Project description:Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for theM. phlei CCUG21000(T)type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is ?0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in theM. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport (potAD,potF) that are absent in other mycobacteria, and 3) strain-specific variations in the number of ?-factor genes. Moreover,M. phlei has as many as 82 mce(mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant toM. smegmatis mc2 155.
Project description:Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including <i>Mycolicibacterium aurum</i> L1, <i>Mycolicibacterium chubuense</i> NBB4, <i>Mycolicibacterium rhodesiae</i> JS60, <i>Mycolicibacterium rhodesiae</i> NBB3 and <i>Mycolicibacterium smegmatis</i> JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus <i>Mycobacterium sensu lato</i>. These results also revealed the presence of an additional <i>xcb</i>F1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, <i>M. aurum</i> L1, <i>M. chubuense</i> NBB4<i>, M. rhodesiae</i> JS60, <i>M. rhodesiae</i> NBB3 and <i>M. smegmatis</i> JS623 were misclassified and form a novel species within the genus <i>Mycobacterium sensu lato</i>. <i>Mycolicibacterium aurum</i> L1<sup>T</sup> (CECT 8761<sup>T</sup> = DSM 6695<sup>T</sup>) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, <i>M. sphagni</i> ATCC 33027<sup>T</sup>. Phenotypic, chemotaxonomic and genomic data considering strain L1<sup>T</sup> (CECT 8761<sup>T</sup> = DSM 6695<sup>T</sup>) as a type strain of novel species with the proposed name, <i>Mycolicibacterium vinylchloridicum</i> sp. nov.