity
    117 short reads
    118 small subunit ribosomal RNA gene sequences
    119 species
    120 spirochaetes
    121 study
    122 subunit (SSU) ribosomal RNA gene sequences
    123 superphyla
    124 taxa
    125 taxa discovery
    126 taxonomic boundaries
    127 taxonomic classification
    128 taxonomic ranks
    129 taxonomic thresholds
    130 taxonomic units
    131 taxonomy
    132 test
    133 threshold
    134 topology
    135 total number
    136 tree topology
    137 uncultured bacteria
    138 uncultured microorganisms
    139 units
    140 usefulness
    141 usefulness of CTUs
    142 work
    143 years
    144 schema:name Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
    145 schema:pagination 635-645
    146 schema:productId N5271811c1cee4f84952e9aca3840db5d
    147 N822792c243494c30bf0d20af3bd58cef
    148 Nc602072f50484b86ae162f00e01523cd
    149 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018109693
    150 https://doi.org/10.1038/nrmicro3330
    151 schema:sdDatePublished 2022-01-01T18:33
    152 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    153 schema:sdPublisher Ne607fb2ec9d2454082b9852707fbb2d6
    154 schema:url https://doi.org/10.1038/nrmicro3330
    155 sgo:license sg:explorer/license/
    156 sgo:sdDataset articles
    157 rdf:type schema:ScholarlyArticle
    158 N062a828eb8784a3d8f7d80c885725ff6 rdf:first sg:person.01100647363.23
    159 rdf:rest Nab32069cb6ed4d89ab6a0f4b92d79d3d
    160 N12877c368183402d97fd18c019603ad1 rdf:first sg:person.01130261667.49
    161 rdf:rest N4f38f325911a4c599bfb2c2d9ff17abd
    162 N291234e812c4472cb349f992ef1fae34 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    163 schema:name Archaea
    164 rdf:type schema:DefinedTerm
    165 N4240fc33cb854196a78d9040e9b9d377 rdf:first sg:person.01142757113.45
    166 rdf:rest N596f2b21c1c64834909d2ec655ceb469
    167 N466e769814014411a84b063be2b382b1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    168 schema:name Sequence Analysis, DNA
    169 rdf:type schema:DefinedTerm
    170 N4c2e0a4656644f1c808bb67b1f3333ad schema:issueNumber 9
    171 rdf:type schema:PublicationIssue
    172 N4f38f325911a4c599bfb2c2d9ff17abd rdf:first sg:person.01301526365.45
    173 rdf:rest Nf0eb6b47aee74d8b85a46287dce57adf
    174 N5271811c1cee4f84952e9aca3840db5d schema:name doi
    175 schema:value 10.1038/nrmicro3330
    176 rdf:type schema:PropertyValue
    177 N596f2b21c1c64834909d2ec655ceb469 rdf:first sg:person.01274774737.70
    178 rdf:rest N062a828eb8784a3d8f7d80c885725ff6
    179 N5e0ec513c5734442b2b4d47a4eaec0f5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    180 schema:name RNA, Ribosomal, 16S
    181 rdf:type schema:DefinedTerm
    182 N6f10081c37744b3090fbefcaad93e6a5 rdf:first sg:person.0664234342.14
    183 rdf:rest rdf:nil
    184 N6fa49afd05384447829d59c8ec8122bc schema:volumeNumber 12
    185 rdf:type schema:PublicationVolume
    186 N75e918d0abfe4fcdbe1ae643570e7814 rdf:first sg:person.01167734006.82
    187 rdf:rest N6f10081c37744b3090fbefcaad93e6a5
    188 N822792c243494c30bf0d20af3bd58cef schema:name pubmed_id
    189 schema:value 25118885
    190 rdf:type schema:PropertyValue
    191 N86aed387884b4852a443d82a9013a2d3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    192 schema:name DNA, Ribosomal
    193 rdf:type schema:DefinedTerm
    194 N88176636015d4b3790bb191e9df2dbaa schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Bacteria
    196 rdf:type schema:DefinedTerm
    197 N93d7f3d7e5b14a48947035a5c297e505 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    198 schema:name DNA, Bacterial
    199 rdf:type schema:DefinedTerm
    200 N95481242bf4c47588ff5d48109e75744 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    201 schema:name Phylogeny
    202 rdf:type schema:DefinedTerm
