- Volume 47, Issue 4, 1997
Volume 47, Issue 4, 1997
- Original Papers Relating To Systematic Bacteriology
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Characterization of Borrelia lusitaniae sp. nov. by 16S Ribosomal DNA Sequence Analysis
More LessWe determined the complete sequence of the rrs gene from five strains of genomic species PotiB2. Both distance and parsimony methods were used to infer the evolutionary relationships of the rrs gene sequence of this genomic species in comparison with the rrs gene sequence of Borrelia valaisiana and the rrs gene sequences of Borrelia burgdorferi sensu lato species obtained from sequence databases. The phylogenetic analysis revealed that the genomic species PotiB2 strains clustered in a separate lineage, which was consistent with data from previous DNA-DNA hybridization experiments (D. Postic, M. V. Assous, P. A. D. Grimont, and G. Baranton, Int. J. Syst. Bacteriol. 44:743–752, 1994). A PCR-restriction fragment length polymorphism analysis was used to identify genomic species PotiB2 and to differentiate it from B. burgdorferi sensu lato species. Moreover, signature nucleotide positions were identified for each B. burgdorferi sensu lato species. In accordance with DNA relatedness values, our findings suggest that genomic species PotiB2 can be more clearly defined and identified, and we propose that it should be referred to as a new species, Borrelia lusitaniae. The type strain is PotiB2.
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Genetic and Phenotypic Analysis of Borrelia valaisiana sp. nov. (Borrelia Genomic Groups VS116 and M19)
To clarify the taxonomic status of two recently described Borrelia genomic groups, groups VS116 and M19, three group VS116 strains and eight group M19 strains isolated from Ixodes ricinus ticks in Switzerland, The Netherlands, and the United Kingdom were characterized. PCR-restriction fragment length polymorphism (RFLP) analysis of the 5S-23S intergenic spacer amplicon, rRNA gene restriction analysis, 16S rRNA gene sequence analysis, randomly amplified polymorphic DNA (RAPD) fingerprinting, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and immunoblotting with monoclonal antibodies were used for genetic and phenotypic analysis. The PCR-RFLP and RAPD patterns of three group VS116 strains and eight group M19 strains were identical but differed from those of Borrelia burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii, and Borrelia japonica. DNAs from all group VS116 and M19 strains yielded three fragments (6.9, 3.2, and 1.4 kb) and four fragments (2.1, 1.2, 0.8, and 0.6 kb) after digestion with EcoRV and Hindlll, respectively, hybridizing with an Escherichia coli 16S+23S cDNA probe. The SDS-PAGE protein profiles of group VS116 and M19 strains were heterogeneous. Phylogenetic analysis of the partial 16S rRNA gene sequences showed that group VS116 and M19 spirochetes were members of a Borrelia species distinct from previously characterized members of the genus Borrelia. Based on our present study and data from previous DNA-DNA hybridizations, a new Borrelia species, Borrelia valaisiana sp. nov., in the B. burgdorferi complex, is proposed. Strain VS116 is the type strain of this new species.
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Nocardioides pyridinolyticus sp. nov., a Pyridine-Degrading Bacterium Isolated from the Oxic Zone of an Oil Shale Column
More LessA bacterial strain which is able to degrade pyridine was previously isolated from the oxic zone of an oil shale column and described as Pimelobacter sp. strain OS4T. However, Pimelobacter species have been transferred to the genera Nocardioides and Terrabacter. Strain OS4T was identified as a member of the genus Nocardioides on the basis of chemotaxonomic analysis and phylogenetic inference based on 16S ribosomal DNA (rDNA) sequence analysis. The G+C content of strain OS4T is 72.5 mol%. The cell wall peptidoglycan contains LL-diaminopimelic acid as the diamino acid. The predominant menaquinone is MK-8(H4). The cellular fatty acid profile of strain OS4T is similar to that of the genus Nocardioides. The 16S rDNA similarity of strain OS4T with previously described Nocardioides species is 94.5% ± 0.7%, and a phylogenetic tree based on 16S rDNA sequences revealed a distinct lineage for strain OS4T within the evolutionary radiation enclosed by the genus Nocardioides. Therefore, on the basis of our data, we propose that strain OS4T should be placed in the genus Nocardioides as a member of a new species, Nocardioides pyridinolyticus. The type strain of the new species is strain OS4 (= KCTC 0074BP).
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Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., Two Extremely Radiation-Resistant and Slightly Thermophilic Species from Hot Springs
AbstractStrains of Deinococcus geothermalis sp. nov. were isolated from the hot spring and runoff at Agnano, Naples, Italy, and from the hot spring at São Pedro do Sul in central Portugal, while strains of Deinococcus murrayi sp. nov. were isolated from the hot springs at São Pedro do Sul, São Gemil, and Alcafache in central Portugal. The strains of D. geothermalis and D. murrayi produce orange-pigmented colonies and have an optimum growth temperature of about 45 to 50°C. The type strains of the two new species are extremely gamma radiation resistant. The fatty acids of these new species are primarily branched-chain fatty acids. The two new species can be distinguished from each other by the lower pH range of D. geothermalis than of D. murrayi, by their fatty acid compositions, and by several biochemical parameters, including the ability of D. geothermalis to grow in minimal medium without yeast extract. 16S rRNA gene sequencing also showed that the isolates constitute two species and that these species are distinct from the other species of the genus Deinococcus. The type strain of D. geothermalis is AG-3a (= DSM 11300), and the type strain of D. murrayi is ALT-1b (= DSM 11303).
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Phylogeny of Photorhabdus and Xenorhabdus Species and Strains as Determined by Comparison of Partial 16S rRNA Gene Sequences †
More LessAbstractPartial 16S rRNA gene sequences of 16 strains of the genera Photorhabdus and Xenorhabdus were determined by direct sequencing of PCR products. Aligned sequences were subjected to phylogenetic analysis by maximum-likelihood and maximum-parsimony methods. Distance matrix and phylogenetic analysis did not separate the genera unambiguously. Taxonomic grouping of the bacteria closely paralleled taxonomic grouping of their nematode associates and their geographic origins. We found at least two well-supported taxonomic groups in Photorhabdus species, which suggests that the genus Photorhabdus is coevolving with the nematodes and may be polyspecific.
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Corynebacterium mucifaciens sp. nov., an Unusual Species from Human Clinical Material
More LessAbstractEight strains of a previously undescribed coryneform bacterium had been isolated from human clinical material over a 5-year period. Colonies of the unknown coryneform bacterium had an unusual appearance as they were slightly yellowish and very mucoid. Biochemical and chemotaxonomic characterization revealed that the unknown coryneform bacterium belonged to the genus Corynebacterium. It could be readily differentiated from all previously described Corynebacterium species. Electron microscopy demonstrated the production of an extracellular substance causing connecting filaments between cells as a morphological correlate to the mucoid colonies. Comparative 16S rRNA gene sequence analysis revealed that the unknown coryneform bacterium represented a new subline within the genus Corynebacterium, for which the name Corynebacterium mucifaciens sp. nov. is proposed. The type strain is CCUG 36878 (= DSM 44265 = CIP 105129).
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Borrelia recurrentis Characterization and Comparison with Relapsing-Fever, Lyme-Associated, and Other Borrelia spp.
More LessBorrelia recurrentis, the cause of louse-borne relapsing fever, has until recently been considered noncultivable, which has prevented characterization of this spirochete. We successfully cultivated 18 strains from patients with louse-borne relapsing fever and present the initial characterization of these isolates. Electron microscopy revealed spirochetal cells with pointed ends, an average wavelength of 1.8 µ.m, an amplitude of 0.8 µm, and 8 to 10 periplasmic flagella. The G+C ratio was 28.4 mol%. Whole DNA-DNA hybridizations showed similarity between the isolates of B. recurrentis but not with Borrelia hermsii, Borrelia parkeri, Borrelia turicatae, or the Lyme-associated borreliae. Sequencing studies of both the flagellin and 16S RNA genes revealed that the greatest similarity was between B. recurrentis and Borrelia duttonii. Analysis of the sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of strains revealed four groups based on the position of a major protein band (one of the groups showed some heterogeneity and was subdivided into four subgroups). Pulsed-field gel electrophoresis revealed five distinct patterns.
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Isolation and Characterization of the Homoacetogenic Thermophilic Bacterium Moorella glycerini sp. nov.
