title: The bacterial pangenome as a new tool for analysing pathogenic bacteria.
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.
authors.affiliation: Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France.
authors.forename: L
authors.initials: L
authors.lastname: Rouli
authors.affiliation: Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France.
authors.forename: V
authors.initials: V
authors.lastname: Merhej
authors.affiliation: Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France.
authors.forename: P-E
authors.initials: PE
authors.lastname: Fournier
authors.affiliation: Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France.
authors.forename: D
authors.initials: D
authors.lastname: Raoult
keywords: Bacteria; bioinformatics tools; comparative genomics; pangenome; pathogenic species