Characterization of ThreeMycobacteriumspp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics

Abstract

We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.

TheMycobacterium phleigenome: expectations and surprises

“…The genomes were annotated and functionally classified into different subsystems (functional roles) using Rapid Annotation using Subsystem Technology ( Aziz et al 2008 , see also Das et al 2015 ). Noncoding RNA genes were predicted using the INFERence RNA ALignment tool (INFERNAL 1.1), and the Rfam database (version 11.0) with a minimum energy cutoff at 34 ( Nawrocki and Eddy 2013 ).…”

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

“…Within the unique region near 3.7 Mb, the σ 2997 gene (MMAR_2997; σ 2997 ) was predicted 235 to be present only in the M and NCTC2275 strains [Figs 1 and S3; σ 2997 is expressed and 236 functional (Pettersson et al, 2015;unpublished)]. Since the σ 2997 gene is missing in the 237 other Mma genomes, it is plausible that it was present in the ancestor but was lost during 238 evolution in the majority of the Mma strains.…”

“…We previously reported the use of core genes to generate robust phylogenetic trees for 337 other mycobacteria (Das et al, 2015;. Hence, we used the 4300 core genes (see (Qi et al 2009;Wang et al 2015;Doig et al 2012).…”

“…Consequently, this 369 has expanded the repertoire of genes that can be used to study the evolutionary 370 relationships among bacteria and that have had an impact on their evolution, diversity and 371 use as biotechnological vehicles and documenting the microbial biosphere. Phylogeny 372 based on multiple genes and genomic information have generated more robust trees and in 373 many cases also provided evidence that known species should be considered as separate 374 species or subspecies of known bacteria (Devulder et al 2005;Das et al 2015;Loman and 375 Pallen 2015). 376…”

“…VIMS9 was isolated from wild striped bass in Virginia, USA 508 and Davis from farmed striped bass in Davis, California, USA. The different strains were 509 cultivated as described elsewhere (Das et al 2015;. 510…”