More LessA thermophilic, anaerobic, spore-forming bacterium (strain JW/AS-Y6T) was isolated from a mixed sediment-water sample from a hot spring (Calcite Spring area) at Yellowstone National Park. The vegetative cells of this organism were straight rods, 0.4 to 0.6 by 3.0 to 6.5 µ.m. Cells occurred singly and exhibited a slight tumbling motility. They formed round refractile endospores in terminal swollen sporangia. Cells stained gram positive. The temperature range for growth at pH 6.8 was 43 to 65°C, with optimum growth at 58°C. The range for growth at 60°C (pH60C; with the pH meter calibrated at 60°C) was 5.9 to 7.8, with an optimum pH600 of 6.3 to 6.5. The substrates utilized included glycerol, glucose, fructose, mannose, galactose, xylose, lactate, glycerate, pyruvate, and yeast extract. In the presence of CO2, acetate was the only organic product from glycerol and carbohydrate fermentation. No H2 was produced during growth. The strain was not able to grow chemolitho-trophically at the expense of H2-CO2; however, suspensions of cells in the exponential growth phase consumed H2. The bacterium reduced fumarate to succinate and thiosulfate to elemental sulfur. Growth was inhibited by ampicillin, chloramphenicol, erythromycin, rifampin, and tetracycline, but not by streptomycin. The G+C content of the DNA was 54.5 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolate in the Gram type-positive Bacillus-Clostridium subphylum. On the basis of physiological properties and phylogenetic analysis we propose that the isolated strain constitutes a new species, Moorella glycerini; the type strain is JW/AS-Y6 (= DSM 11254 = ATCC 700316).
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Helicobacter salomonis sp. nov., a Canine Gastric Helicobacter sp. Related to Helicobacter felis and Helicobacter bizzozeronii
More LessDuring a study of the prevalence and distribution of gastric helicobacters in domestic pets, a novel group of Helicobacter-like organisms were identified. These “Helicobacter group 2 strains were initially distinguished from the species Helicobacter felis and Helicobacter bizzozeronii by their cellular morphology and the type of motility exhibited. Bacterial cells were only slightly spiral, 5 to 7 µm long, and 0.8 to 1.2 µm wide and showed an unusual slow wavelike motion. Each cell had tufts of sheathed flagella at one or both ends. Phylogenetic analysis by 16S ribosomal DNA sequence comparison revealed that H. felis, H. bizzozeronii, “Gastrospirillum hominis” 2, and the new group of helicobacters formed a distinct cluster with intraspecies similarity values of more than 98%. These taxa were clearly separated from all other known Helicobacter species. Dot blot DNA-DNA hybridization studies indicated that the Helicobacter group 2 strains are genetically homogeneous and distinct from other canine and feline gastric helicobacters. Quantitative DNA-DNA hybridization experiments showed that Helicobacter group 2 strains exhibit >;90% DNA homology to each other, but <39% homology to the phylogenetically related taxa H. felis and H. bizzozeronii. We propose the name Helicobacter salomonis for the novel Helicobacter group 2 strains. The type strain is H. salomonis Inkinen (= CCUG 37845).
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Description of Nocardiopsis synnemataformans sp. nov., Elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb, nov., and Designation of Nocardiopsis antarctica and Nocardiopsis alborubida as Later Subjective Synonyms of Nocardiopsis dassonvillei
AbstractData from chemotaxonomic and 16S ribosomal DNA sequence analyses of an isolate obtained from the sputum of a kidney transplant patient identified the isolate as a member of the genus Nocardiopsis. DNA-DNA hybridization data, as well as physiological characteristics, indicated that the isolate represents a new species of the genus Nocardiopsis, designated Nocardiopsis synnemataformans; the type strain is strain IMMIB D-1215 (= DSM 44143). In addition, DNA-DNA hybridization data, as well as the results of biochemical tests, indicated that Nocardiopsis alborubida DSM 40465T, Nocardiopsis antarctica DSM 43884T, and Nocardiopsis dassonvillei DSM 43111T represent a single species designated N. dassonvillei. We also found that Nocardiopsis alba subsp. alba DSM 43377T and N. alba subsp. prasina DSM 43845T are genetically different and therefore propose that N. alba subsp. prasina be elevated to species status as Nocardiopsis prasina comb, nov., whose type strain is strain DSM 43845.
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Vibrio diabolicus sp. nov., a New Polysaccharide-Secreting Organism Isolated from a Deep-Sea Hydrothermal Vent Polychaete Annelid, Alvinella pompejana
More LessAbstractA deep-sea, facultatively anaerobic, heterotrophic, mesophilic new organism was isolated from the polychaete annelid Alvinella pompejana collected from a deep-sea hydrothermal field in the East Pacific Rise. On the basis of phenotypic characteristics, phylogenetic analyses, and DNA-DNA relatedness, this organism was identified as a new species of the genus Vibrio, for which the name Vibrio diabolicus is proposed. In batch cultures in the presence of glucose, this organism produced an innovative exopolysaccharide. This polymer had high contents of both uronic acids and hexosamines and was similar to other polysaccharides with interesting biological activities.
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Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris Nodules
More LessAbstractThirty-one strains of two new genomic species (genomic species 1 and 2) of rhizobia isolated from root nodules of Phaseolus vulgaris and originating from various locations in France were compared with reference strains of rhizobia by performing a numerical analysis of 64 phenotypic features. Each genomic species formed a distinct phenon and was separated from the other rhizobial species. A comparison of the complete 16S rRNA gene sequences of a representative of genomic species 1 (strain R602spT) and a representative of genomic species 2 (strain H152T) with the sequences of other rhizobia and related bacteria revealed that each genomic species formed a lineage independent of the lineages formed by the previously recognized species of rhizobia. Genomic species 1 clustered with the species that include the bean-nodulating rhizobia, Rhizobium legumino-sarum, Rhizobium etli, and Rhizobium tropici, and branched with unclassified rhizobial strain OK50, which was isolated from root nodules of Pterocarpus klemmei in Japan. Genomic species 2 was distantly related to all other Rhizobium species and related taxa, and the most closely related organisms were Rhizobium galegae and several Agrobacterium species. On the basis of the results of phenotypic and phylogenetic analyses and genotypic data previously published and reviewed in this paper, two new species of the genus Rhizobium, Rhizobium gallicum and Rhizobium giardinii, are proposed for genomic species 1 and 2, respectively. Each species could be divided in two subgroups on the basis of symbiotic characteristics, as shown by phenotypic (host range and nitrogen fixation effectiveness) and genotypic data. For each species, one subgroup had the same symbiotic characteristics as R. leguminosarum biovar phaseoli and R. etli biovar phaseoli. The other subgroup had a species-specific symbiotic phenotype and genotype. Therefore, we propose that each species should be subdivided into two biovars, as follows: R. gallicum biovar gallicum and R. gallicum biovar phaseoli; and R. giardinii biovar giardinii and R. giardinii biovar phaseoli.
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Recognition of Two New Species of Intestinal Spirochetes: Serpulina intermedia sp. nov. and Serpulina murdochii sp. nov.
On the basis of DNA-DNA hybridization data, nine intestinal spirochete strains were grouped into five genospecies. Three of these genospecies were previously recognized Serpulina species, Serpulina hyodysenteriae (type strain, B78), Serpulina innocens (type strain, B256), and Serpulina pilosicoli (type strain, P43/6/78; previously “Anguillina coli”). The other two genospecies were found to be new Serpulina species, for which we propose the names Serpulina intermedia sp. nov. (with type strain PWS/A) and Serpulina murdochii sp. nov. (with type strain 56–150). S. intermedia and S. murdochii cells had a typical spirochete ultrastructure with 22 to 28 periplasmic flagella per cell. Various soluble sugars were growth substrates for S. intermedia and S. murdochii. During growth in basal heart infusion broth supplemented with fetal calf serum beneath an O2-N2 (1:99) atmosphere, cells of these new species consumed oxygen and glucose and produced H2, CO2, acetate, butyrate, and ethanol. The G+C content of the DNA of S. murdochii 56–150T was 27 mol%, and the G+C content of the DNA of S. intermedia PWS/AT was 25 mol%. In addition, a restriction fragment length polymorphism-PCR assay for the detection of intestinal spirochetes was developed. The assay was based on generation and restriction endonuclease analysis (with Hinfl, TaqI, Sau3A, and MboII) of a 558-bp amplicon of ribosomal DNA (rDNA) encoding 16S rRNA. The PCR amplification was specific for Serpulina species and Brachyspira aalborgi. Four restriction digest patterns were found for the five Serpulina species. Hinfl. restriction differentiated S. murdochii and S. innocens from the other species. Sau3A and TaqI restrictions gave unique fragment patterns for S. murdochii and S. pilosicoli, respectively. S. hyodysenteriae and S. intermedia DNAs gave the same fragment pattern regardless of the enzyme tested. B. aalborgi was differentiated from the Serpulina species by MboII digestion of the 16S rDNA amplicon.
