Careful use of 16S rRNA gene sequence similarity values for the identification of Mycobacterium species

M Beye; N Fahsi; D Raoult; P-E Fournier

doi:10.1016/j.nmni.2017.12.009

Careful use of 16S rRNA gene sequence similarity values for the identification of Mycobacterium species

New Microbes New Infect. 2017 Dec 29:22:24-29. doi: 10.1016/j.nmni.2017.12.009. eCollection 2018 Mar.

Authors

M Beye¹, N Fahsi¹, D Raoult^{1

2}, P-E Fournier¹

Affiliations

¹ URMITE, UM63, CNRS7278, IRD198, Inserm1095, Institut Hospitalo-Universitaire Méditerranée-infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France.
² Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia.

Abstract

In order to evaluate the suitability of 16S rRNA nucleotide sequence similarity for the classification of new Mycobacterium isolates at the species level, we systematically studied the pairwise identity values of this gene for 131 Mycobacterium species with standing in nomenclature. Only one of the studied species, M. poriferae (0.76%), strictly respected the 95% and 98.65% threshold values currently recommended to determine the affiliation of bacterial isolates to an existing or new genus or species, respectively. All other species exhibited at least an identity value >98.65% and/or <95% with another Mycobacterium species. Therefore, we suggest that interpretation of interspecies 16S rRNA identity values should be made cautiously when classifying a new mycobacterial isolate at the species level.

Keywords: 16S rRNA; Mycobacterium; sequence similarity; taxonomy; threshold value.