- Volume 51, Issue 6, 2001
Volume 51, Issue 6, 2001
- Articles
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Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 . as mMrinibacillus marinus gen nov., comb. nov.
More LessA moderately halophilic, round-endospore-forming bacterium (strain YKJ-13T) was isolated from jeotgal, a traditional Korean fermented seafood, and studied by a polyphasic taxonomic approach. This organism was related to the phylogenetic clade comprising members of Bacillus rRNA group 2 and formed a cluster with Bacillus marinus with a bootstrap fidelity value of 93.6%. The peptidoglycan type was A1alpha linked directly through L-Lys. Based on cell morphology, peptidoglycan type and phylogeny, strain YKJ-13T, together with B. marinus, is considered to be a member of Bacillus rRNA group 2. Strain YKJ-13T was also characterized by having MK-7 and MK-8 as the predominant menaquinones and iso-C15:0 as the major fatty acid. The DNA G+C content was 44 mol%. Strain YKJ-13T exhibited a 16S rDNA similarity value of 95.7% with B. marinus DSM 1297T, its closest phylogenetic relative. Levels of 16S rDNA similarity between strain YKJ-13T and other Bacillus spp. were less than 94.2%. Therefore, on the basis of the data presented, the name Jeotgalibacillus alimentarius gen. nov., sp. nov. is proposed for strain YKJ-13T (= KCCM 80002T = JCM 10872T). It is also proposed that B. marinus be reclassified in Marinibacillus gen. nov. as Marinibacillus marinus comb. nov.
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Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov.
More LessOn the basis of 16S rRNA gene sequencing and DNA-DNA reassociation, industrial solvent-producing clostridia have been assigned to four species. In this study, the phenotypic characteristics of Clostridium acetobutylicum, Clostridium beijerinckii, 'Clostridium saccharoperbutylacetonicum', and an unnamed Clostridium sp. represented by the strains NCP 262T and NRRL B643 are compared. In addition, a further 40 strains of solvent-producing clostridia have been classified by biotyping, DNA fingerprinting and 16S rRNA gene sequencing. These included 14 C. beijerinckii strains, two strains currently designated as 'Clostridium kaneboi' and 'Clostridium butanologenum', and 24 production strains used in the commercial acetone-butanol fermentation. All of the C. beijerinckii strains were confirmed to have been classified correctly. The 'C. kaneboi' and 'C. butanologenum' strains require reclassification as C. acetobutylicum and C. beijerinckii, respectively. The commercial production strains were found to belong either to C. beijerinckii or to the unnamed Clostridium sp. For the comparative phenotypic studies of the four species, representative strains were selected from each of the DNA-fingerprint subgroups within each species. These strains were analysed for their ability to utilize different carbohydrates, hydrolyse gelatin or aesculin, and produce indole, and were tested for the presence of catalase and urease. On the basis of these results, several phenotypic traits were found to be useful for differentiating between the four species. The descriptions of C. acetobutylicum and C. beijerinckii have been emended. The names Clostridium saccharoperbutylacetonicum sp. nov. [type strain = N1-4 (HMT) = ATCC 27021T] and Clostridium saccharobutylicum sp. nov. (type strain = DSM 13864T = ATCC BAA-117T) are proposed for the two new species.
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Metabolism of cinnamic acids by some Clostridiales and emendation of the descriptions of Clostridium aerotolerans, Clostridium celerecrescens and Clostridium xylanolyticum.
M Chamkha, J L Garcia and M LabatThe ability of Clostridium aerotolerans DSM 5434T, Clostridium celerecrescens DSM 5628T, Clostridium methoxybenzovorans DSM 12182T, Clostridium stercorarium ATCC 35414T, Clostridium subterminale DSM 2636, Clostridium termitidis DSM 5398T, Clostridium thermolacticum DSM 2910T, Clostridium thermopalmarium DSM 5974T and Clostridium xylanolyticum DSM 6555T to metabolize cinnamic acid and various derivatives, with or without glucose supplementation, was examined. Only C aerotolerans DSM 5434T and C. xylanolyticum DSM 6555T, closely related species, transformed cinnamic acid to 3-phenylpropionic acid. Both species also reduced a wide range of cinnamic acid derivatives, including o-, m- and p-coumaric, o-, m- and p-methoxycinnamic, p-methylcinnamic, caffeic, ferulic, isoferulic and 3,4,5-trimethoxycinnamic acids to their corresponding 3-phenylpropionic acid derivatives. C. aerotolerans DSM 5434T, however, also decarboxylated p-coumaric acid into 4-vinylphenol, which was then reduced to 4-ethylphenol. C. celerecrescens was grouped with C. aerotolerans and C. xylanolyticum in subcluster XIVa of the Clostridiales. C. celerecrescens DSM 5628T only metabolized m- and p-methoxycinnamic and p-methylcinnamic acids to their corresponding 3-phenylpropionic acid derivatives, reducing the double bond in the C3 aliphatic side chain. Addition of glucose markedly increased the yield of the biotransformations by these three species. An emendation of the descriptions of C. aerotolerans, C. celerecrescens and C. xylanolyticum is proposed, based on these observations.
