title: Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.
abstract: Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.
authors.affiliation: 1] Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190 Esporles, Balearic Islands, Spain. [2] Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany. [3] Ribocon GmbH, Fahrenheitstrasse 1, D-28359 Bremen, Germany.
authors.forename: Pablo
authors.initials: P
authors.lastname: Yarza
authors.affiliation: Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
authors.forename: Pelin
authors.initials: P
authors.lastname: Yilmaz
authors.affiliation: Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
authors.forename: Elmar
authors.initials: E
authors.lastname: Pruesse
authors.affiliation: 1] Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany. [2] Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Glöckner
authors.affiliation: Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Ludwig
authors.affiliation: Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany.
authors.forename: Karl-Heinz
authors.initials: KH
authors.lastname: Schleifer
authors.affiliation: Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, Georgia 30605-2605, USA.
authors.forename: William B
authors.initials: WB
authors.lastname: Whitman
authors.affiliation: Société de Bactériologie Systématique et Vétérinaire (SBSV) and École Nationale Vétérinaire de Toulouse (ENVT), F-31076 Toulouse cedex 03, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Euzéby
authors.affiliation: Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Amann
authors.affiliation: Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190 Esporles, Balearic Islands, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Rosselló-Móra
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D019295:Computational Biology; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D030561:Databases, Nucleic Acid; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics*; D021521:Ribotyping; D017422:Sequence Analysis, DNA
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S