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Thermotoga hypogea sp. nov., a Xylanolytic, Thermophilic Bacterium from an Oil-Producing Well
A new thermophilic, xylanolytic, strictly anaerobic, rod-shaped bacterium, strain SEBR 7054T, was isolated from an African oil-producing well. Based on the presence of an outer sheath (toga) and 16S rRNA sequence analysis data, this organism was identified as a member of the genus Thermotoga. Strain SEBR 7054T possessed lateral flagella, had a G+C content of 50 mol%, produced traces of ethanol from glucose but no lactate, and grew optimally in the presence of 0 to 0.2% NaCl at 70°C. Its phenotypic and phylogenetic characteristics clearly differed from those reported for the five previously validly described Thermotoga species. Therefore, we propose that strain SEBR 7054T is a member of a new species of the genus Thermotoga, Thermotoga hypogea sp. nov. The type strain of T. hypogea is SEBR 7054 (= DSM 11164).
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Taxonomy of Pseudomonas Strains Isolated from Tomato Pith Necrosis: Emended Description of Pseudomonas corrugata and Proposal of Three Unnamed Fluorescent Pseudomonas Genomospecies
More LessThirty-three fluorescent Pseudomonas strains isolated from tomato pith necrosis (FPTPN strains) and 89 Pseudomonas corrugata strains were studied by numerical taxonomy. In the dendrogram of distances, the P. corrugata strains constituted a single phenon (phenon 1), whereas 17 of the 33 FPTPN strains clustered in a separate phenon (phenon 2). The other 16 FPTPN strains were included in phena consisting of well-characterized fluorescent Pseudomonas species or were isolated phenotypes. Phena 1 and 2 were distinguished by fluorescence on King B medium, accumulation of poly-β;-hydroxybutyrate, production of levan, and assimilation of sorbitol. DNA-DNA hybridization showed that P. corrugata is a true genomic species (66 to 100% DNA relatedness) and that the FPTPN strains of phenon 2 were divided into three genomic groups. Genomic groups 1 and 2 were not distinct from each other phenotypcally, and genomic group 3 could be distinguished from genomic groups 1 and 2 only on the basis of assimilation of citraconate and laevulinate. Genomic groups 1 and 2 are related to P. corrugata (40 to 55% DNA relatedness), whereas genomic group 3 is less closely related to P. corrugata (20 to 23% DNA relatedness). The lipopolysaccharide patterns on electrophoresis gels and fatty acid profiles of strains belonging to genomic groups 1 through 3 are different from each other and from the lipopolysaccharide patterns and fatty acid profiles of P. corrugata. However, cross-reactions were observed between P. corrugata and the FPTPN strain genomic groups, indicating that there are common epitopes of the lipopolysaccharides. The three FPTPN strain genomic groups were not named as species but were designated Pseudomonas genomospecies FP1, FP2, and FP3.
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Shewanella woodyi sp. nov., an Exclusively Respiratory Luminous Bacterium Isolated from the Alboran Sea
Thirty-four strains of nonfermentative, respiratory, luminous bacteria were isolated from samples of squid ink and seawater from depths of 200 to 300 m in the Alboran Sea. Although these strains had a few properties similar to properties of Shewanella (Alteromonas) hanedai, they did not cluster phenotypically with any previously described bacterium. The nucleotide sequence of a 740-bp segment of luxA was not homologous with other known luxA sequences but clustered with the luxA sequences of Shewanella hanedai, Vibrio logei, Vibrio fischeri, and Photobacterium species. The 16S RNA gene from two strains was sequenced and was found to be most closely related to the S. hanedai 16S RNA gene. Based on the differences observed, we describe the new isolates as members of a new species, Shewanella woodyi sp. nov. Strain ATCC 51908 (= MS32) is the type strain of this new species.
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Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., Novel Antarctic Species with the Ability To Produce Eicosapentaenoic Acid (20:5ω3) and Grow Anaerobically by Dissimilatory Fe(III) Reduction
A polyphasic taxonomic study was performed to characterize dissimilatory iron-reducing strains mostly isolated from Antarctic sea ice. The strains were isolated from samples of congelated (land-fast) sea ice, grease ice, and ice algal biomass collected from the coastal areas of the Vestfold Hills in eastern Antarctica (68°S 78°E). The strains were facultatively anaerobic, motile, and rod shaped, were capable of anaerobic growth either by fermentation of carbohydrates or by anaerobic respiration, and utilized a variety of electron acceptors, including nitrate, ferric compounds, and trimethylamine N-oxide. A phylogenetic analysis performed with 16S rRNA sequences showed that the isolates formed two groups representing novel lineages in the genus Shewanella. The first novel group included seawater-requiring, psychrophilic, chitinolytic strains which had DNA G+C contents of 48 mol%. The members of the second strain group were psychrotrophic and did not require seawater but could tolerate up to 9% NaCl. The strains of this group were also unable to degrade polysaccharides but could utilize a number of monosaccharides and disaccharides and had G+C contents of 40 to 43 mol%. The whole-cell-derived fatty acid profiles of the sea ice isolates were found to be similar to the profiles obtained for other Shewanella species. The omega-3 polyunsaturated fatty acid eicosapentaenoic acid (EPA) (20:5ω3) was detected in all of the sea ice isolates at levels ranging from 2 to 16% of the total fatty acids. EPA was also found at high levels in Shewanella hanedai (19 to 22%) and Shewanella benthica (16 to 18%) but was absent in Shewanella alga and Shewanella putrefaciens. On the basis of polyphasic taxonomic data, the Antarctic iron-reducing strains are placed in two new species, Shewanella frigidimarina sp. nov. (type strain, ACAM 591) and Shewanella gelidimarina sp. nov. (type strain, ACAM 456).
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A Proposal To Revive the Genus Kitasatospora (Omura, Takahashi, Iwai, and Tanaka 1982)
More LessWe determined almost complete 16S ribosomal DNA sequences for 12 actinomycete strains which were either previously classified as Kitasatospora strains or defined as Streptomyces strains but shown to contain major Amounts of meso-diaminopimelic acid in their whole-cell hydrolysates. These sequences were subjected to phylogenetic analyses together with the sequences of 34 Streptomyces species. Phylogenetic trees were reconstructed by using both neighbor-joining and maximum-parsimony methods. The Kitasatospora species always formed a stable monophyletic clade. However, the genus Kitasatospora appeared to be either a sister taxon of the genus Streptomyces or a lineage that originated from within Streptomyces species, depending on the outgroup used. Phylogenetic trees were also constructed by using the sequences of the 16S-23S rRNA gene spacers. Sereptomyces and Kitasatospora species were consistently recovered as two distinct clades independent of the outgroup used. On the basis of phylogenetic, chemotaxonomic, and phenotypic evidence, we propose that the genus Kitasatospora Omura et al. 1982 should be revived.
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Campylobacter hyoilei Alderton et al. 1995 and Campylobacter coli Véron and Chatelain 1973 Are Subjective Synonyms
The taxonomic affiliation of Campylobacter hyoilei was reevaluated by examining a variety of phenotypic and genotypic criteria. Whole-cell protein electrophoresis and a comparison of 66 phenotypic characters revealed that reference strains of C. hyoilei were indistinguishable from Campylobacter coli strains. These data were confirmed by a DNA-DNA hybridization level of 67% between the type strains of the two species. Several species-specific assays based on PCR amplification or probe hybridization further substantiated that C. coli strains and C. hyoilei strains are indistinguishable. It is therefore concluded that C. hyoilei and C. coli represent the same species and that the former name should be regarded as a junior synonym of the latter name.
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Phylogenetic Analysis of Erwinia Species Based on 16S rRNA Gene Sequences †
More LessThe phylogenetic relationships of the type strains of 16 Erwinia species were investigated by performing a comparative analysis of the sequences of the 16S rRNA genes of these organisms. The sequence data were analyzed by the neighbor-joining method, and each branch was supported by moderate bootstrap values. The phylogenetic tree and sequence analyses confirmed that the genus Erwinia is composed of species that exhibit considerable heterogeneity and form four clades that are intermixed with members of other genera, such as Escherichia coli, Klebsiella pneumoniae, and Serratia marcescens. Cluster I includes the type strains of Erwinia herbicola, Erwinia millltiae, Erwinia ananas, Erwinia uredovora, and Erwinia stewartii and corresponds to Dye’s herbicola group. Cluster II consists of Erwinia persicinus, Erwinia rhapontici, Erwinia amylovora, and Erwinia cypripedii. Cluster III consists of Erwinia carotovora subspecies and Erwinia chrysanthemi and is characterized by the production of pectate lyases and cellulases. Erwinia salicis, Erwinia rubrifaciens, and Erwinia nigrifluens form the cluster that is most distantly related to other Erwinia species. The data from the sequence analyses are discussed in the context of biochemical and DNA-DNA hybridization data.
