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Review
. 2006 Nov 29;361(1475):1911-6.
doi: 10.1098/rstb.2006.1915.

Stepping stones towards a new prokaryotic taxonomy

Dirk Gevers  1 , Peter Dawyndt, Peter Vandamme, Anne Willems, Marc Vancanneyt, Jean Swings, Paul De Vos
Affiliations
Review

Stepping stones towards a new prokaryotic taxonomy

Dirk Gevers et al. Philos Trans R Soc Lond B Biol Sci. .

Abstract

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.

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Figures

Figure 1
Figure 1
The present polyphasic practice consists of screening the isolates using different techniques to cluster-relate isolates. On the basis of the consensus clustering, a set of representative strains is subjected to 16S rRNA gene sequencing to determine the phylogenetic position. The second level thus represents a gain in information for a reduced set of strains. If necessary, DNA–DNA hybridization (DDH) is performed on a selection of strains.
Figure 2
Figure 2
Landscaping of the prokaryotic systems. Going from microbial data towards landscaping prokaryotic systems requires improvements in three directions: (i) microbiologists should accumulate more useful data, (ii) mathematicians should develop objective classification methods and (iii) computer scientists should contribute by constructing information gateways of integrated microbial data.
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