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Re-evaluating prokaryotic species

Nature Reviews Microbiology volume 3, pages 733–739 (2005)Cite this article

Abstract

There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.

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Figure 1: Failure of threshold methods in delineating prokaryotic species.

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Acknowledgements

This paper is the outcome of a workshop entitled ‘The prokaryotic species: genome plasticity, microevolution and taxonomy’, organized by F. Thompson and J. Swings in Ghent, Belgium, 25 October 2004, and has the intention to stir up the interdisciplinary debate on the prokaryotic species. We thank all participants as well as D. Mazel, G. Manfio and T. Iida for their contributions. T.C., P.V. and J.S. are indebted to the Fund for Scientific Research — Flanders (Belgium) for a position as postdoctoral fellow and research funding, respectively. F.M.C. acknowledges funding from the National Science Foundation.

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Authors and Affiliations

  1. Laboratory of Microbiology and the Bioinformatics and Evolutionary Genomics Research Group, Ghent University/VIB, Ghent, Belgium

    Dirk Gevers

  2. Department of Biology, Wesleyan University, Middletown, Connecticut, USA

    Frederick M. Cohan

  3. Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

    Jeffrey G. Lawrence

  4. Department of Infectious Disease Epidemiology, Imperial College London, London, UK

    Brian G. Spratt

  5. Laboratory of Microbiology, Ghent University, Ghent, Belgium

    Tom Coenye & Peter Vandamme

  6. Department of Biology and Biochemistry, University of Bath, Bath, UK

    Edward J. Feil

  7. Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany

    Erko Stackebrandt

  8. Bioinformatics and Evolutionary Genomics Research Group, Ghent University/VIB, Ghent, Belgium

    Yves Van de Peer

  9. Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Campinas, Brazil

    Fabiano L. Thompson

  10. Laboratory of Microbiology and the BCCM™/LMG Bacteria Collection, Ghent University, Ghent, Belgium

    Jean Swings

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Correspondence to Dirk Gevers.

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FURTHER INFORMATION

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Glossary

MLST

Multilocus sequence typing, a method for the genotypic characterization of prokaryotes at the infraspecific level, using the allelic mismatches of a small number (usually 7) of housekeeping genes. Designed as a tool in molecular epidemiology and used for recognizing distinct strains within named species.

MLSA

Multilocus sequence analysis, a method for the genotypic characterization of a more diverse group of prokaryotes (including entire genera) using the sequences of multiple protein-coding genes.

SPECIES CONCEPT

A framework to understand how and why an observer can sort organisms into species; that is, what kind of unit do we think the term species embraces, and what characteristics are shared between all members of a species.

SPECIES DEFINITION

A more practical outline of how to assign isolates to a named species or identify new species.

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Gevers, D., Cohan, F., Lawrence, J. et al. Re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733–739 (2005). https://doi.org/10.1038/nrmicro1236

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