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Methanogenium frigidum sp. nov., a Psychrophilic, H2-Using Methanogen from Ace Lake, Antarctica
Methanogenium frigidum sp. nov. was isolated from the perennially cold, anoxic hypolimnion of Ace Lake in the Vesfold Hills of Antarctica. The cells were psychrophilic, exhibiting most rapid growth at 15°C and no growth at temperatures above 18 to 20°C. The cells were irregular, nonmotile coccoids (diameter, 1.2 to 2.5 μm) that occurred singly and grew by CO2 reduction by using H2 as a reductant Formate could replace H2, but growth was slower. Acetate, methanol, and trimethylamine were not catabolized. Cells grew with acetate as the only organic compound in the culture medium, but growth was much faster in medium also supplemented with peptones and yeast extract. The cells were slightly halophilic; good growth occurred in medium supplemented with 350 to 600 mM Na+, but no growth occurred with 100 or 850 mM Na+. The pH range for growth was 6.5 to 7.9; no growth occurred at pH 6.0 or 8.5. Growth was slow (maximum specific growth rate, 0.24 day−1; doubling time, 2.9 days). This is the first report of a psychrophilic methanogen growing by CO2 reduction.
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Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov., from the Genital Tract of Sows
Two groups of strains isolated from sows were shown to belong to new sublines in the genus Streptococcus. Based on phenotypic and phylogenetic analyses, we propose that these bacteria should be classified as two new species, Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov. These two species are found in the genital tract, but the capnophilic species S. thoraltensis may also occur in the intestinal tract of pigs. The type strain of S. hyovaginalis is SHV515 (= LMG 14710), and S69 (= LMG 13593) is the type strain of S. thoraltensis.
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Spiroplasma lineolae sp. nov., from the Horsefly Tabanus lineola (Diptera: Tabanidae)
Spiroplasma strain TALS-2T from the viscera of the striped horsefly, Tabanus lineola, collected in Georgia was serologically distinct from other Spiroplasma species, groups, putative groups, and subgroups. Light and electron microscopy of cells of strain TALS-2T revealed helical motile cells surrounded only by a single cytoplasmic membrane. The organism grew in M1D and SP-4 liquid media. Growth also occurred in 1% serum fraction medium and in conventional horse serum medium. Growth in liquid media was serum dependent. The strain passed through 220-nm filter pores, but was retained in filters with 100-nm pores. The optimum temperature for growth was 30°C. Multiplication occurred at temperatures from 20 to 37°C, with a doubling time at the optimum temperature of 5.6 h in M1D broth. Strain TALS-2T catabolized glucose but hydrolyzed neither arginine nor urea. The guanine-plus-cytosine content of the DNA was 25 ± 1 mol%. The genome size was 1,390 kbp. Six isolates serologically similar to strain TALS-2T were obtained from the same host in coastal Georgia. Three strains closely related to strain TALS-2T were isolated from the horsefly Poeciloderas quadripunctatus in Costa Rica. Strain TALS-2T (= ATCC 51749), a representative of group XXVII, is designated the type strain of a new species, Spiroplasma lineolae (Mollicutes: Entomoplasmatales).
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Corynebacterium mastitidis sp. nov., Isolated from Milk of Sheep with Subclinical Mastitis
Fourteen strains of a hitherto unknown catalase-positive, aerobic, gram-positive coryneformlike organism were isolated from the milk of sheep with subclinical mastitis from different regions of Spain. The strains phenotypically closely resembled one another and biochemically were similar to Corynebacterium urealyticum and Corynebacterium afermentans subsp. lipophilum. The results of chemotaxonomic investigations were consistent with membership in the genus Corynebacterium, and comparative 16S rRNA gene sequencing studies showed that the unknown bacterium from sheep was indeed a member of the genus Corynebacterium. Within the genus Corynebacterium the new bacterium formed a distinct subline that exhibited >4% sequence divergence with other species. Based on both phenotypic and phylogenetic findings, a new species, Corynebacterium mastitidis, is proposed for the organisms from mastitic sheep. The type strain of C. mastitidis is CECT 4843 (= S-8).
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Biodiversity of Bradyrhizobia Nodulating Lupinus spp.
The genetic structure of Bradyrhizobium isolates recovered from three Lupinus species (Lupinus campestris, Lupinus montanus, and Lupinus exaltatus) grown in Mexico was examined. Among 41 Bradyrhizobium isolates, 18 electrophoretic types (ETs) were distinguished by multilocus enzyme electrophoresis of five metabolic enzymes. The mean genetic diversity, 0.64, indicated that there was great genetic diversity in the population sampled. Most isolates (63%) fell into two closely related clusters (clusters I and II) and were the types most frequently isolated from the root nodules of L. montanus and L. campestris. ET cluster III isolates were frequent nodule occupants of L. exaltatus. The isolates also were assigned to three main groups by using Curie point pyrolysis mass spectrometry. In general, the multilocus enzyme electrophoretic data and pyrolysis mass spectrometric data agreed. We determined the 16S rRNA sequences of representative Lupinus isolates and of Bradyrhizobium japonicum USDA 6T and found that the lupine isolates were highly related to the B. japonicum type strain, although not all B. japonicum type strains (subcultures maintained in different bacterial collections) had identical small-subunit rRNA.
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Corynebacterium singulare sp. nov., a New Species for Urease-Positive Strains Related to Corynebacterium minutissimum
We studied two coryneform strains from clinical specimens. These strains had type IV and corynemycolic acids in their cell walls and also had phenotypic characteristics, such as urease activity and fermentation of glucose and sucrose but not trehalose, which did not permit assignment to any previously recognized taxon. According to DNA-DNA hybridization data, these two strains are members of the same species (level of DNA similarity, 86%). Phylogenetic analysis based on comparisons of almost complete small-subunit ribosomal DNA sequences revealed that these strains are closely related to Corynebacterium minutissimum, but DNA relatedness experiments clearly showed that they constitute a distinct new species with a level of DNA relatedness to the C. minutissimum type strain of less than 40%. This new species can be differentiated from C. minutissimum strains by its enzymatic activities and carbon source utilization, and the name Corynebacterium singulare is proposed for it. The type strain is strain IBS B52218 (= CCUG 37330), which was isolated from a semen specimen.
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Classification of Austrian Rhizobia and the Mexican Isolate FL27 Obtained from Phaseolus vulgaris L. as Rhizobium gallicum
More LessThe phylogenetic positions of four rhizobial strains obtained from nodules of common bean plants (Phaseolus vulgaris L.) grown in an Austrian soil and of the Mexican bean isolate FL27 are described. Analysis of the 16S rRNA genes revealed sequences almost identical to that of the Rhizobium gallicum type strain, R602sp, with a maximum of two nucleotide substitutions. Comparison of the 16S rRNA gene sequences with those from other bacteria indicated highest similarity to Rhizobium sp. strain OK-50, Rhizobium leguminosarum IAM 12609, and Rhizobium etli. DNA homology determined by DNA-DNA hybridization was high among the Austrian isolates and R602spT (45 to 90%) and ranged from 21 to 65% with FL27, but hybridization analysis revealed very low homology to the recognized common bean-nodulating species, R. leguminosarum bv. phaseoli, R. etli, and Rhizobium tropici. Ribosomal gene organization was studied by Southern hybridization with the 16S rRNA gene and temperature gradient gel electrophoresis, indicating identical organizations and the presence of three identical 16S rRNA copies in the genome of this species. The six strains investigated showed different plasmid profiles based on their geographical origins. We propose that the Austrian isolates and the Mexican strain FL27 are members of the species R. gallicum.
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Corynebacterium durum sp. nov., from Human Clinical Specimens
More LessA new Corynebacterium species, Corynebacterium durum, was isolated from respiratory tract specimens of five human patients. The strains of this species exhibited similar morphologic and biochemical features that differentiated them from all recognized species. Notably, all of these strains developed irregular and strongly adherent colonies under aerobic conditions and produced acid from mannitol and galactose. The cells are long pleomorphic rods with some filaments. This species has characteristics of the genus Corynebacterium, such as 55 mol% guanine plus cytosine in the DNA and the presence of corynomycolic acids, meso-diaminopimelic acid, arabinose, and galactose in the cell wall. These isolates formed a homogeneous group in which the DNA-DNA similarity values (as determined by an SI nuclease procedure) compared with reference strain IBS G15036T (T = type strain) ranged from 71 to 100%. The analysis of the nearly complete 16S rRNA gene sequence of IBS G15036T indicated that this new species represents a distinct taxon within the genus Corynebacterium. This new species can be identified on the basis of its colony morphology, fermentation of sugars, and enzymatic activities. Strain IBS G15036 (= CCUG 37331) is the type strain of C. durum.
