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Volume 44,
Issue 1,
1994
Volume 44, Issue 1, 1994
- Original Papers Relating To Systematic Bacteriology
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Nucleotide Sequence Comparison of the Mycobacterial dnaJ Gene and PCR-Restriction Fragment Length Polymorphism Analysis for Identification of Mycobacterial Species
AbstractWe recently reported a genus-specific PCR for the mycobacterial dnaJ gene. In the present study, we have determined the nucleotide sequences of the dnaJ gene from 19 mycobacterial species (Mycobacterium tuberculosis, M. bovis, M. bovis BCG, M. africanum, M. microti, M. marinum, M. kansasii, M. gastri, M. simiae, M. scrofulaceum, M. szulgai, M. gordonae, M. avium, M. intracellulare, M. xenopi, M. fortuitum, M. chelonae, M. hemophilum, and M. paratuberculosis). On the basis of the amplified dnaJ gene nucleotide sequences, we constructed a phylogenetic tree of the mycobacterial species by using the neighbor-joining method and unweighted pairwise grouping method of arithmetic average. We found that the phylogenetic relationship inferred within the slowly growing species was in good agreement with the traditional classification, with three major branches corresponding to Runyon’s groups I, II, and III. An exception was M. simiae, which was phylogenetically closer to the cluster including members of Runyon’s group III than to that of Runyon’s group I. On the other hand, the rapid growers, such as M. fortuitum and M. chelonae, did not form a coherent line corresponding to Runyon’s group IV, indicating that our phylogenetic analysis based on the dnaJ gene reflects the phenotypic characteristics such as pigmentation but not the growth rate. Finally, we revealed the species-specific restriction sites within the amplified dnaJ gene to differentiate most of the mycobacterial DNA by a combination of PCR with restriction fragment length polymorphism analysis.
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Assignment of Human-Derived CDC Group 1 Coryneform Bacteria and CDC Group 1-Like Coryneform Bacteria to the Genus Actinomyces as Actinomyces neuii subsp. neuii sp. nov., subsp. nov., and Actinomyces neuii subsp. anitratus subsp. nov.
More LessAlmost the entire 16S rRNA gene sequences of some strains of CDC group 1 and group 1-like coryneform bacteria, isolated from human sources, were determined. Comparative analysis of the rRNA sequence data revealed that both groups of coryneforms belong to the genus Actinomyces. On the basis of the present molecular findings and previous biochemical studies, we propose a new Actinomyces species, Actinomyces neuii sp. nov., containing Actinomyces neuii subsp. neuii subsp. nov. for CDC group 1 coryneform bacteria and Actinomyces neuii subsp. anitratus subsp. nov. for CDC group 1-like coryneform bacteria.
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Bacillus galactophilus Is a Later Subjective Synonym of Bacillus agri
More LessWe confirm that Bacillus galactophilus Takagi, Shida, Kadowaki, Komagata, and Udaka 1993 is a later subjective synonym of Bacillus agri Nakamura 1993 on the basis of chemosystematic data and DNA relatedness data.
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- Matters Relating To The International Committee On Systematic Bacteriology
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Taxonomic Notes: A Proposal for Recording the Properties of Putative Taxa of Procaryotes fn1
More LessThe problem that the proposal for recording the properties of putative taxa of procaryotes attempts to redress arises because the International Code of Nomenclature of Bacteria is not able to provide sensible regulation of nomenclature for new taxa defined by very limited data, such as a nucleotide sequence for a small portion of the genome. The constructors of the original code (1957) and the Judicial Commission considering the 1976 and 1990 revisions did not foresee or act upon the possibilities for molecular description and typification of procaryotes that were not yet cultivable. As a result, formal names are being proposed for uncultivated procaryotes whose uniqueness is defined only by very limited characteristics, such as differences in a molecular sequence. As the editors of two journals concerned with the systematics of procaryotes, we recognize that the problem will increase as the available technology gains wider use and becomes easier to apply. Accordingly, this note is presented in advance of discussions by the International Committee on Systematic Bacteriology at the forthcoming congress (July 1994) so that there may be discussions and reaction by colleagues.
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Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on Requests for Opinions Published Between January 1985 and July 1993
More LessEleven requests were published between January 1985 and July 1993. Four of these requests were granted and have been published as Opinion 64, replacing and recognizing type strains of Methanobacterium formicicum and Methanobacterium bryantii, respectively; Opinion 65, replacing the type strain of Selenomonas sputigena; Opinion 66, replacing the type strain of Streptococcus mitis; and Opinion 67, rejecting Citrobacter diversum. Six requests were denied, including requests for conservation or recognition of “Rhodococcus lentifragmentus,” “Pediococcus acidilactici” and “Salmonella enterica,” rejection of Erwinia camegieana, Pectobacterium camegieana, and Lactobacillus paracasei, and transfer of the type strain of Methanosaeta concilii to Methanothrix soehngenii. A request based on a proposal for reinterpretation of the position of Xanthomonas maltophilia was not considered by the Judicial Commission because it represented a substantive taxonomic issue rather than a nomenclatural question governed by the Bacteriological Code.
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- Minireview
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Taxonomy of the Genus Frankia (Actinomycetales)
More LessMembers of the genus Frankia have been classified in the order Actinomycetales on the basis of morphology, cell chemistry, and 16S rRNA sequences and catalogs. This genus, which is presently defined by morphology, cell chemistry, the ability to fix nitrogen, and infectivity for and ability to enter into symbiotic relationships with certain plant hosts, may be heterogeneous. Frankia species groups have been difficult to delineate by classical phenotypic methods. The recent use of DNA-DNA pairing and low-frequency restriction fragment analysis, as well as probes composed of certain sequences from the nif (nitrogen fixation) genes or the variable regions of 16S rRNA, has contributed to substantial progress in developing species concepts. In this review I trace the taxonomic history of the genus and outline some of the problems to be resolved in the future.
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Volumes and issues
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Volume 75 (2025)
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