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Nat Rev Microbiol. 2014 Sep;12(9):635-45. doi: 10.1038/nrmicro3330.

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.

Author information

1
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.
2
Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
3
1] Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany. [2] Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
4
Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany.
5
Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, Georgia 30605-2605, USA.
6
Société de Bactériologie Systématique et Vétérinaire (SBSV) and École Nationale Vétérinaire de Toulouse (ENVT), F-31076 Toulouse cedex 03, France.
7
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.

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.

PMID:
25118885
DOI:
10.1038/nrmicro3330
[Indexed for MEDLINE]
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