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Borrelia burgdorferi Sensu Stricto, a Bacterial Species “Made in the U.S.A.”?
More LessAmong the three main species of Borrelia burgdorferi sensu lato associated with Lyme borreliosis, B. burgdorferi sensu stricto (B. burgdorferi) is the sole species present both in North America and in Europe, where Borrelia garinii and Borrelia afzelii also occur. The greater genetic diversity together with the greater clinical polymorphism observed in the Old World suggests that this is the birthplace of the complex B. burgdorferi sensu lato. However, the genetic proximity of some North American and European B. burgdorferi strains is quite mystifying. A previous study of the whole genome (M. Foretz, D. Postic, and G. Baranton, Int. J. Syst. Bacteriol. 47:11-18, 1997) compared the diversity of North American and European B. burgdorferi strains. To further investigate the geographical origin and the migration of B. burgdorferi, we have focused on the study of the single variable and highly adaptive gene ospC. Both approaches demonstrated the greater diversity of North American strains and the close relatedness between European strains and between some isolates from the two areas. We discuss the significance of these features and suggest that they might be evidence of the anteriority of North American B. burgdorferi strains.
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Thermosipho melanesiensis sp. nov., a New Thermophilic Anaerobic Bacterium Belonging to the Order Thermotogales, Isolated from Deep-Sea Hydrothermal Vents in the Southwestern Pacific Ocean
More LessA new thermophilic, anaerobic rod-shaped bacterium, strain BI429T was isolated from the gills of a deep-sea vent hydrothermal mussel, Bathymodiolus brevior, from the Lau Basin (Southwestern Pacific Ocean). Pheno-typically, this isolate exhibited characteristics similar to those described for members of the order Thermotogales. This organism was identified as a member of the genus Thermosipho on the basis of the presence of the typical outer sheath-like structure (toga), its 16S rRNA sequence, and its ability to grow on carbohydrates (sucrose, starch, glucose, maltose, lactose, cellobiose, and galactose). The cells of this organism were gram negative and rod shaped and generally occurred singly or in pairs, rarely occurring as chains with a maximum of five rods. At the optimum temperature for growth (70°C), optimum pH (6.5), and optimum salinity (30 g of NaCl per liter), the doubling time was 100 min. In spite of the high percentage of similarity of its 16S rRNA sequence with that of Thermosipho africanus (98.6%), the weak level of DNA-DNA reassociation with this strain (2%) and particular physiological characteristics allowed us to differentiate this new organism from the sole species of the genus Thermosipho previously described (T. africanus). On the basis of these observations, we propose that the new organism should be described as a new species, Thermosipho melanesiensis. The type strain of T. melanesiensis is BI429.
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Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System
More LessA mesophilic, gram-negative, vibrio-shaped, marine, acetate-oxidizing sulfate reducer (strain B54) was isolated from a water-oil separation system on a North Sea oil platform. The optimum conditions for growth were 33°C, pH 6.8 to 7.0, and concentrations of NaCI and MgCl2 6H2O of at least 1 and 0.3%, respectively. Of various organic acids tested, only acetate was used as an electron and carbon source. The presence of 2-oxoglutarate:dye oxidoreductase suggests acetate oxidation via an operative citric acid cycle. Even though growth of most Desulfobacter strains (including strain B54) did not occur on hydrogen, hydrogenase was detected at low activity. The growth yields were 4.6, 13.1, and 9.6 g of (dry weight) cells per mol of acetate oxidized with sulfate, sulfite, and thiosulfate, respectively, as electron acceptors. Strain B54 was able to fix dinitrogen. Desulforubidin and cytochromes of the c and b types were present. The G+C content of the DNA was 47 mol%. Strain B54 is most closely related to Desulfobacter latus, with a 16S rDNA sequence similarity of 98.1%. The DNA-DNA relatedness between them was 40.5%. On the basis of differences in genotypic, pheno-typic, and immunological characteristics, we propose that strain B54 is a member of a new species, D. vibrioformis. It can be easily identified and distinguished from other Desulfobacter species by its large, vibrio-shaped cells.
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Demetria terragena gen. nov., sp. nov., a New Genus of Actinomycetes Isolated from Compost Soil
More LessA novel actinomycete was isolated from compost soil and was studied taxonomically and phylogenetically. Cells of this organism were gram positive, not acid fast, nonmotile, nonsporulating, irregular coccoid to short rod shaped, and microaerophilic. The cell wall peptidoglycan contained lysine and was cross-linked via an l-Lys←.-Ser←D-Asp interpeptide bridge. The major menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and two unknown phospholipids. Mycolic acids were absent The cellular fatty acid profile was complex, with large amounts of saturated and monounsaturated straight-chain acids and smaller amounts of iso and anteiso branched-chain acids. The G+C content of the DNA was 66 mol%. Comparative 16S ribosomal DNA studies revealed that strain HKI0089T represents a novel lineage within Actinobacteria (32) distinct from all previously described genera and most closely related to members of the genera Kytococcus, Dermacoccus, and Dermatophilus of the family Dermatophilaceae. On the basis of our results, we suggest that strain HKI 0089 should be classified in a new genus and species, for which we propose the name Demetria terragena. The type strain and the only strain of the genus and species is HKI 0089 (DSM 11295).
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Phylogenetic Analysis of the Genus Desulfotomaculum: Evidence for the Misclassification of Desulfotomaculum guttoideum and Description of Desulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov.
Almost complete 16S ribosomal DNA (rDNA) sequences were determined for the type strains of nine species belonging to the genus Desulfotomaculum and for seven strains described as strains of this genus. The sequences were compared with previously published 16S rDNA and rRNA sequences of the type strains of the other species of the genus. The majority of the species form a phylogenetically coherent cluster within the Clostridium-Bacillus subphylum of gram-positive bacteria. The cluster consists of phylogenetically well-separated lineages containing (i) Desulfotomaculum nigrificans, Desulfotomaculum aeronauticum, and Desulfotomaculum ruminis, (ii) Desulfotomaculum geothermicum, Desulfotomaculum thermosapovorans, and Desulfotomaculum sapomandens, (iii) Desulfotomaculum kuznetsovii, Desulfotomaculum australicum, and Desulfotomaculum thermocisternum, (iv) Desulfotomaculum thermobenzoicum and Desulfotomaculum thermoacetoxidans, and (v) Desulfotomaculum acetoxidans. Some as-yet-undescribed Desulfotomaculum strains are phylogenetically well-separated from strains of the described species. Desulfotomaculum guttoideum shares extremely high 16S rDNA similarity with certain Clostridium species (e.g., Clostridium sphenoides and Clostridium celerecrescens) and is most likely a misidentified species. Desulfotomaculum orientis represents a new genus which branches most closely to the genus Desulfitobacterium. The name Desulfosporosinus orientis gen. nov., comb. nov., is proposed for this taxon.
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In Vitro Culture and Phylogenetic Analysis of “Candidatus Arsenophonus triatominarum,” an Intracellular Bacterium from the Triatomine Bug, Triatoma infestans
More LessAn intracellular symbiotic bacterium was isolated from the hemolymph of Triatoma infestans and cultured in an Aedes albopictus cell line. 16S ribosomal DNA sequence analysis revealed that the bacterium was a member of the γ-3 subgroup of the class Proteobacteria, having 96.2% sequence identity with the most closely related bacterium, Arsenophonus nasoniae, the causative agent of the son-killer trait in the parasitoid wasp Nasonia vitripennis. These bacteria share morphological features and a common tissue distribution and transmission mode. The A. nasoniae-T, infestans symbiont branch represents a lineage of insect symbionts which may be capable of horizontal transmission between phylogenetically distant host insects. We propose that the intracellular symbiont from T. infestans be classified as “Candidatus Arsenophonus triatominarum.” The bacterium found in the hemocytes of T. infestans is designated the type strain of this species.
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Discovery and Classification of Ecological Diversity in the Bacterial World: The Role of DNA Sequence Data
More LessAll living organisms fall into discrete clusters of closely related individuals on the basis of gene sequence similarity. Evolutionary genetic theory predicts that in the bacterial world, each sequence similarity cluster should correspond to an ecologically distinct population. Indeed, surveys of sequence diversity in protein-coding genes show that sequence clusters correspond to ecological populations. Future population surveys of protein-coding gene sequences can be expected to disclose many previously unknown ecological populations of bacteria. Sequence similarity clustering in protein-coding genes is recommended as a primary criterion for demarcating taxa.
