- Volume 46, Issue 3, 1996
Volume 46, Issue 3, 1996
- Original Papers Relating To Systematic Bacteriology
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Legionella waltersii sp. nov. and an Unnamed Legionella Genomospecies Isolated from Water in Australia
More LessTwo Legionella-like organisms were isolated from water samples obtained in Adelaide, Australia. One organism was isolated from a drinking water distribution system, and the other was isolated from a cooling tower at a sewage treatment plant. Both strains required l-cysteine for growth and contained cellular branched-chain fatty acids and ubiquinones typical of the genus Legionella. These strains were serologically distinct from each other as determined by a slide agglutination test. Strain 2074-AUS-ET (T = type strain) was serologically distinct from all previously described Legionella species and serotypes. Strain 2055-AUS-E could not be differentiated biochemically or serologically from Legionella quinlivanii. Both strains were shown by DNA hybridization studies (hydroxyapatite method) to be members of new Legionella species. Legionella waltersii sp. nov. is the name proposed for strain 2074-AUS-ET (= ATCC 51914T). L. waltersii was less than 10% related to other Legionella species. Strain 2055-AUS-E (= ATCC 51913) was informally named Legionella genomospecies 1, since it could not be phenotypically distinguished from L. quinlivanii. Legionella genomospecies 1 was closely related to L. quinlivanii strains (53 to 69% related with 4.5 to 6.5% divergence at 60°C and 31 to 52% related at 75°C).
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Streptomyces caviscabies sp. nov., from Deep-Pitted Lesions in Potatoes in Québec, Canada
More LessEight deep-pitted-scab-inducing streptomycetes isolated from potato lesions in Québec (Canada) were phenotypically compared with representative strains of the principal plant-pathogenic Streptomyces species. These eight strains could be distinguished from representatives of Streptomyces scabies, Streptomyces aureofaciens, Streptomyces ipomoeae, and Streptomyces acidiscabies on the basis of their morphological or physiological properties. They were characterized by a gold mycelium on yeast-malt extract medium and a white mass of spores borne in flexuous chains. The spores of these organisms were cylindrical and smooth. Their cell walls contained the LL-diaminopimelic acid isomer, and their DNA guanine-plus-cytosine content was 71 mol%. The strains which we studied did not produce melanin. All of the strains grew on proline or methionine as a sole nitrogen source and utilized raffinose as a sole carbon source. Bacterial growth was inhibited at pH 4.5. The levels of DNA relatedness between the deep-pitted-scab-inducing strains and strains of the other plant-pathogenic Streptomyces species were low. We place these deep-pitted-scab-inducing strains in a new bacterial species, for which we propose the name Streptomyces caviscabies. The type strain of this species is strain ATCC 51928.
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The Differentiation of Bordetella parapertussis and Bordetella bronchiseptica from Humans and Animals as Determined by DNA Polymorphism Mediated by Two Different Insertion Sequence Elements Suggests Their Phylogenetic Relationship
More LessWe describe a novel insertion sequence (IS) element, IS1002, which was found to be closely related to IS481, which is found only in Bordetella pertussis; we found that these two IS eleemnts have a level of sequence identity of 61.5% and also have almost identical terminal inverted repeats. IS1002 was present both B. pertussis and Bordetella parapertussis strains isolated from humans. In contrast, IS1002 was absent from B. parapertussis strains isolated from sheep. A DNA fingerprint analysis performed with anothe IS element, IS1001, which is present in B. parapertussis and Bordetella bronchiseptica, revealed that B. parapertussis isolates obtained from sheep are distinct from human isolates. Thus, human and ovine B. parapertussis strains comprise two distinct populations, indicatng that little or no transmission occurs between sheep and humans. An IS-associated restriction frragment length polymorphism analysis revealed that B. parapertussis strains isolated from sheep are genetically more polymorphic that the human B. parapertussis population, which is genetically very homogeneous. This suggests that human B. parapertussis strains diverged from a single clone only recently. IS1001 is present in a subset of B. bronchiseptica strains that were derived mainly from pigs and rabbits, suggesting that these strains and to have adapted to different hosts (sheep and humans). Once in the human host, B. parapertussis probably acquired IS1002 from B. pertussis. In contrast to human B. parapertussis isolates, B. pertussis strains produced polymorphic IS1002-related DNA fingerprint patterns.
