The advancement of genetic techniques has greatly boosted taxonomic studies in recent years. Within the genus Mycobacterium, 42 new species have been detected since 1990, most of which were grown from clinical samples. Along with species for which relatively large numbers of strains have been reported, some of the new species of mycobacteria have been detected rarely or even only once. From the phenotypic point of view, among the new taxa, chromogens exceed nonchromogens while the numbers of slowly and rapidly growing species are equivalent. Whereas conventional identification tests were usually inconclusive, an important role was played by lipid analyses and in particular by high-performance liquid chromatography. Genotypic investigations based on sequencing of 16S rRNA gene have certainly made the most important contribution. The investigation of genetic relatedness led to the redistribution of the species previously included in the classically known categories of slow and rapid growers into new groupings. Within slow growers, the intermediate branch related to Mycobacterium simiae and the cluster of organisms related to Mycobacterium terrae have been differentiated; among rapid growers, the group of thermotolerant mycobacteria has emerged. The majority of species are resistant to isoniazid and, to a lesser extent, to rifampin. Many of the new species of mycobacteria are potentially pathogenic, and there are numerous reports of their involvement in diseases. Apart from disseminated and localized diseases in immunocompromised patients, the most frequent infections in immunocompetent people involve the lungs, skin, and, in children, cervical lymph nodes. The awareness of such new mycobacteria, far from being a merely speculative exercise, is therefore important for clinicians and microbiologists.

/pdf/impact-of-genotypic-studies-on-mycobacterial-taxonomy-the-4yzf7jd4kb.pdf

Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s

Mycolic acids: structure, biosynthesis and physiological functions.

The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.

/pdf/phylogenomics-and-comparative-genomic-studies-robustly-qvcysqwp4x.pdf

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

Cultures of Mycobacterium sp. strain PYR-1 were dosed with anthracene or phenanthrene and after 14 days of incubation had degraded 92 and 90% of the added anthracene and phenanthrene, respectively. The metabolites were extracted and identified by UV-visible light absorption, high-pressure liquid chromatography retention times, mass spectrometry, 1H and 13C nuclear magnetic resonance spectrometry, and comparison to authentic compounds and literature data. Neutral-pH ethyl acetate extracts from anthracene-incubated cells showed four metabolites, identified ascis-1,2-dihydroxy-1,2-dihydroanthracene, 6,7-benzocoumarin, 1-methoxy-2-hydroxyanthracene, and 9,10-anthraquinone. A novel anthracene ring fission product was isolated from acidified culture media and was identified as 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid. 6,7-Benzocoumarin was also found in that extract. When Mycobacterium sp. strain PYR-1 was grown in the presence of phenanthrene, three neutral metabolites were identified as cis- andtrans-9,10-dihydroxy-9,10-dihydrophenanthrene andcis-3,4-dihydroxy-3,4-dihydrophenanthrene. Phenanthrene ring fission products, isolated from acid extracts, were identified as 2,2′-diphenic acid, 1-hydroxynaphthoic acid, and phthalic acid. The data point to the existence, next to already known routes for both gram-negative and gram-positive bacteria, of alternative pathways that might be due to the presence of different dioxygenases or to a relaxed specificity of the same dioxygenase for initial attack on polycyclic aromatic hydrocarbons.

Degradation of phenanthrene and anthracene by cell suspensions of mycobacterium sp. strain pyr-1

Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.

/pdf/aerobic-bacteria-degrading-both-n-alkanes-and-aromatic-3zwiqq3lmf.pdf

Aerobic bacteria degrading both n -alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

A bacterial strain isolated from a fluoranthene-polluted soil was characterized with respect to its metabolic and chemotaxonomic properties, and its phylogenetic position was determined. This bacterium exhibits all of the genus-specific properties of the genus Mycobacterium and clusters phylogenetically with the group of fast-growing mycobacteria. On the basis of its unique fatty acid pattern, the distinctness of its physiological properties and the uniqueness of the primary structure of its 16S ribosomal DNA, we propose that the new isolate should be assigned to a new species, Mycobacterium hodleri. This novel species is phylogenetically closely related to Mycobacterium diernhoferi and Mycobacterium neoaurum. The type strain of M. hodleri is strain EMI2 (= DSM 44183).

/pdf/mycobacterium-hodleri-sp-nov-a-new-member-of-the-fast-3sukwfmi4b.pdf

Mycobacterium hodleri sp. nov., a new member of the fast-growing mycobacteria capable of degrading polycyclic aromatic hydrocarbons

A bacterial strain isolated from a fluoranthene-polluted soil was characterized with respect to its metabolic and chemotaxonomic properties, and its phylogenetic position was determined. This bacterium exhibits all of the genus-specific properties of the genus Mycobacterium and clusters phylogenetically with the group of fast-growing mycobacteria. On the basis of its unique fatty acid pattern, the distinctness of its physiological properties and the uniqueness of the primary structure of its 16s ribosomal DNA, we propose that the new isolate should be assigned to a new species, Mycobacterium hodleri. This novel species is phylogenetically closely related to Mycobacterium diernhoferi and Mycobacterium neoaurum. The type strain of M. hodleri is strain EM12 (= DSM 44183).

Mycobacterium hodleri sp. nov., a New Member Mycobacteria Capable of Degrading Aromatic Hydrocarbons of the Fast-Growing Polycyclic

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Mycobacterium hodleri sp. nov., a new member of the fast-growing mycobacteria capable of degrading polycyclic aromatic hydrocarbons

Mycobacterium hodleri sp. nov., a New Member Mycobacteria Capable of Degrading Aromatic Hydrocarbons of the Fast-Growing Polycyclic