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Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group.
More LessThe taxonomic positions of species of the Lactobacillus casei group have been evaluated by sequencing and phylogenetic analysis of a 277 bp recA gene fragment. High sequence similarity between strain ATCC 393T, currently designated as the type strain of L. casei, and the type strain of Lactobacillus zeae, LMG 17315T, has been established, while L. casei ATCC 334 and Lactobacillus paracasei NCDO 151T form a single phylogenetic group. The taxonomic status of species and strains at issue is discussed.
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Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and 'Actinoplanes aurantiacus' to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.
More LessThe phylogenetic structure of the genus Actinoplanes was determined by comparative 16S rDNA sequence analysis of the type strains of all validly described Actinoplanes species and other strains of Actinoplanes. Actinoplanes minutisporangius IFO 15962T and 'Actinoplanes aurantiacus' IFO 13967 were placed outside the family Micromonosporaceae and appeared to be closely related to the genus Cryptosporangium. On the basis of their morphological and chemotaxonomic characteristics and phylogenetic analysis, these strains were reclassified into the genus Cryptosporangium. DNA-DNA hybridization revealed that these strains differed from the species previously described in this genus. Therefore, the transfer is proposed of Actinoplanes minutisporangius Ruan et al. 1986 and 'Actinoplanes aurantiacus' IFO 13967 to the genus Cryptosporangium as Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.
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Nocardia ignorata sp. nov.
More LessAn isolate that was received during a mycobacterial quality control test and which was thought to be a Mycobacterium species was subjected to a polyphasic taxonomic study after mycolic acid analysis showed that it possessed mycolates characteristic of the nocardiae. Further chemotaxonomic and 16S rRNA gene sequence analyses of this isolate demonstrated that it belongs to the genus Nocardia. 16S rRNA gene sequence data, DNA-DNA hybridization studies and the biochemical characteristics of the isolate indicate that it belongs to a novel species that differs from previously described members of the genus Nocardia. The name Nocardia ignorata sp. nov. is proposed for this isolate with the type strain IMMIB R-1434T (= DSM 44496T = NRRL B-24141T).
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Alcalilimnicola halodurans gen. nov., sp. nov., an alkaliphilic, moderately halophilic and extremely halotolerant bacterium, isolated from sediments of soda-depositing Lake Natron, East Africa Rift Valley.
An alkaliphilic, halotolerant, Gram-negative, heterotrophic, aerobic and rod-shaped organism was isolated from drying soda and at a water-covered site of Lake Natron, Tanzania, by means of the most-probable-number technique developed for anoxygenic, phototrophic sulfur bacteria. It had an absolute requirement for alkalinity, but not for salinity; growth occurred at salt concentrations of 0-28% (w/v), with optimal growth at 3-8% (w/v) NaCl. The bacterium preferentially metabolized volatile fatty acids and required vitamins for growth. The name Alcalilimnicola halodurans gen. nov., sp. nov. is proposed for the novel isolate, placed in the gamma-Proteobacteria within the family Ectothiorhodospiraceae on the basis of analysis of the 16S rDNA sequence, polar lipids, fatty acids and DNA base composition. Although Alcalilimnicola halodurans is closely related to the extreme anoxygenic, phototrophic sulfur bacteria of the genus Halorhodospira, it is not phototrophic.
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Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and 'HGE agent' as subjective synonyms of Ehrlichia phagocytophila.