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Actinobacillus delphinicola sp. nov., a New Member of the Family Pasteurellaceae Pohl (1979) 1981 Isolated from Sea Mammals
More LessWe performed phenotypic and phylogenetic studies of a gram-negative, rod-shaped bacterium isolated from cetaceans. The results of a 16S rRNA gene sequence analysis demonstrated that this bacterium represents a previously unknown line of descent in the family Pasteurellaceae. On the basis of the results of our phylogenetic analysis and phenotypic criteria, we propose that this organism should be classified as a new species, Actinobacillus delphinicola sp. nov. The type strain of A. delphinicola sp. nov. is strain NCTC 12870.
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Propionic Acid-Producing Strains Previously Designated as Corynebacterium xerosis, C. minutissimum, C. striatum, and CDC Group I2 and Group F2 Coryneforms Belong to the Species Corynebacterium amycolatum
More LessPropionic acid-producing Corynebacterium strains that lacked mycolic acids and were formerly identified as Corynebacterium minutissimum, Corynebacterium xerosis, Corynebacterium striatum, and CDC group I2 and F2 strains were studied to determine their relatedness to Corynebacterium amycolatum. A total of 60 strains were used for phenotypic characterization studies, and 26 of these strains were used for genetic studies. DNA-DNA hybridization experiments performed at 65°C revealed that the levels of relatedness between the propionic acid-producing strains and the type strain of C. amycolatum were more than 70% and that the ΔT m values ranged from 0 to 5°C (ΔT m is the difference between the denaturation temperature of a homoduplex and the denaturation temperature of a heteroduplex); these values are consistent with inclusion of these strains in the species C. amycolatum. Currently used conventional tests, such as urease, nitrate reduction, and sugar fermentation tests, were not suitable for accurate identification of C. amycolatum. Phenotypic differentiation of this species from related taxa should be based on the following characteristics in addition to propionic acid production: Lipid requirement, Tween esterase activity, tyrosine clearing, alkaline phosphatase activity, α-glucosidase activity, and β-glucuronidase activity.
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Phylogenetic Analysis Reveals New Relationships among Members of the Genera Microtetraspora and Microbispora
More LessThe 16S rRNA gene sequences of 7 Microbispora strains, 14 Microtetraspora species, 9 Streptosporangium species, and 12 Actinomadura species were determined. A phylogenetic analysis showed that Microtetraspora fusca, Microtetraspora glauca, and Microtetraspora niveoalba formed a coherent cluster with the members of the genus Microbispora. This cluster is distantly related to two other clusters, one of which consists of the Microtetraspora species transferred from the former Actinomadura pusilla group and one of which consists of members of the genus Streptosporangium. Our results show that it is necessary to review the taxonomic definitions of the genera Microtetraspora and Microbispora, which have been separated by a single morphological characteristic, the number of spores on spore chains.
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Phenotypic and Genotypic Characterization of Atypical Lactococcus garvieae Strains Isolated from Water Buffalos with Subclinical Mastitis and Confirmation of L. garvieae as a Senior Subjective Synonym of Enterococcus seriolicida
During a survey of bacterial agents that cause subclinical mastitis in water buffalos, we isolated several strains of gram-positive cocci that appeared to be enterococci except that they grew very slowly at 45°C and grew slowly in broth containing 6.5% NaCl. On the basis of the results of conventional physiologic tests, these strains were identified as Enterococcus durans. However, none of the strains reacted with the AccuProbe Enterococcus genetic probe. The whole-cell protein profiles of these organisms were compared with the profiles of Enterococcus and Lactococcus reference strains. Apart from minor quantitative differences, the mastitis isolates had indistinguishable protein profiles that were similar to the profiles of the Lactococcus garvieae and Enterococcus seriolicida type strains. The results of DNA relatedness studies performed by using the hydroxy-apatite method at 55 and 70°C indicated that all of the mastitis isolates were related to the type strain of L. garvieae at the species level, despite the fact that they exhibited several uncommon phenotypic characteristics (growth at 45°C, growth in broth containing 6.5% NaCl, and failure to produce acid from mannitol and sucrose). The high levels of DNA relatedness between strains of L. garvieae and E. seriolicida demonstrated that these taxa are members of a single species. Since L. garvieae is a senior synonym of E. seriolicida, L. garvieae should be retained as the species name and strain ATCC 43921 should remain the type strain of this species.
