Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm

Aurélia Caputo (1) , Vicky Merhej (1) , Kalliopi Georgiades (2) , Pierre-Edouard Fournier (1) , Olivier Croce (1) , Catherine Robert (1) , Didier Raoult (1)

1 URMITE - Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes
2 Departement of Biological Sciences

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.

Keywords: Pan-genome; Klebsiella pneumoniae; Taxonomy Definitions Background; CONVERGENT EVOLUTION; COXIELLA-BURNETII; SEQUENCE-ANALYSIS; RNA GENES; STRAIN; DATABASE; CLASSIFICATION; PATHOGENS; BACTERIA; REVEALS

Domains: Life Sciences [q-bio]; Cellular Biology

Aurélia Caputo, Vicky Merhej, Kalliopi Georgiades, Pierre-Edouard Fournier, Olivier Croce, et al.. Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm. Biology Direct, 2015, 10 (55), ⟨10.1186/s13062-015-0085-2⟩. ⟨hal-01236715⟩