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Journal of Bacteriology, January 2009, p. 91-99, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01202-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera {triangledown} ,{dagger}

Marc Deloger,{ddagger} Meriem El Karoui, and Marie-Agnès Petit*

INRA, UR888, F78350, Jouy en Josas, France

Received 27 August 2008/ Accepted 22 October 2008

The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

* Corresponding author. Mailing address: UBLO, INRA, 78352 Jouy en Josas Cedex, France. Phone: 33 1 34 65 20 77. Fax: 33 1 34 65 20 65. E-mail: marie-agnes.petit{at}jouy.inra.fr

{triangledown} Published ahead of print on 31 October 2008.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} Present address: Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, 5 rue Anselme, 69004 Lyon, France.

Journal of Bacteriology, January 2009, p. 91-99, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01202-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

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  • Zhulin, I. B. (2009). It Is Computation Time for Bacteriology!. J. Bacteriol. 191: 20-22 [Full Text]  


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