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Comparative Analysis of 16S and 23S rRNA Sequences of Listeria Species
More LessIn order to establish the taxonomic value of 16S rRNA and 23S rRNA for distinguishing Listeria species, the complete 23S rRNA sequences for all Listeria species were determined by using the type strains. We designed and experimentally validated a universal 23S rRNA sequencing method, which included PCR amplification of the rDNA gene and direct cycle sequencing of the amplicon with eubacterial primers. The results of our sequence comparison indicated that the genus Listeria can be divided into two subgroups; one subgroup is composed of Listeria monocytogenes, Listeria innocua, Listeria ivanovii, Listeria seeligeri, and Listeria welshimeri, whereas the other subgroup includes Listeria grayi subsp. grayi and Listeria grayi subsp. murrayi. A phylogenetic analysis revealed that these species diverged recently. These results are consistent with 16S rRNA sequence analysis data. For application purposes, one 16S rRNA region that can be used to distinguish each Listeria species except L. monocytogenes and L. innocua has been described. In this study we found four 23S rRNA signature regions which, when used in combination, can be used to distinguish the species.
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Polyphasic Approach to the Classification and Identification of Gardnerella vaginalis and Unidentified Gardnerella vaginalis-Like Coryneforms Present in Bacterial Vaginosis
A taxonomic study of Gardnerella vaginalis and G. vaginalis-like coryneforms was performed in order to clarify the phylogenetic affiliation of these organisms and to improve future identification. We examined 50 strains by performing whole-cell protein and fatty acid analyses, a 16S rRNA sequence analysis, and an extensive phenotypic characterization analysis. The results of both chemotaxonomic techniques which we used divided the organisms into two main clusters, and the 16S rRNA sequence analysis revealed that the clusters represent different genera, which were easily distinguished by the results of classical phenotypic tests. The cluster I strains were identified as G. vaginalis, which was shown to be a close relative of the genus Bifidobacterium. An improved description of G. vaginalis is presented. The cluster II strains belong to or are closely related to Actinomyces turicensis.
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Mycobacterium hodleri sp. nov., a New Member of the Fast-Growii Mycobacteria Capable of Degrading Polycyclic Aromatic Hydrocarbons
More LessA bacterial strain isolated from a fluoranthene-polluted soil was characterized with respect to its metabolic and chemotaxonomic properties, and its phylogenetic position was determined. This bacterium exhibits all of the genus-specific properties of the genus Mycobacterium and clusters phylogenetically with the group of fast-growing mycobacteria. On the basis of its unique fatty acid pattern, the distinctness of its physiological properties and the uniqueness of the primary structure of its 16S ribosomal DNA, we propose that the new isolate should be assigned to a new species, Mycobacterium hodleri. This novel species is phylogenetically closely related to Mycobacterium diernhoferi and Mycobacterium neoaurum. The type strain of M. hodleri is strain EMI2 (= DSM 44183).
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Paenibacillus apiarius sp. nov.