More LessThe genera Anaplasma, Ehrlichia, Cowdria, Neorickettsia and Wolbachia encompass a group of obligate intracellular bacteria that reside in vacuoles of eukaryotic cells and were previously placed in taxa based upon morphological, ecological, epidemiological and clinical characteristics. Recent genetic analyses of 16S rRNA genes, groESL and surface protein genes have indicated that the existing taxa designations are flawed. All 16S rRNA gene and groESL sequences deposited in GenBank prior to 2000 and selected sequences deposited thereafter were aligned and phylogenetic trees and bootstrap values were calculated using the neighbour-joining method and compared with trees generated with maximum-probability, maximum-likelihood, majority-rule consensus and parsimony methods. Supported by bootstrap probabilities of at least 54%, 16S rRNA gene comparisons consistently clustered to yield four distinct clades characterized roughly as Anaplasma (including the Ehrlichia phagocytophila group, Ehrlichia platys and Ehrlichia bovis) with a minimum of 96.1% similarity, Ehrlichia (including Cowdria ruminantium) with a minimum of 97.7% similarity, Wolbachia with a minimum of 95.6% similarity and Neorickettsia (including Ehrlichia sennetsu and Ehrlichia risticii) with a minimum of 94.9% similarity. Maximum similarity between clades ranged from 87.1 to 94.9%. Insufficient differences existed among E. phagocytophila, Ehrlichia equi and the human granulocytic ehrlichiosis (HGE) agent to support separate species designations, and this group was at least 98.2% similar to any Anaplasma species. These 16S rRNA gene analyses are strongly supported by similar groESL clades, as well as biological and antigenic characteristics. It is proposed that all members of the tribes Ehrlichieae and Wolbachieae be transferred to the family Anaplasmataceae and that the tribe structure of the family Rickettsiaceae be eliminated. The genus Anaplasma should be emended to include Anaplasma (Ehrlichia) phagocytophila comb. nov. (which also encompasses the former E. equi and the HGE agent), Anaplasma (Ehrlichia) bovis comb. nov. and Anaplasma (Ehrlichia) platys comb. nov., the genus Ehrlichia should be emended to include Ehrlichia (Cowdria) ruminantium comb. nov. and the genus Neorickettsia should be emended to include Neorickettsia (Ehrlichia) risticii comb. nov. and Neorickettsia (Ehrlichia) sennetsu comb. nov.
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Candida thermophila sp. nov., a novel thermophilic yeast isolated from soil.
More LessYeast strain Y94T, which is capable of growth at high temperature, was isolated from soil in Korea. Characteristics of the strain include asexual reproduction by multilateral budding, the absence of extracellular starch-like compounds, a negative Diazonium blue B colour reaction, and the absence of arthrospores, ballistoconidia and ascospores; the strain can therefore be placed in the genus Candida. A maximum growth temperature of 50-51 degrees C, along with certain other physiological characteristics, and a unique 26S rDNA partial sequence separate this strain from other ascomycetous yeasts. Taken together, these results suggest that the strain is a novel species and the name Candida thermophila sp. nov. (type strain is Y94T = JCM 10994T = KCCM 50661T) is proposed.
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Candida bituminiphila, a novel anamorphic species of yeast.
More LessA novel anamorphic species of yeast belonging to the genus Candida was isolated from tar in Canada. Morphological and physiological observations, as well as phylogenetic analyses, were performed. Conidiophores were produced, were usually short and had sympodial growth, numerous bud scars and a rachis-like structure. They bore one or more conidia. Pseudomycelium was scarcely produced and true mycelium was sparse. No sexual reproduction was observed on corn meal, malt, Gorodkowa, Dextrose Yeast Peptone or V8 agars. Zygoascus hellenicus was physiologically the most closely related species, but it differed from the novel species by its ability to assimilate D-galacturonate and L-rhamnose, ferment sucrose and grow at 37 degrees C. From sequence analysis of the 26S rDNA D1/D2 region, Z. hellenicus and Candida bertae var. bertae were the closest species with 54 and 56 bp substitutions, respectively. Similar results have been obtained from analysis of the 18S rDNA. All these data support the hypothesis that the yeast, named Candida bituminiphila, is a novel species closely related to Z. hellenicus. The holotype and only isolate of C. bituminiphila is strain CBS 8813T (= MUCL 41424T).
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Phylogenetic analysis of strains originally assigned to Bullera variabilis: descriptions of Bullera pseudohuiaensis sp. nov., Bullera komagatae sp. nov. and Bullera pseudoschimicola sp. nov.
F Y Bai, M Takashima and T NakaseTwenty strains previously assigned to the species Bullera variabilis Nakase & Suzuki were reclassified using a molecular taxonomic approach. The strains were regrouped first by nucleotide sequence comparison of the rDNA internal transcribed spacer (ITS) regions, including the 5.8S gene. Phylogenetic positions of B. variabilis strains with different ITS region sequences were then analysed based on their 18S rDNA sequences. The taxonomic status of the original Bullera variabilis strains was clarified further by DNA-DNA hybridization experiments. Of the 20 strains studied, five remained in the species B. variabilis, six strains were reassigned to the species Bullera mrakii and three novel species were proposed for eight of the nine remaining strains, namely Bullera pseudohuiaensis sp. nov. (one strain; type strain JCM 5984T = AS 2.2203T), Bullera komagatae sp. nov. (one strain; type strain JCM 5983T = AS 2.2202T) and Bullera pseudoschimicola sp. nov. (six strains; type strain JCM 391ST = AS 2.2201T). The remaining strain, JCM 6140, was closely related to B. pseudoschimicola. However, differences in ITS region sequences between strain JCM 6140 and strains of B. pseudoschimicola, and the intermediate DNA-DNA relatedness to representative strains of B. pseudoschimicola did not allow a definite taxonomic decision to be made for strain JCM 6140.
