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

Maria J Garcia,Susanne Gola

doi:10.1111/1751-7915.12336

Abstract

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 Mycobacterium 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 Mycobacterium. 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 Mycobacterium. These analyses showed that all relevant genome parameters of JS623 clearly separate this strain from M. smegmatis. The strain JS623 should be corrected as Mycobacterium 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.

Highlights

Mycobacterium smegmatis (Trevisan) Lehmann and Neumann 1899 is a typical environmental rapid-growingThe type strain, M. smegmatis ATCC 19420, is an offspring of the ancient isolate of Alvarez and Tavel, who recovered the microorganism from smegma
In order to cover a broad range of fast-growing Mycobacterium species, analysing at the same time the longest 16S rRNA coding region possible, the sequences from 22 representative rapid growers with approved names were obtained from the National Center for Biotechnology Information (NCBI) genome database during October 2014
The 16S rRNA gene sequences from M. goodii, M. moriokaense and M. wolinskyi were obtained from GenBank (Supporting Information Table S2)

Summary

Unexpected differences were found between the genome of strain JS623, used in bioremediation studies, and the genome of strain mc2155, a model organism for investigating basic biology of mycobacteria Both strains are currently assigned in the databases to the species Mycobacterium smegmatis and, the environmental isolate JS623 is increasingly included as a representative of that species in comparative genomebased approaches aiming at identifying distinctive traits of the different members of the genus Mycobacterium. Modern whole genome-based in silico methods where performed in a comprehensive molecular phylogenetic analysis of JS623 and other members of the genus Mycobacterium. These analyses showed that all relevant genome parameters of JS623 clearly separate this strain from M. smegmatis. The strain JS623 should be corrected as Mycobacterium sp. 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

Introduction

Results and discussion

Conclusions