More LessThe name “Bacillus apiarius” Katznelson 1955 was not included on the Approved Lists of Bacterial Names and thus lost standing in bactenal nomenclature. The genetic homogeneity of “B. apiarius” strains was assessed by determining their G+C contents by the buoyant density method and by measuring the levels of DNA relatedness by spectrophotometric reassociation procedures. The G+C contents of the 15 strains examined, ranged from 52 to 54 mol%. DNA reassociation revealed the presence of two clusters each with high levels of intragroup relatedness (60 to 100%). One cluster consisted of six strains highly related to Bacillus thiaminolyticus, and the other consisted of nine strains related to the designated type strain of “B. apiarius.” The strains in the second cluster were not closely related genetically to the type strains of organisms frequently associated with honey bees (namely, Paenibacillus alvei, Paenibacillus larvae, Bacillus laterosporus, and Paenibacillus pulvifaciens). The “B. apiarius” strains in the second cluster were also phenotypically homogeneous and distinguishable from the previously described species. Comparative analyses of the 16S rRNA gene DNA sequence showed that the proper phylogenetic position of the second cluster was in the genus Paenibacillus. These findings justify the proposal of a new species with the name Paenibacillus apiarius. The type strain is NRRL NRS-1438.
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Two New Leptospiral Serovars in the Hebdomadis Serogroup Isolated from Zimbabwe Cattle
More LessFour strains belonging to the genus Leptospira serogroup Hebdomadis were isolated from Zimbabwe cattle at slaughter. These isolates were subjected to cross-agglutinin absorption tests and to restriction fragment length polymorphism and pulsed-field gel electrophoresis analyses of their genomic DNAs. One of these strains repreents a new serovar, for which the name mhou is proposed; strain SBF 40 is the reference strain of this serovar. The other three strains belong to a second new serovar, for which the name marondera is proposed; the reference strain of this serovar is strain SBF 5. The three strains of serovar marondera could be differentiated by their restriction fragment polymorphism and pulsed-field gel electrophoretic patterns.
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DNA Relatedness among Verticil-Forming Streptomyces Species (Formerly Streptoverticillium Species)
More LessLevels of DNA relatedness among 35 strains of Streptomyces species originally classified in the genus Streptoverticillium were determined spectrophotometrically. These strains represent eight of the phenotypic cluster groups described for the genus Streptoverticillium in Bergey’s Manual of Systematic Bacteriology. Average linkage clustering of the DNA relatedness data resulted in 20 clusters including 13 single-member clusters, at a level of relatedness of >70%. Several species could be reduced to synonymy on the basis of DNA homology data, but these taxa were not generally equivalent to the clusters suggested by phenotypic numerical taxonomy data.
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Bartonella vinsonii subsp. berkhoffii subsp. nov., Isolated from Dogs; Bartonella vinsonii subsp. vinsonii; and Emended Description of Bartonella vinsonii
Two bacterial strains, one isolated from the blood of a dog with valvular endocarditis and one isolated from the blood of a healthy dog, were similar to Bartonella species, as determined by a number of phenotypic criteria, including growth characteristics, biochemical reactions, and cell wall fatty acid composition. The results of 16S rRNA gene sequence similarity studies confirmed that these strains are closely related and belong in the genus Bartonella and that Bartonella vinsonii is their closest relative (the 16S rRNA of isolate 93-C01T [T = type strain] was 99.37% identical to the 16S rRNA of the type strain of B. vinsonii, the 16S rRNA of isolate G7464 was 99.61% identical to the 16S rRNA of the type strain, and the 16S rRNAs of the dog isolates were 99.77% identical to each other). The 16S rRNAs of both strains contained a 12-base insertion that was not present in the 16S rRNA of the type strain of any Bartonella species. DNA relatedness tests revealed that these strains were related at the species level to the type strain of B. vinsonii. They were, however, significantly more closely related to each other than to B. vinsonii. On the basis of their unique 16S rRNA sequence insertion, their preferentially high level of relatedness, and their similar origins (dogs), we believe that strains 93-C01T and G7464 should be placed in a separate subspecies of B. vinsonii, for which we propose the name B. vinsonii subsp. berkhoffii subsp. nov. The type strain of B. vinsonii subsp. berkhoffii is strain 93-C01 (= ATCC 51672). The description of B. vinsonii is emended to accommodate the new subspecies, and B. vinsonii subsp. vinsonii is described.