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Inclusion of Aeromonas DNA Hybridization Group 11 in Aeromonas encheleia and Extended Descriptions of the Species Aeromonas eucrenophila and A. encheleia
The recently reported chemotaxonomic and genotypic description of two well-separated subgroups (I and II) in Aeromonas eucrenophila and their affiliation to Aeromonas encheleia and the unnamed Aeromonas DNA hybridization group (HG) 11 (G. Huys, M. Altwegg, M.-L. HÄnninen, M. Vancanneyt, L. Vauterin, R. Coopman, U. U. Torck, J. Lüthy-Hottenstein, P. Janssen, and K. Kersters, Syst. Appl. Microbiol. 19:616-623, 1996) has questioned the original species descriptions of A. eucrenophila and A. encheleia. In order to elucidate the uncleartaxonomic status of these taxa in the genus Aeromonas, we have further investigated a collection of 14 reference strains and 14 related isolates encompassing the taxa A. eucrenophila subgroups I and II, A. encheleia, and HG11 by DNA-DNA hybridization (on 17 of the 28 strains) and phenotypic characterization (on all 28 strains). Genotypically, the investigated strains could be grouped into two DNA hybridization groups that exhibited between-group homologies ranging from 42 to 52%. The members of DNA homology group I (DNA binding, 76 to 100%) were strains of A. eucrenophila subgroup I, including the type strain LMG 3774, and two A. eucrenophila-like isolates, leading to the conclusion that these strains should be considered true representatives of the species A eucrenophila. The strains of A eucrenophila subgroup II, HG11, and A. encheleia, on the other hand, were closely joined in DNA homology group II (DNA binding, 74 to 105%) together with two presumptive A. encheleia isolates. The fact that strain LMG 16330T A. encheleia was the only type strain residing in DNA homology group I1 implies that HG11 and A. eucrenophila subgroup II should be classified in the species A. encheleia. Except for the somewhat aberrant phenotypic positions of HG11 strains LMG 13075 and LMG 13076, the establishment of DNA homology groups I and II was supported by the delineation of phena 1 and 2 (level of correlation, 90%), respectively, as revealed by numerical analysis of 136 phenotypic test results. These data indicate A. eucrenophila and A encheleia are phenotypically highly related but can be easily separated by testing the production of acid from d-cellobiose. and lactose and the assimilation of d-cellobiose. Extended descriptions of both species are given.
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Aeromonas popoffii sp. nov., a Mesophilic Bacterium Isolated from Drinking Water Production Plants and Reservoirs
We examined the taxonomic position of seven Aeromonas isolates, recovered from Flemish and Scottish drinking water production plants and reservoirs, which were previously recognized by numerical analysis of genomic AFLP fingerprints as members of an unknown Aeromonas taxon that most closely resembled the species Aeromonas bestiarum (DNA hybridization group [HG] 2). The new phenotypic and DNA-DNA hybridization data obtained in this study show that the A. bestiarum-like strains constitute a separate Aeromonas species, for which the name Aeromonas popoffii sp. nov. is being proposed. The new species exhibited an internal DNA relatedness ranging from 79 to 100% and was 22 to 63% related to the type or reference strains of other Aeromonas spp. The highest DNA binding values were determined with A. bestiarum (51 to 63%), followed by Aeromonas hydrophila sensu stricto (HG1; 50 to 60%) and Aeromonas salmonicida (HG3; 39 to 55%). Although fingerprints generated by ribotyping and cellular fatty acid analysis often were highly similar, minor differences between the respective fingerprints were of significance for the differentiation of A. popoffii from its closest taxonomic neighbors, HG1, HG2, and HG3. Phenotypically, all seven strains of A. popoffii were positive for acid and gas production from d-glucose and glycerol, growth in KCN broth, arginine dihydrolase, DNase, Voges-Proskauer reaction, and resistance to vibriostatic agent O/129 and ampicillin but displayed negative reactions for production of urease, tryptophan deaminase, ornithine decarboxylase, and lysine decarboxylase (LDC). None of the strains displayed strong hemolytic activity. The lack of d-sucrose fermentation and LDC production and the ability to utilize dl-lactate as the sole energy and carbon source were useful characteristics for the biochemical separation of A. popoffii from A. bestiarum. Other Aeromonas spp. could be differentiated phenotypically from the new species by at least two features. The chromosomal G+C content of A. popoffii ranges from 57.7 to 59.6 mol%. Strain LMG 17541 is proposed as the type strain.
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Reorganization of the Genus Erythromicrobium: Description of “Erythromicrobium sibiricum” as Sandaracinobacter sibiricus gen. nov., sp. nov., and of “Erythromicrobium ursincola” as Erythromonas ursincola gen. nov., sp. nov.
More LessThe results of investigations on the morphology, physiology, pigment composition, light-harvesting antenna and reaction center organization, and electron carriers of five Erythromicrobium representatives, and on phylogenetic relations among them, are summarized. On the basis of clear phenotypic differences and distinct phylogenetic positions shown by 16S ribosomal DNA analysis, the tentative species “Erythromicrobium sibiricum” and “Erythromicrobium ursincola” are formally described as the type species of two new genera: Sandaracinobacter sibiricus gen. nov., sp. nov., and Erythromonas ursincola gen. nov., sp. nov., respectively. The genus Erythromicrobium is at present composed of the type species, E. ramosum, and two species, “E. hydrolyticum” and “E. ezovicum,” whose nomenclature is yet to be validated. All species studied group within the α-4 subclass of Proteobacteria.
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Discrimination of Acinetobacter Genomic Species by AFLP Fingerprinting
AFLP is a novel genomic fingerprinting method based on the selective PCR amplification of restriction fragments. The usability of this method for the differentiation of genomic species in the genus Acinetobacter was investigated. A total of 151 classified strains (representing 18 genomic species, including type, reference, and field strains) and 8 unclassified strains were analyzed. By using a single set of restriction enzymes (HindIII and TaqI) and one particular set of selective PCR primers, all strains could be allocated to the correct genomic species and all groups were properly separated, with minimal intraspecific similarity levels ranging from 29 to 74%. Strains belonging to genomic species 8 (Acinetobacter lwoffii sensu stricto) and 9 grouped together in one cluster. The closely related DNA groups 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3, and 13TU (sensu Tjernberg & Ursing 1989) were clearly distinguishable, with intraspecific linkage levels above 50%. Strains of the independently described genomic species 13BJ (sensu Bouvet & Jeanjean 1989) and 14TU linked together at a relatively low level (33%). Although a previous DNA-DNA hybridization study seemed to justify the unification of these genomic species, AFLP analysis actually divides the 13BJ-14TU group into three well-separated subgroups. Finally, four unclassified strains obtained from diverse sources and origins grouped convincingly together, with a similarity linkage level of approximately 50%. These strains showed no similarities in their AFLP patterns with any of the other 155 strains studied and may represent a thus-far-undescribed Acinetobacter species. Based on these results, AFLP should be regarded as an important auxiliary method for the delineation of genomic species. Furthermore, because AFLP provides a detailed insight into the infraspecific structure of Acinetobacter taxa, the method also represents a highly effective means for the confirmation of strain identity in the epidemiology of acinetobacters.
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Occurrence of Multiple Genomovars of Burkholderia cepacia in Cystic Fibrosis Patients and Proposal of Burkholderia multivorans sp. nov.
We performed an integrated genotypic and phenotypic analysis of 128 strains of the genera Burkholderia, Ralstonia, and Pseudomonas in order to study the taxonomic structure of Burkholderia cepacia and its relationships with other Burkholderia species. Our data show that presumed B. cepacia strains isolated from cystic fibrosis patients belong to at least five distinct genomic species, one of which was identified as Burkholderia vietnamiensis. This group of five phenotypically similar species is referred to as the B. cepacia complex. The name Burkholderia multivorans is proposed for one of these genomic species, which was formerly referred to as B. cepacia genomovar II; the remaining B. cepacia groups are referred to as genomovars I, III, and IV, pending additional differential phenotypic tests. The role and pathogenic potential of each of these taxa, particularly in view of the potentially fatal infections in cystic fibrosis patients, need further evaluation. The data presented also demonstrate that Pseudomonas glathei and Pseudomonas pyrrocinia should be reclassified as Burkholderia species.
