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. 2015 Jun 26:7:72-85.
doi: 10.1016/j.nmni.2015.06.005. eCollection 2015 Sep.

The bacterial pangenome as a new tool for analysing pathogenic bacteria

L Rouli  1 , V Merhej  1 , P-E Fournier  1 , D Raoult  1
Affiliations

The bacterial pangenome as a new tool for analysing pathogenic bacteria

L Rouli et al. New Microbes New Infect. .

Abstract

The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.

Keywords: Bacteria; bioinformatics tools; comparative genomics; pangenome; pathogenic species.

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Figures

Fig. 1
Fig. 1
Study of the core/pangenome ratio function of the number of genomes added in several bacterial species. A closed pangenome is defined when reaching a plateau.
Fig. 2
Fig. 2
(a) Shigella flexneri. (b) All Shigella. (c) Escherichia coli and E. coli + Shigella. In black, the trend curves, in blue the core/pangenome ratio, in red the pangenome and in green the core. Number at left corresponded to percentage and number at right corresponded to number of genes.
Fig. 3
Fig. 3
Summary of the difference between closed and open pangenome.
Fig. 4
Fig. 4
Strategy of analyses of the pangenome.
See this image and copyright information in PMC

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