title: Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm.
abstract: BACKGROUND
  Various methods are currently used to define species and are based on the phylogenetic marker 16S ribosomal RNA gene sequence, DNA-DNA hybridization and DNA GC content. However, these are restricted genetic tools and showed significant limitations.
  
  
  RESULTS
  In this work, we describe an alternative method to build taxonomy by analyzing the pan-genome composition of different species of the Klebsiella genus. Klebsiella species are Gram-negative bacilli belonging to the large Enterobacteriaceae family. Interestingly, when comparing the core/pan-genome ratio; we found a clear discontinuous variation that can define a new species.
  
  
  CONCLUSIONS
  Using this pan-genomic approach, we showed that Klebsiella pneumoniae subsp. ozaenae and Klebsiella pneumoniae subsp. rhinoscleromatis are species of the Klebsiella genus, rather than subspecies of Klebsiella pneumoniae. This pan-genomic analysis, helped to develop a new tool for defining species introducing a quantic perspective for taxonomy.
authors.affiliation: URMITE, UMR CNRS 7278-IRD 198, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, Cedex 5, France. aurelia.caputo@univ-amu.fr.
authors.forename: Aurélia
authors.initials: A
authors.lastname: Caputo
authors.affiliation: URMITE, UMR CNRS 7278-IRD 198, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, Cedex 5, France. vicky.merhej@univ-amu.fr.
authors.forename: Vicky
authors.initials: V
authors.lastname: Merhej
authors.affiliation: Departement of Biological Sciences, University of Cyprus, P.O. Box 20537-1678, Nicosia Cyprus, Greece. popigeorgiades@hotmail.com.
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Georgiades
authors.affiliation: URMITE, UMR CNRS 7278-IRD 198, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, Cedex 5, France. pierre-edouard.fournier@univ-amu.fr.
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
authors.affiliation: URMITE, UMR CNRS 7278-IRD 198, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, Cedex 5, France. olivier.croce@gmail.com.
authors.forename: Olivier
authors.initials: O
authors.lastname: Croce
authors.affiliation: URMITE, UMR CNRS 7278-IRD 198, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, Cedex 5, France. catherine.robert@univ-amu.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Robert
authors.affiliation: URMITE, UMR CNRS 7278-IRD 198, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, Cedex 5, France. didier.raoult@gmail.com.
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D002965:Classification; D016680:Genome, Bacterial; D023281:Genomics; D007709:Klebsiella / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny