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Abstract
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.
Keywords
SPECIES DEFINITION, DNA-DNA HYBRIDIZATION, HORIZONTAL GENE-TRANSFER, BACTERIAL-INFECTIONS, POLYPHASIC TAXONOMY, PROKARYOTES, SIGNATURES, Genomics, Evolution, Microbes, Taxonomy, MULTILOCUS SEQUENCE-ANALYSIS, VIBRIO-CHOLERAE, PHYLOGENETIC ANALYSIS

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MLA
Thompson, Cristiane C., et al. “Microbial Genomic Taxonomy.” BMC GENOMICS, vol. 14, 2013, doi:10.1186/1471-2164-14-913.
APA
Thompson, C. C., Chimetto, L., Edwards, R. A., Swings, J., Stackebrandt, E., & Thompson, F. L. (2013). Microbial genomic taxonomy. BMC GENOMICS, 14. https://doi.org/10.1186/1471-2164-14-913
Chicago author-date
Thompson, Cristiane C, Luciane Chimetto, Robert A Edwards, Jean Swings, Erko Stackebrandt, and Fabiano L Thompson. 2013. “Microbial Genomic Taxonomy.” BMC GENOMICS 14. https://doi.org/10.1186/1471-2164-14-913.
Chicago author-date (all authors)
Thompson, Cristiane C, Luciane Chimetto, Robert A Edwards, Jean Swings, Erko Stackebrandt, and Fabiano L Thompson. 2013. “Microbial Genomic Taxonomy.” BMC GENOMICS 14. doi:10.1186/1471-2164-14-913.
Vancouver
1.
Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL. Microbial genomic taxonomy. BMC GENOMICS. 2013;14.
IEEE
[1]
C. C. Thompson, L. Chimetto, R. A. Edwards, J. Swings, E. Stackebrandt, and F. L. Thompson, “Microbial genomic taxonomy,” BMC GENOMICS, vol. 14, 2013.
@article{4378670,
  abstract     = {{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.}},
  articleno    = {{913}},
  author       = {{Thompson, Cristiane C and Chimetto, Luciane and Edwards, Robert A and Swings, Jean and Stackebrandt, Erko and Thompson, Fabiano L}},
  issn         = {{1471-2164}},
  journal      = {{BMC GENOMICS}},
  keywords     = {{SPECIES DEFINITION,DNA-DNA HYBRIDIZATION,HORIZONTAL GENE-TRANSFER,BACTERIAL-INFECTIONS,POLYPHASIC TAXONOMY,PROKARYOTES,SIGNATURES,Genomics,Evolution,Microbes,Taxonomy,MULTILOCUS SEQUENCE-ANALYSIS,VIBRIO-CHOLERAE,PHYLOGENETIC ANALYSIS}},
  language     = {{eng}},
  pages        = {{8}},
  title        = {{Microbial genomic taxonomy}},
  url          = {{http://doi.org/10.1186/1471-2164-14-913}},
  volume       = {{14}},
  year         = {{2013}},
}

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