Mycolicibacterium nivoides sp. nov isolated from a peat bog.
ABSTRACT: A fast-growing, non-chromogenic, acid-fast-staining bacterium (DL90T) was isolated from a peat bog in northern Minnesota. On the basis of 16S rRNA gene sequence similarity (99.8 % identity with Mycolicibacterium septicum and 98 % with Mycolicibacterium peregrinum) and chemotaxonomic data (fatty acid content), strain DL90T represents a member of the genus Mycolicibacterium. Physiological tests (growth curves, biofilm formation, antibiotic sensitivity, colony morphologies and heat tolerance) and biochemical analysis (arylsulfatase activity and fatty acid profiles) distinguish DL90T from its closest relative M. septicum. Phylogenomic reconstruction of the 'Fortuitium-Vaccae' clade, digital DNA-DNA hybridization (DDH) values of 61 %, and average nucleotide identity (ANI) values of approximately 95 % indicate that DL90T is likely to be diverged from M. septicum. Thus, we propose that DL90T represents a novel species, given the name Mycolicibacterium nivoides with the type strain being isolate DL90T (=JCM 32796T=NCCB 100660T).
Project description:The understanding of species distribution and inducible macrolide resistance in the Mycobacterium fortuitum complex (MFC) is limited. Of 90 mostly respiratory MFC clinical isolates, half were M. fortuitum, followed by M. peregrinum, M. porcinum, M. septicum, and M. conceptionense Most M. fortuitum, M. por cinum, and M. septicum isolates were inducibly resistant to clarithromycin, whereas two-thirds of the M. peregrinum isolates were clarithromycin susceptible. Clarithromycin-resistant M. fortuitum isolates exhibited common mutations of erm(39), potentially involved in clarithromycin resistance.
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.
Project description:Tap and shower water at two locations in the Netherlands was examined for the presence of rapidly growing nontuberculous mycobacteria. Cultures yielded Mycobacterium peregrinum, M. salmoniphilum, M. llatzerense, M. septicum, and three potentially novel species, a distribution different from that in clinical samples.
Project description:Mycolicibacterium litorale is a rapidly growing mycobacterial organism with unknown pathogenic features. Here, we report the complete genome sequence of Mycolicibacterium sp. strain NIID-NTM18, which was isolated from a cardiac implantable electronic device infection and which is most similar to M. litorale This sequence will provide essential information for future studies of the pathogenicity of these mycobacteria.
Project description:<i>Clostridium septicum</i> is a Gram-positive, toxin-producing, and spore-forming bacterium that is recognized, together with <i>C. perfringens</i>, as the most important etiologic agent of progressive gas gangrene. <i>Clostridium septicum</i> infections are almost always fatal in humans and animals. Despite its clinical and agricultural relevance, there is currently limited knowledge of the diversity and genome structure of <i>C. septicum</i>. This study presents the complete genome sequence of <i>C. septicum</i> DSM 7534<sup>T</sup> type strain as well as the first comparative analysis of five <i>C. septicum</i> genomes. The taxonomy of <i>C. septicum</i>, as revealed by 16S rRNA analysis as well as by genomic wide indices such as protein-based phylogeny, average nucleotide identity, and digital DNA-DNA hybridization indicates a stable clade. The composition and presence of prophages, CRISPR elements and accessory genetic material was variable in the investigated genomes. This is in contrast to the limited genetic variability described for the phylogenetically and phenotypically related species <i>Clostridium chauvoei</i>. The restriction-modification (RM) systems between two <i>C. septicum</i> genomes were heterogeneous for the RM types they encoded. <i>C. septicum</i> has an open pangenome with 2,311 genes representing the core genes and 1,429 accessory genes. The core genome SNP divergence between genome pairs varied up to 4,886 pairwise SNPs. A vast arsenal of potential virulence genes was detected in the genomes studied. Sequence analysis of these genes revealed that sialidase, hemolysin, and collagenase genes are conserved compared to the α-toxin and hyaluronidase genes. In addition, a conserved gene found in all <i>C. septicum</i> genomes was predicted to encode a leucocidin homolog (beta-channel forming cytolysin) similar (71.10% protein identity) to <i>Clostridium chauvoei</i> toxin A (CctA), which is a potent toxin. In conclusion, our results provide first, valuable insights into strain relatedness and genomic plasticity of <i>C. septicum</i> and contribute to our understanding of the virulence mechanisms of this important human and animal pathogen.
Project description:A nonidentifiable mycolicibacterium was isolated from a malignant lymphoma patient treated with intensive chemoimmunotherapy. Multilocus sequence analysis showed that this isolate was close to "Mycolicibacterium (Mycobacterium) ratisbonense," but the details of this species were still unknown. Here, we report the draft genome sequence data of Mycolicibacterium sp. strain NCC-Tsukiji.