Microbial genomic taxonomy

Cristiane C. Thompson, Luciane Chimetto, Robert A. Edwards, Jean Swings, Erko Stackebrandt, Fabiano L. Thompson

Research output: Contribution to journalComment/debate

227 Citations (Scopus)
3 Downloads (Pure)


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.

Original languageEnglish
Article number913
JournalBMC Genomics
Publication statusPublished - 23 Dec 2013
Externally publishedYes

Bibliographical note

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


  • Evolution
  • Genomics
  • Microbes
  • Taxonomy


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