A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species
Dhamodharan Ramasamy, Ajay Kumar Mishra, Jean-Christophe Lagier, Roshan Padhmanabhan, Morgane Rossi, Erwin Sentausa, Didier Raoult and Pierre-Edouard Fournier
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France.
Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.