Taxonomy and Phylogeny of Prokaryotes

  • Pierre Caumette
  • Céline Brochier-Armanet
  • Philippe Normand


Classification of prokaryotes is hierarchically organized into seven levels: kingdoms, phyla, classes, orders, families, genera, and species. In prokaryotes, because they reproduce by clonal fission, the species, considered as the basic unit of the biological diversity, faces several problems such as the definition of an individual. A bacterial strain can be recognized as an individual belonging to a species. However, many inconsistencies exist between phenotypic similarity levels and evolutionary relationships deduced from molecular phylogenies. Most taxonomic groups have been reconsidered through phylogenetic analysis in the 1980s, and a consensus has been reached on the need for coherence between taxonomy and phylogeny. Thus, the multiple revisions of species, genera, or higher taxonomic levels pose many complex problems that are solved gradually. Prokaryotic microorganisms correspond to two of the three domains of life: Archaea and Bacteria. Their systematics is described in the “Bergey’s Manual for Systematic Bacteriology, second edition” published in five volumes.

In the text, the Latin terms used are those accepted by the Nomenclature Committee, and the organization of the bacterial and archaeal domains is presented as they appear in the “Bergey’s Manual for Systematic Bacteriology.” They are discussed according to the recent data of the hierarchical classification of Prokaryotes.


16S RNA homology Archaea Bacteria Bacterial taxonomy Dendrogram DNA/DNA hybridization Domains G + C% Genotypic criteria Phenotypic criteria Phylogenetic tree Phyla Systematics of prokaryotes 


Websites This site is managed by Jean Euzéby of the ENV Toulouse; it maintains bacterial taxonomy entries based on the publications validly made in journals of bacterial taxonomy. This site is managed by the American NCBI. It is complementary to the first; however, it incorporates several nonvalid taxa.


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Pierre Caumette
    • 1
  • Céline Brochier-Armanet
    • 2
  • Philippe Normand
    • 3
  1. 1.Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM)UMR CNRS 5254, Université de Pau et des Pays de l’AdourPau CedexFrance
  2. 2.Laboratoire de Biométrie et Biologie ÉvolutiveUMR CNRS 5558, Université Claude Bernard Lyon 1Villeurbanne CedexFrance
  3. 3.Microbial Ecology CenterUMR CNRS 5557 / USC INRA 1364, Université Lyon 1VilleurbanneFrance

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