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Desulfovibrio gabonensis sp. nov., a New Moderately Halophilic Sulfate-Reducing Bacterium Isolated from an Oil Pipeline
Two moderately halophilic sulfate-reducing bacteria were isolated from an African oil pipeline and designated strains SEBR 3640 and SEBR 2840T (T = type strain). Both of these strains possessed traits that define the genus Desulfovibrio. The cells of both isolates were motile curved rods that had a single polar flagellum and contained desulfoviridin, and both isolates utilized lactate, pyruvate, malate, fumarate, succinate, and ethanol in the presence of sulfate. Sulfite, thiosulfate, and elemental sulfur were also used as electron acceptors in the presence of lactate. However, both strains tolerated higher concentrations of NaCI (up to 17%) than all other Desulfovibrio species except Desulfovibrio halophilus, which tolerated a similar level of NaCI. The results of a 16S rRNA gene sequence analysis also placed the designated type strain, strain SEBR 2840, in the genus Desulfovibrio but revealed that this organism was significantly different from D. halophilus and all other validly described Desulfovibrio species. On the basis of our results, we propose that strain SEBR 2840T is a member of a new species of the genus Desulfovibrio, Desulfovibrio gabonensis. The type strain of D. gabonensis is strain SEBR 2840 (= DSM 10636).
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Mycoplasma sturni sp. nov., from the Conjunctiva of a European Starling (Sturnus vulgaris)
Strain UCMFT (T = type strain) was isolated from the conjunctiva of a European starling (Sturnus vulgaris) with conjunctivitis. Colonies grown on conventional mycoplasma agar possessed the typical fried-egg appearance observed with many mycoplasmal species. Electron micrographs of ultrathin sections of UCMFT revealed a pleomorphic cellular morphology; the cells ranged from spherical to elliptical or flask shaped. The cell size ranged from 0.3 to 0.5 μm. Strain UCMFT grows well in a variety of mycoplasma broth formulations at 25°C with rapid and heavy growth at 37°C. No growth occurs at 42°C. This organism ferments glucose but does not hydrolyze urea or arginine and has an absolute requirement for sterol for growth. Strain UCMFT does not hemagglutinate or hemadsorb chicken erythrocytes. The genome size is 870 kbp, and the guanine-plus-cytosine content is 31 mol%. Sequence analysis of the 16S rRNA gene demonstrated that this organism is unique and has not been described previously. Serological analysis confirmed that strain UCMFT is distinct from all previously identified Mycoplasma, Acholeplasma, Spiroplasma, Entomoplasma, and Mesoplasma species. This organism represents a new species, for which we propose the name Mycoplasma sturni. Strain UCMF (= ATCC 51945) is the type strain of M. sturni sp. nov.
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Erwinia alni, a New Species Causing Bark Cankers of Alder (Alnus Miller) Species
More LessThe causal agent of an undetermined disease of black alder (Alnus glutinosa) and Italian alder (Alnus cordata) was identified as an Erwinia species. This alder bacterium induces dark brown necrotic cankers on alder plants; these cankers are often longitudinally elongated and occur in the bark of the trunks and also in the bark of branches, twigs, and suckers. A dark watery liquid often exudes from small cracks in the cankers and stains the bark surface. Disease symptoms were produced on the trunks of 2-year-old black and Italian alder trees after artificial inoculation of selected strains of bacteria obtained from typical bark cankers (G. Surico and L. Mugnai, Inf. tore Fitopatol. 12:41-43, 1992). Morphological examination of the pathogen by electron microscopy showed that it is a motile rod-shaped organism. All of the strains examined were gram negative, oxidase negative, and facultatively anaerobic with fermentative metabolism and had the general characteristics and fatty acids of members of the family Enterobacteriaceae. Strains PVFi 20T (T = type strain), PVFi 23, PVFi 25, and PVFi 27 were chosen for further characterization. These four strains exhibited 96 to 100% DNA homology in hybridization experiments performed at 40 and 50°C. They were most closely related to Erwinia nigrifluens (levels of homology 40°C, 49 to 65%). Phenotypic differentiation from E. nigrifluens, which induces a similar disease on Persian walnut but is nonpathogenic on alder, is based on positive reactions by the alder strains for acetoin (Voges-Proskauer reaction), endoglucanase activity, and acid production from maltose and negative reactions for esculin hydrolysis and acid production from raffinose, melibiose, sorbitol, and inositol. The fatty acid profiles of the alder strains were quantitatively different from those of all previously validly named plant-pathogenic species belonging to the Enterobacteriaceae. On the basis of data described above, the name Erwinia alni is proposed for the new organism.