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Three new species of Saccharomyces sensu lato van der Walt from Yaku Island in Japan: Saccharomyces naganishii sp. nov., Saccharomyces humaticus sp. nov. and Saccharomyces yakushimaensis sp. nov.
More LessThree new yeast species were isolated from soil and partially decayed leaves in Yaku Island and Iriomote Island in the Nansei Islands of Japan. Based on DNA hybridization and physiological characters, these represent novel taxa. These are designated Saccharomyces naganishii sp. nov. (type strain IFO 10181T = CBS 8797T), Saccharomyces humaticus sp. nov. (type strain IFO 10673T = CBS 8893T) and Saccharomyces yakushimaensis sp. nov. (type strain IFO 1889T = CBS 8894T). The phylogenetic relationships of the three new species with members of other ascomycetous genera (e.g. Kluyveromyces, Saccharomyces, Torulaspora and Zygosaccharomyces) were estimated by 18S rDNA gene sequence analysis.
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Reclassification of the Cryptococcus humicola complex.
M Takashima, T Sugita, T Shinoda and T NakaseTen strains of the Cryptococcus humicola complex were reclassified on the basis of sequence analyses of 18S rDNA and internal transcribed spacer regions and DNA-DNA reassociation experiments. They were differentiated into seven species including C humicola. Five novel species are proposed: Cryptococcus daszewskae sp. nov. (type strain CBS 5123T = JCM 11166T = MUCL 30649T), Cryptococcus fragicola sp. nov. (type strain JCM 1530TT = CBS 88981), Cryptococcus longus sp. nov. (type strain CBS 5920T = JCM 11167T = MUCL 30690T), Cryptococcus musci sp. nov. (type strain JCM 1531T = CBS 8899T) and Cryptococcus pseudolongus sp. nov. (type strain JCM 9712T = CBS 8297T). A syntype of Sporobolomyces albidus JCM 1460T is also revealed to be a distinct species; the name Cryptococcus ramirezgomezianus nom. nov. is therefore proposed for Sporobolomyces albidus Ramírez Gómez (type strain IJFM 502T = CBS 2839T = JCM 1460T = NRRL Y-2478T), since the name Cryptococcus albidus (Saito) C. E. Skinner has already been recognized for a distinct species within the genus Cryptococcus. Strains possessing either Q-9 or Q-10 have been reported to occur in C. humicola; however, after reclassification, the ubiquinone type of the species in each phylogenetic group was shown to be uniform, indicating that it is a useful criterion for the taxonomy of the Trichosporonales.
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New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence.
More LessThe phylum Euglenozoa consists of three distinct groups: the euglenoids, diplonemids and kinetoplastids. The phylogenetic position of the diplonemids within this phylum remains unsettled, since both morphological and molecular data produce weak and contradictory results. It is shown here that taxonomic sampling, G+C content bias, mutational saturation and differences of evolutionary rate among lineages are major factors affecting the topology of the small-subunit rRNA euglenozoan tree. When these problems are minimized by using a larger diplonemid sampling (including a sequence of environmental origin) and correcting for G+C bias (by using both paralinear distances or an unbiased dataset), a diplonemids+euglenoids sisterhood is retrieved. Bootstrap support for this relationship is still moderate, but it is retrieved by all analysis methods, overcoming previously reported disagreements. In addition, the inclusion of a large number of euglenoid sequences in the analysis improves some phylogenetic relationships within this group. Some problematic taxa, such as the species Khawkinea quartana, are now placed with high bootstrap support and monophyly is found for two interesting groups (the photosynthetic genera Eutreptia+Eutreptiella and the loricate genera Strombomonas+Trachelomonas), although with weak statistical support.
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Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision).
More LessFrom 1990 to 2000, the number of published named taxa based upon new isolates at species and genus levels in International Journal of Systematic and Evolutionary Microbiology, formerly International Journal of Systematic Bacteriology, have increased by approximately four- and sevenfold, respectively. New taxa based upon characterization of only a single isolate remained at around 40% for both categories. The Bacteriological Code (1990 Revision) has no recommendations on the number of strains required for definition of new taxa. For a few groups, a minimum number of 5-10 strains has been suggested in minimal standards. Since an exponential increase in new taxa can be expected in the future, the authors discuss problems related to naming new species and genera based upon descriptions of a single isolate and suggest that this practice is re-evaluated. It is proposed that the following should be added to Recommendation 30b of the Bacteriological Code: 'Descriptions should be based on as many strains as possible (minimum five), representing different sources with respect to geography and ecology in order to be well characterized both phenotypically and genotypically, to establish the centre (from which the type strain could be chosen) and the extent of the cluster to be named. In addition, comparative studies should be performed, including reference strains that represent neighbouring species and/or genera, in order to give descriptions that are sufficiently detailed to allow differentiation from these neighbours.'
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Volumes and issues
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Volume 74 (2024)
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