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Phenotypic and Phylogenetic Characterization of Some Eubacterium-Like Isolates Containing a Novel Type B Wall Murein from Human Feces: Description of Holdemania filiformis gen. nov., sp. nov.
More LessA group of Eubacterium-like strains (designated group S14), isolated from the feces of healthy people, was characterized by biochemical tests, fatty acid analysis, cell wall murein analysis, and 16S rDNA analysis. Our results indicate that group S14 is phylogenetically a member of the Clostridium subphylum of the gram-positive bacteria. Despite a phenotypic resemblance to the genus Eubacterium, group S14 was shown to be phylogenetically distantly related to the type species of the genus, Eubacterium limosum. Group S14 showed a specific phylogenetic association with Erysipelothrix rhusiopathiae. Group S14 resembled Erysipelothrix in possessing the uncommon type B cell wall murein. Structural analyses, however, revealed the presence of a previously unknown B1δ (l-Ala)-d-Glu-Gly-l-Lys murein type. Based on a 16S rRNA sequence divergence of greater than 10% with E. rhusiopathiae and the presence of a unique murein type, a new genus, Holdemania, is proposed for group S14, with one species, Holdemania filiformis. Type strain of H. filiformis is ATCC 51649.
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Mycobacterium novocastrense sp. nov., a Rapidly Growing Photochromogenic Mycobacterium
More LessA strain isolated from a biopsy sample taken from a slowly spreading skin granulation on a child’s hand was found to have properties consistent with its classification in the genus Mycobacterium. An almost complete gene sequence of the 16S rRNA of the strain was determined following the cloning and sequencing of the amplified gene. The sequence was aligned with those available for mycobacteria, and phylogenetic trees were inferred with four tree-making algorithms. The organism, which formed a distinct phyletic line within the evolutionary radiation occupied by rapidly growing mycobacteria, was readily distinguished from members of validly described species of rapidly growing mycobacteria on the basis of its mycotic acid pattern and a number of other phenotypic features, notably its ability to form yellow pigmented colonies when incubated in the light. The name proposed for this new species is Mycobacterium novocastrense. The type strain is DSM 44203.
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Mycoplasma lagogenitalium sp. nov., from the Preputial Smegma of Afghan Pikas (Ochotona rufescens rufescens)
Organisms with characteristics typical of mycoplasmas were isolated from the preputial smegma of Afghan picas (Ochotona rufescens rufescens). The results of growth inhibition tests, metabolic inhibition tests, and immunobinding assays showed that the isolated strains were identical and that they were distinct from previously described Mycoplasma, Entomoplasma, Mesoplasma, and Acholeplasma species. These organisms represent a new species, for which the name Mycoplasma lagogenitalium is proposed. M. lagogenitalium ferments glucose, does not hydrolyze arginine or urea, reduces tetrazolium chloride, possesses phosphatase activity, does not digest gelatin or casein, and does not produce films or spots. It lyses sheep erythrocytes and does not adsorb sheep, rabbit, or horse erythrocytes. Cholesterol or serum is required for growth. The growth temperature is 37°C. The guanine-plus-cytosine content of the DNA is 23.0 ± 1.0 mol%. The type strain is M. lagogenitalium 12MS (= ATCC 700289T).
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Sulfurospirillum arcachonense sp. nov., a New Microaerophilic Sulfur-Reducing Bacterium
More LessThe isolation of a new motile, gram-negative, heterotrophic, sulfur-reducing, microaerophilic, vibrioid bacterium, strain F1F6, from oxidized marine surface sediment (Arcachon Bay, French Atlantic coast) is described. Hydrogen (with acetate as the carbon source), formate (with acetate as the carbon source), pyruvate, lactate, α-ketoglutarate, glutarate, glutamate, and yeast extract supported growth with elemental sulfur under anaerobic conditions. Apart from H2 and formate, the oxidation of the substrates was incomplete. Microaerophilic growth was supported with hydrogen (acetate as the carbon source), formate (acetate as the carbon source), acetate, propionate, pyruvate, lactate, α-ketoglutarate, glutamate, yeast extract, fumarate, succinate, malate, citrate, and alanine. The isolate grew fermentatively with fumarate, succinate being the only organic product. Elemental sulfur and oxygen were the only electron acceptors used. Vitamins or amino acids were not required. The isolate was oxidase, catalase, and urease positive. Comparative 16S rDNA sequence analysis revealed a tight cluster consisting of the validly described species Sulfurospirillum deleyianum and the strains SES-3 and CCUG 13942 as the closest relatives of strain F1F6 (level of sequence similarity, 91.7 to 92.4%). Together with strain F1F6, these organisms form a novel lineage within the epsilon subclass of proteobacteria clearly separated from the described species of the genera Arcobacter, Campylobacter, Wolinella, and Helicobacter. Due to the phenotypic characteristics shared by strain F1F6 and S. deleyianum and considering their phylogenetic relationship, we propose the inclusion of strain F1F6 in the genus Sulfurospirillum, namely, as S. arcachonense sp. nov. Based on the results of this study, an emended description of the genus Sulfurospirillum is given.
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Terracoccus luteus gen. nov., sp. nov., an LL-Diaminopimelic Acid-Containing Coccoid Actinomycete from Soil
More LessA gram-positive, aerobic actinomycete was isolated from soil. Spherical cells of this organism occur singly or form packets, which may cluster. The diagnostic diamino acid of the cell wall peptidoglycan is LL-diaminopimelic acid. The predominate menaquinone is MK-8 (H4), and the main fatty acids are 13-methyl tetradecanoic acid and 12-methyl tetradecanoic acid. The diagnostic polar lipids are phosphatidylethanolamine and phosphatidylinositol. The DNA base composition is 73 mol% G+C. Comparison of 16S ribosomal DNA sequences showed that this isolate is a phylogenetic neighbor of Terrabacter tumescens and Intrasporangium calvum. Genotypic, chemotaxonomic, morphological, and physiological characteristics are used to describe a new genus and species, Terracoccus luteus gen. nov., sp. nov. The type strain is strain IMET 7848 (= DSM 44267).
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Meiothermus cerbereus sp. nov., a New Slightly Thermophilic Species with High Levels of 3-Hydroxy Fatty Acids
More LessStrains of Meiothermus cerbereus sp. nov. were isolated from the hot springs within the Geysir geothermal area of Iceland. The strains of Meiothermus cerbereus produce red-orange-pigmented colonies, have an optimum growth temperature of about 55°C, and have higher levels of 3-OH fatty acids than the strains of the other species of the genus Meiothermus. These strains, unlike all other strains of the species of the genus Meiothermus examined previously, require cysteine, thiosulfate, or thioglycolate for growth in liquid Thermus medium, but not in the corresponding medium solidified with agar. Several strains belonging to Meiothermus silvanus, isolated from Geysir, also required reduced sulfur compounds for growth in liquid medium, leading to the hypothesis that this requirement is not a taxonomic characteristic of the new species. The new species represented by strains GY-1T and GY-5 can be distinguished from the other species of the genus Meiothermus by biochemical characteristics, fatty acid composition, DNA-DNA reassociation values, and 16S ribosomal DNA sequence. The type strain for Meiothermus cerbereus is GY-1 (= DSM 11376).
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Polyphasic Taxonomy of Nesterenkonia halobia
More LessA phenotypic study has been carried out on six moderately halophilic gram-positive nonmotile cocci isolated from ponds of a saltern located in Huelva, Spain. These strains were examined for 150 morphological, physiological, biochemical, and nutritional traits and showed phenotypic characteristics similar to those of Nesterenkonia halobia (formerly Micrococcus halobius). The guanine-plus-cytosine (G+C) content of their DNA ranged between 70 and 72 mol%, values quite similar to those described for N. halobia (71.5 mol%). The 16S rDNA sequence analysis of one representative isolate showed that it is phylogenetically quite close to N. halobia, within the high-G+C-content gram-positive branch. DNA-DNA hybridization experiments showed a high degree of homology (72 to 100%) among the six isolates and the type strain N. halobia ATCC 21727. All data demonstrate quite clearly that the six isolates are members of the species N. halobia. Since this species was described on the basis of a single strain isolated from unrefined solar salt, and its description is not complete (especially in the utilization of different compounds), our study contributes to a better description of the moderate halophile N. halobia.
