Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species M ycobacterium smegmatis

Unexpected differences were found between the genome of strain JS623, used in bioremediation studies, and the genome of strain mc(2)155, a model organism for investigating basic biology of mycobacteria. Both strains are currently assigned in the databases to the species M ycobacterium smegmatis and, consequently, the environmental isolate JS623 is increasingly included as a representative of that species in comparative genome‐based approaches aiming at identifying distinctive traits of the different members of the genus M ycobacterium. We applied traditional molecular taxonomic procedures – inference of single and concatenated gene trees – to re‐evaluate the membership of both strains to the same species, adopting the latest accepted cut‐off values for species delimitation. Additionally, modern whole genome‐based in silico methods where performed in a comprehensive molecular phylogenetic analysis of JS623 and other members of the genus M ycobacterium. These analyses showed that all relevant genome parameters of JS623 clearly separate this strain from M . smegmatis. The strain JS623 should be corrected as M ycobacterium sp. not only in the literature but, even more importantly, in the database entries, as inclusion of the genome wrongly attributed to the M . smegmatis species in comparative studies will result in misleading conclusions.