    203 Nab32069cb6ed4d89ab6a0f4b92d79d3d rdf:first sg:person.0764345020.82
    204 rdf:rest N12877c368183402d97fd18c019603ad1
    205 Nb87e4c0e38f14e14925ed30dd5d1a562 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    206 schema:name Databases, Nucleic Acid
    207 rdf:type schema:DefinedTerm
    208 Nc59998ee282c4d5db7dec0971a8ae16b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    209 schema:name Ribotyping
    210 rdf:type schema:DefinedTerm
    211 Nc602072f50484b86ae162f00e01523cd schema:name dimensions_id
    212 schema:value pub.1018109693
    213 rdf:type schema:PropertyValue
    214 Ncca0010416b041fe96bed3aa089f6f44 rdf:first sg:person.0601714613.51
    215 rdf:rest N75e918d0abfe4fcdbe1ae643570e7814
    216 Ne607fb2ec9d2454082b9852707fbb2d6 schema:name Springer Nature - SN SciGraph project
    217 rdf:type schema:Organization
    218 Nf01e408e366e4d3ca7fbe12898665cf0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    219 schema:name DNA, Archaeal
    220 rdf:type schema:DefinedTerm
    221 Nf0eb6b47aee74d8b85a46287dce57adf rdf:first sg:person.01351157720.95
    222 rdf:rest Ncca0010416b041fe96bed3aa089f6f44
    223 Nf2a59843d7e4461ea8b4da691127a430 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    224 schema:name Computational Biology
    225 rdf:type schema:DefinedTerm
    226 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    227 schema:name Biological Sciences
    228 rdf:type schema:DefinedTerm
    229 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
    230 schema:name Microbiology
    231 rdf:type schema:DefinedTerm
    232 sg:grant.3781187 http://pending.schema.org/fundedItem sg:pub.10.1038/nrmicro3330
    233 rdf:type schema:MonetaryGrant
    234 sg:grant.3782531 http://pending.schema.org/fundedItem sg:pub.10.1038/nrmicro3330
    235 rdf:type schema:MonetaryGrant
    236 sg:grant.3796246 http://pending.schema.org/fundedItem sg:pub.10.1038/nrmicro3330
    237 rdf:type schema:MonetaryGrant
    238 sg:journal.1032854 schema:issn 1740-1526
    239 1740-1534
    240 schema:name Nature Reviews Microbiology
    241 schema:publisher Springer Nature
    242 rdf:type schema:Periodical
    243 sg:person.01100647363.23 schema:affiliation grid-institutes:grid.419529.2
    244 schema:familyName Pruesse
    245 schema:givenName Elmar
    246 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01100647363.23
    247 rdf:type schema:Person
    248 sg:person.01130261667.49 schema:affiliation grid-institutes:grid.6936.a
    249 schema:familyName Ludwig
    250 schema:givenName Wolfgang
    251 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01130261667.49
    252 rdf:type schema:Person
    253 sg:person.01142757113.45 schema:affiliation grid-institutes:grid.437298.3
    254 schema:familyName Yarza
    255 schema:givenName Pablo
    256 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01142757113.45
    257 rdf:type schema:Person
    258 sg:person.01167734006.82 schema:affiliation grid-institutes:grid.419529.2
    259 schema:familyName Amann
    260 schema:givenName Rudolf
    261 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167734006.82
    262 rdf:type schema:Person
    263 sg:person.01274774737.70 schema:affiliation grid-institutes:grid.419529.2
    264 schema:familyName Yilmaz
    265 schema:givenName Pelin
    266 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01274774737.70
    267 rdf:type schema:Person
    268 sg:person.01301526365.45 schema:affiliation grid-institutes:grid.6936.a
    269 schema:familyName Schleifer
    270 schema:givenName Karl-Heinz
    271 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01301526365.45
    272 rdf:type schema:Person
    273 sg:person.01351157720.95 schema:affiliation grid-institutes:grid.213876.9
    274 schema:familyName Whitman
    275 schema:givenName William B.