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Phylogeny and Taxonomy of Mesophilic Methanococcus spp. and Comparison of rRNA, DNA Hybridization, and Phenotypic Methods
More LessThe phylogeny and taxonomy of the mesophilic methane-producing archaea of the order Methanococcales were examined by DNA relatedness, 16S rRNA sequence analysis, cellular protein pattern, and phenotypic methods. The mesophilic species Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltaei, and “Methanococcus aeolicus” formed a deep group with 5 to 30% DNA relatedness and 92 to 96% 16S rRNA sequence similarity. Twenty-two additional isolates and Methanococcus deltae were similar to the type strain of either M. voltaei or M. maripaludis. Two isolates, strains A2 and A3, exhibited 37% DNA relatedness and 99.2% 16S rRNA sequence similarity to M. voltaei PST (T = type strain). In the absence of phenotypic differences, these organisms were assigned to M. voltaei. Similarly, four autotrophic isolates, strains C5, C6, C7, and C8, exhibited 54 to 69% DNA relatedness and 99.2% 16S rRNA sequence similarity to M. maripaludis JJT and were assigned to M. maripaludis. While these isolates were sufficiently genetically diverse to justify classification in novel species, few differences were apparent in the phenotypic properties available for measurement. Thus, the phenotypic properties of these lithotrophic archaea were highly conserved and poor indicators of genetic diversity. Partial sequencing of about 200 bases of both the 16S and 23S rRNAs of the isolates demonstrated allelic diversity within methanococcal species. This allelic diversity did not correlate with diversity measured by DNA relatedness, cellular protein pattern, and other methods. Similarly, antisera to whole cells of the type strains did not cross-react strongly to whole cells of strains that were genetically similar, and serological cross-reactivity was not a useful taxonomic method for methanococci. Lastly, on the basis of the results of 16S rRNA sequence analyses and biochemical data, the ancestor of the mesophilic methanococci may have been an autotrophic thermophile.
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Phylogenetic Relationships and Diversity within the Pasteurella haemolytica Complex Based on 16S rRNA Sequence Comparison and Outer Membrane Protein and Lipopolysaccharide Analysis
More LessThe outer membrane protein (OMP) and lipopolysaccharide (LPS) profiles of 30 untypeable isolates of Pasteurella haemolytica were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and compared with the profiles of typeable isolates. The phylogenetic relationships of 28 isolates representing each of the serotypes of P. haemolytica and Pasteurella trehalosi, as well as untypeable isolates of P. haemolytica, were determined by comparing 16S rRNA sequences. The analysis of the OMP and LPS profiles of the untypeable isolates revealed five groups, which were designated untypeable groups 1 (UG1) through UG5. The UG1 and UG2 isolates had OMP and LPS profiles identical to the profiles of certain serotype A1 and A2 isolates, respectively. Furthermore, UG1 isolates originating from cattle and sheep could be clearly differentiated on the basis of their OMP profiles. The OMP and LPS profiles of UG3 isolates were similar in appearance to the profiles of serotype A11 isolates, suggesting that these two groups are closely related. The OMP profiles of UG4 and UG5 isolates were unique and different from the OMP profiles of the UG1 through UG3 isolates. A comparison of 16S rRNA sequences revealed that typeable isolates of P. haemolytica could be divided into the following three groups: (i) serotype A1, A5 through A9, A12 through A14, and A16 isolates, (ii) serotype A2 isolates, and (iii) serotype A11 isolates. The isolates belonging to the first group all had identical sequences, whereas the sequences of isolates belonging to the second and third groups differed from the sequences of the isolates belonging to the first group at two and four base positions, respectively. The sequence data for the untypeable isolates confirmed the conclusions derived from the OMP and LPS analysis. Isolates belonging to UG1 and UG2 were identical to serotype A1 and A2 isolates, respectively; isolates