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A Novel Pathogenic Taxon of the Mycobacterium tuberculosis Complex, Canetti: Characterization of an Exceptional Isolate from Africa
In an attempt to characterize an unusual mycobacterial strain isolated from a 2-year-old Somali patient with lymphadenitis, we applied various molecular methods not previously used for the taxonomic classification of mycobacteria. This isolate, designated So93, did not differ from Mycobacterium tuberculosis in the biochemical tests and in its 16S rRNA sequence, but produced smooth and glossy colonies, which is highly exceptional for this species. This smooth phenotype was unstable and switched nonreversibly to a rough colony morphology with a low frequency. The two colony types were equally virulent for the guinea pig, exhibiting characteristic tuberculous disease. Both morphotypes had shorter generation times than the M. tuberculosis reference laboratory strain H37Rv and clinical isolates of M. tuberculosis and Mycobacterium bovis. Furthermore, the So93 isolate differed from all M. tuberculosis complex strains described thus far by having only a single copy of insertion sequence IS1081, an unusual composition of the direct repeat cluster, and a characteristic phenolic glycolipid and lipooligosaccharide. This glycolipid had previously been observed only in a smooth isolate of M. tuberculosis obtained in 1969 by Canetti in France. Analysis of the Canetti strain showed that it shared virtually all genetic properties characteristic of So93, distinguishing these two strains from the known M. tuberculosis complex taxa, M. tuberculosis, Mycobacterium africanum, M. bovis, and Mycobacterium microti. The natural reservoir, host range, and mode of transmission of the group of bacteria described in this paper are presently unknown. This study, partly based on not previously used molecular criteria, supports the idea that the established members within the M. tuberculosis complex and the newly described Canetti grouping should be regarded as a single species, which likely will be designated “M. tuberculosis”.
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Notes: Rapid Identification of Heterotrophic, Thermophilic, Spore-Forming Bacteria Isolated from Hot Composts
More LessThe restriction enzyme profiles of 16S ribosomal DNAs (rDNAs) amplified by PCR from thermophilic heterotrophic bacterial strains isolated from composts were compared with those of reference strains. This allowed us to assign all but 1 of 16 strains to four different Bacillus species (namely, Bacillus stearothermophilus, Bacillus pallidus, Bacillus thermoglucosidasius, and “Bacillus thermodenitrificans”). This study showed that PCR restriction analysis of 16S rDNA contributes to rapid and reliable identification of newly isolated strains belonging to recognized species.
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Proposal To Reclassify Zoogloea ramigera IAM 12670 (P. R. Dugan 115) as Duganella zoogloeoides gen. nov., sp. nov.
More LessThe taxonomic position of a misclassified strain, Zoogloea ramigera IAM 12670T (= ATCC 25925T = P. R. Dugan 115T), was reevaluated. A phylogenetic analysis based on 16S ribosomal rDNA sequences revealed that this organism was located in the beta subclass of the class Proteobacteria with members of the genus Telluria as its closest relatives. On the basis of phenotypic and phylogenetic information, we propose that this organism should be reclassified in a new taxon with the name Duganella zoogloeoides gen. nov., sp. nov.
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Phylogenetic Relationships of Salmonella typhi and Salmonella typhimurium Based on 16S rRNA Sequence Analysis
More LessThe 16S rRNA gene sequences of Salmonella typhi and Salmonella typhimurium were amplified by PCR, cloned, and sequenced. These sequences were analyzed by comparison with reference organisms from the family Enterobacteriaceae. Both S. typhi and S. typhimurium belong to the gamma subdivision of the class Proteobacteria.
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Reassessment of the Taxonomic Position of Rickettsiella grylli
V. Roux, M. Bergoin, N. Lamaze and D. RaoultWe determined the 16S rRNA gene sequence of Rickettsiella grylli, an intracellular parasite of Gryllus bimaculatus and related species of crickets. Phylogenetic inferences made from alignment of this sequence with the sequences of other bacteria demonstrated that R. grylli is most closely related to Coxiella burnetii and Legionella species in the γ subclass of the phylum Proteobacteria. R. grylli was previously thought to be related to members of the order Rickettsiales, but the representatives of this order have been shown to be members of the α1 subclass of the Proteobacteria. Our results indicate that R. grylli should be removed from the order Rickettsiales.
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Isolation of an Aceticlastic Strain of Methanosarcina siciliae from Marine Canyon Sediments and Emendation of the Species Description for Methanosarcina siciliae
More LessA newly described strain of the genus Methanosarcina was isolated from submarine canyon sediments and is shown by comparative sequence analyses of 16S ribosomal DNA and the gene encoding methyl coenzyme M reductase, mcrI, to be a strain of Methanosarcina siciliae. Morphological and physiological characteristics are described. In contrast to the two previously described strains that grow exclusively on methanol, methylamines, and dimethylsulfide, M. siciliae C2J is also capable of growth on and methanogenesis from acetate. We propose that the species description for M. siciliae be amended to include aceticlastic strains.
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Desulfuromonas chloroethenica sp. nov. Uses Tetrachloroethylene and Trichloroethylene as Electron Acceptors
More LessStrain TT4B, isolated from freshwater sediments contaminated with chlorinated ethylenes, is described as Desulfuromonas chloroethenica sp. nov. This organism grows with acetate or pyruvate as electron donors and tetrachloroethylene, trichloroethylene, fumarate, polysulfide, and Fe(III) nitriloacetate as electron acceptors. D. chloroethenica is unique among the desulfuromonads in using chloroethylenes as electron acceptors. It is phenotypically and phylogenetically most closely related to Desulfuromonas acetexigens and shares many other features with this species.
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Another View on the Role of Photosynthetic Pigments in Taxonomy of Oxygenic-Phototrophic Bacteria: Proposed Rejection of the Order Prochlorales Florenzano, Balloni, and Materassi 1986 (Emend. Burger-Wiersma, Stal, and Mur 1989), the Family Prochloraceae Florenzano, Balloni, and Materassi 1986, and the Family Prochlorotrichaceae Burger-Wiersma, Stal, and Mur 1989
More LessWe propose that the order Prochlorales Florenzano, Balloni, and Materassi 1986 (emend. Burger-Wiersma, Stal, and Mur 1989), the family Prochloraceae Florenzano, Balloni, and Materassi 1986, and the family Prochlorotrichaceae Burger-Wiersma, Stal, and Mur 1989, validly published in the International Journal of Systematic Bacteriology under the rules of the Bacteriological Code, be rejected because of the imperfection of ordinal diagnosis. The oxygenic-phototrophic prokaryotes involved are proposed to be incorporated under their validly published names into the orders Chroococcales and Oscillatoriales of the “Cyanobacteria” group. Correspondingly, the latter is proposed to be upgraded to equal “Oxygenic photosynthetic bacteria” (Section 19 in Bergey’s Manual).
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PCR-Restriction Fragment Length Polymorphism Analysis of Genes Coding for 16S rRNA in Veillonella spp.
More LessRestriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA (16S rDNA PCR-RFLP) was used to generate restriction profiles of the American Type Culture Collection type strains of the genus Veillonella, i.e., V. atypica, V. caviae, V. criceti, V. dispar, V. parvula, V. ratti, and V. rodentium. Whole-cell protein profiles were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis for comparative purposes. The 16S rRNA genes were amplified by PCR, and RFLP analysis of the 16S rDNA was performed with MnlI and Sau3AI.MnlI produced six RFLP patterns for seven type strains, since the patterns for V. atypica and V. caviae were the same. RFLP patterns with Sau3AI could distinguish between V. atypica and V. caviae. The type strains of Veillonella species were easily distinguished by 16S rDNA PCR-RFLP.
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- Original Papers Relating To The Systematics Of Yeasts
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Reexamination of Yeast Strains Classified as Torulaspora delbrueckii (Lindner)
More LessTwenty-eight yeast strains presumed to represent Torulaspora delbrueckii were analyzed by randomly amplified polymorphic DNA-PCR analysis. Four strains (HUT 7161, IFO 1138, IFO 1145, and IFO 1956) that were considerably different from the type strain were further investigated. Morphological and physiological characteristics revealed that strains HUT 7161 and IFO 1145 belong to the genus Debaryomyces rather than the genus Torulaspora, and the former strain may represent Debaryomyces hansenii. Strains IFO 1138 and IFO 1956 were classified as either Saccharomyces castellii or Saccharomyces dairensis by identification keys involving physiological tests. On the basis of analysis of the sequences of two rRNA internal spacer regions, strains IFO 1138 and IFO 1956 were closely related to S. castellii and strains HUT 7161 and IFO 1145 were outside members of the genera Torulaspora, Zygosaccharomyces, and Saccharomyces.
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- Matters Relating To The International Committee On Systematic Bacteriology
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Corrigenda to the Approved Lists of Bacterial Names and to the Amended Edition of the Approved Lists of Bacterial Names
More LessThis paper contains corrections to the Approved Lists of Bacterial Names and to the amended edition of the Approved Lists of Bacterial Names.
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- Letters To The Editor
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