    276 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351157720.95
    277 rdf:type schema:Person
    278 sg:person.0601714613.51 schema:affiliation grid-institutes:grid.418686.5
    279 schema:familyName Euzéby
    280 schema:givenName Jean
    281 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601714613.51
    282 rdf:type schema:Person
    283 sg:person.0664234342.14 schema:affiliation grid-institutes:grid.466857.e
    284 schema:familyName Rosselló-Móra
    285 schema:givenName Ramon
    286 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0664234342.14
    287 rdf:type schema:Person
    288 sg:person.0764345020.82 schema:affiliation grid-institutes:grid.15078.3b
    289 schema:familyName Glöckner
    290 schema:givenName Frank Oliver
    291 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764345020.82
    292 rdf:type schema:Person
    293 sg:pub.10.1007/978-0-387-21609-6_8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015420409
    294 https://doi.org/10.1007/978-0-387-21609-6_8
    295 rdf:type schema:CreativeWork
    296 sg:pub.10.1007/s00203-013-0888-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043406325
    297 https://doi.org/10.1007/s00203-013-0888-4
    298 rdf:type schema:CreativeWork
    299 sg:pub.10.1023/a:1000665216662 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043457281
    300 https://doi.org/10.1023/a:1000665216662
    301 rdf:type schema:CreativeWork
    302 sg:pub.10.1038/417017a schema:sameAs https://app.dimensions.ai/details/publication/pub.1028561703
    303 https://doi.org/10.1038/417017a
    304 rdf:type schema:CreativeWork
    305 sg:pub.10.1038/500016a schema:sameAs https://app.dimensions.ai/details/publication/pub.1017195767
    306 https://doi.org/10.1038/500016a
    307 rdf:type schema:CreativeWork
    308 sg:pub.10.1038/ismej.2010.87 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035301217
    309 https://doi.org/10.1038/ismej.2010.87
    310 rdf:type schema:CreativeWork
    311 sg:pub.10.1038/ismej.2011.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010316628
    312 https://doi.org/10.1038/ismej.2011.109
    313 rdf:type schema:CreativeWork
    314 sg:pub.10.1038/ismej.2012.82 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015690230
    315 https://doi.org/10.1038/ismej.2012.82
    316 rdf:type schema:CreativeWork
    317 sg:pub.10.1038/nrmicro2367 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052470816
    318 https://doi.org/10.1038/nrmicro2367
    319 rdf:type schema:CreativeWork
    320 grid-institutes:grid.15078.3b schema:alternateName Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
    321 schema:name Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
    322 Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
    323 rdf:type schema:Organization
    324 grid-institutes:grid.213876.9 schema:alternateName Department of Microbiology, University of Georgia, 527 Biological Sciences Building, 30605–2605, Athens, Georgia, USA
    325 schema:name Department of Microbiology, University of Georgia, 527 Biological Sciences Building, 30605–2605, Athens, Georgia, USA
    326 rdf:type schema:Organization
    327 grid-institutes:grid.418686.5 schema:alternateName Société de Bactériologie Systématique et Vétérinaire (SBSV) and École Nationale Vétérinaire de Toulouse (ENVT), F-31076, Toulouse cedex 03, France
    328 schema:name Société de Bactériologie Systématique et Vétérinaire (SBSV) and École Nationale Vétérinaire de Toulouse (ENVT), F-31076, Toulouse cedex 03, France
    329 rdf:type schema:Organization
    330 grid-institutes:grid.419529.2 schema:alternateName Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
    331 schema:name Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
    332 rdf:type schema:Organization
    333 grid-institutes:grid.437298.3 schema:alternateName Ribocon GmbH, Fahrenheitstrasse 1, D-28359, Bremen, Germany
    334 schema:name Department of Ecology and Marine Resources, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190, Esporles, Balearic Islands, Spain
    335 Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
    336 Ribocon GmbH, Fahrenheitstrasse 1, D-28359, Bremen, Germany
    337 rdf:type schema:Organization
    338 grid-institutes:grid.466857.e schema:alternateName Department of Ecology and Marine Resources, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190, Esporles, Balearic Islands, Spain
    339 schema:name Department of Ecology and Marine Resources, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190, Esporles, Balearic Islands, Spain
    340 rdf:type schema:Organization
    341 grid-institutes:grid.6936.a schema:alternateName Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350, Freising, Germany
    342 schema:name Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350, Freising, Germany
    343 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...