belonging to UG3 were related to serotype A11 isolates, although there was some sequence heterogeneity within this group; and isolates belonging to UG4 and UG5 were more distantly related to P. haemolytica than were isolates belonging to UG1 through UG3 and were clearly members of two different species. As expected, isolates of P. trehalosi were even more distantly related to P. haemolytica than were the untypeable isolates, but there was significantly more sequence variation among the four serotypes of this species than there was among the serotypes of P. haemolytica. The correlation of the OMP and LPS data with the 16S rRNA sequence data suggested that OMP and LPS analyses might be useful for preliminary screening and comparing large numbers of isolates in taxonomic and epidemiological studies of the Pasteurellaceae.
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Treponema maltophilum sp. nov., a Small Oral Spirochete Isolated from Human Periodontal Lesions
More LessA novel culture medium for cultivation of fastidious oral anaerobes is described. This medium, OMIZ-Pat, consists of a rich chemically defined basal medium supplemented with asialofetuin, as well as yeast extract and Neopeptone fractions. Addition of 1 mg of rifampin per liter and 100 mg of fosfomycin per liter allowed routine isolation of spirochetes by a limit dilution method in 96-well plates containing liquid OMIZ-Pat. In addition to members of the four previously recognized species of oral treponemes (Treponema denticola, Treponema pectinovorum, Treponema socranskii, and Treponema vincentii), 26 previously undescribed spirochete strains belonging to one group were isolated. We propose the name Treponema maltophilum sp. nov. for these small spirochetes, which have two endoflagella; one endoflagellum is attached at each cell pole, and the endoflagella overlap in the middle of the cell. Growth of these organisms was dependent on a carbohydrate like d-arabinose, l-fucose, d-maltose, l-rhamnose, d-ribose, d-sucrose, or d-trehalose and was inhibited by fetal bovine serum. T. maltophilum is distinguished from other oral Treponema species by its 16S rRNA sequence, its protein and antigen patterns as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immuno-blotting, and its characteristic α-glucosidase activity. The strains included in the new species on the basis of their 16S rRNA sequences are heterogeneous with respect to their α-fucosidase and β-glucuronidase activities, their dependence of N-acetylglucosamine, and their antigens as detected with patient antibodies. Strain BR is designated the type strain, and strains HO2A and PNA1 are reference strains of the new species.
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Clostridium proteoclasticum sp. nov., a Novel Proteolytic Bacterium from the Bovine Rumen
More LessA novel proteolytic bacterium was isolated from rumen contents of New Zealand cattle grazing fresh forage and was designated strain B316T (T = type strain). Strain B316T cells were straight to slightly curved rods (width, 0.4 to 0.6 μm; length, 1.3 to 3.0 μm) that were gram-positive and possessed a single subterminal flagellum. This isolate did not produce catalase, indole, ammonia, lipase, or lecithinase or reduce nitrate, but it did produce a curd reaction with milk. Strain B316T was proteolytic, hydrolyzing casein and fraction I leaf protein. The crude proteinase was predominantly the serine type, but some cysteine proteinase and metallo-proteinase activities were also detected. The DNA base composition of strain B316T was 28 mol% G+C. A 16S ribosomal DNA sequence analysis of strain B316T indicated that it was most closely related to a member of clostridial cluster XIVa, viz., Clostridium aminophilum, an amino acid-fermenting organism isolated from the rumen; the similarity value was 92.2%. The results of the phenotypic characterization analysis, G+C content analysis, and phylogenetic analysis of the 16S ribosomal DNA sequence set strain B316T apart from all of the members of cluster XIVa. We propose that strain B316T should be designated a new species of the genus Clostridium, Clostridium proteoclasticum. Strain B316 is the type strain and has been deposited in the American Type Culture Collection as strain ATCC 51982.
