Open Access Highly Accessed Commentary

Microbial genomic taxonomy

Cristiane C Thompson1*, Luciane Chimetto1, Robert A Edwards2, Jean Swings3, Erko Stackebrandt4 and Fabiano L Thompson1*

Author Affiliations

1 Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil

2 San Diego State University (SDSU), 5500 Campanile Drive, GMCS 411, San Diego, CA 92182, USA

3 Ghent University, K. L. Ledeganckstraat 35, 9000 Gent, Belgium

4 Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany

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BMC Genomics 2013, 14:913  doi:10.1186/1471-2164-14-913

Published: 23 December 2013


A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

Microbes; Taxonomy; Genomics; Evolution