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Bacillus sporothermodurans, a New Species Producing Highly Heat-Resistant Endospores
More LessBacteria that differentiate into highly heat-resistant endospores (HHRS strains) may survive ultrahigh-temperature treatment of milk and germinate in the final product. They do not noticeably spoil the milk and are nonpathogenic. The complete (>96%) 16S rRNA genes from three HHRS strains were identical, and phylogenetic analysis placed them alongside Bacillus firmus in the B. megaterium group of the genus Bacillus. Moreover, the approximately 550 nucleotides between regions U2 and U5 were invariant for seven HHRS strains. However, three cloned 16S rRNA genes from one HHRS strain, M215, showed marked size and sequence variations within the V1 and V2 regions. DNA reassociation assays confirmed the distinction between a reference HHRS strain and closely related members of the B. megaterium group, notably, B. firmus (30%), B. benzoevorans (28%), and B. circulans (20%). Ribotyping and pyrolysis mass spectrometry both indicated that the HHRS strains belong to a homogeneous, species-ranked taxon, an exception being strain TP1248, which is slightly atypical. The HHRS strains are unusual in that they grow poorly, if at all, on nutrient agar; good growth is obtained on brain heart infusion agar. On subculture, most HHRS strains form long, filamentous rods which stain unevenly in the Gram reaction. They are strictly aerobic and do not produce acid from sugars. We propose the name Bacillus sporothermodurans for these bacteria, which are phenotypically and phylogenetically distinct from other Bacillus species. The type strain is M215 (= DSMZ 10599).
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16S Ribosomal DNA Analysis of the Genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and Emendation of the Family Micromonosporaceae
More LessIn order to determine the phylogenetic structure of the actinomycete family Micromonosporaceae, the 16S ribosomal DNA sequences of 17 type species of the genera Actinoplanes, Dactylosporangium, and Pilimelia were compared with the 16S ribosomal DNA sequences of species of the genera Catellatospora, Catenuloplanes, and Couchioplanes and with those of species of the genus Micromonospora and other actinomycete genera for which the sequences have been previously determined. All genera of the family, together with the genera Catellatospora, Catenuloplanes, and Couchioplanes, form a phylogenetically coherent cluster that is well separated from other families of the order Actinomycetales. Except for one species of the genus Catellatospora, all species cluster according to their genus affiliation. The inclusion of the genera Catellatospora, Catenuloplanes, and Couchioplanes into the family broadens the phenotypic and chemotaxonomic heterogeneity of this taxon. An emendation of the family Micromonosporaceae is given.
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Isolation and Identification of Poly(3-Hydroxyvalerate)-Degrading Strains of Pseudomonas lemoignei
By using selective enrichment of polyhydroxyalkanoate-degrading bacteria and poly(3-hydroxyvalerate)-containing granules from Chromobacterium violaceum as the carbon source, 10 new Pseudomonas lemoignei strains were isolated; these strains were able to degrade poly(3-hydroxyvalerate), as well as poly(3-hydroxybutyrate), in vitro. The new isolates were characterized and identified by comparing them with P. lemoignei LMG 2207T (T = type strain). Like P. lemoignei LMG 2207T cells, the cells of the 10 new isolates contained mainly hexadecenoic, hexadecanoic, octadecenoic, and dodecanoic acids, as well as hydroxylated fatty acids, and exhibited respiration in the presence of methylpyruvate, 3-hydroxybutyrate, and 4-hydroxybutyrate, but not in the presence of the 92 other carbon sources included in Biolog GN microplates. The protein patterns of the new isolates were almost identical to each other and very similar to the protein pattern of P. lemoignei LMG 2207T. Some of the new isolates, but not P. lemoignei LMG 2207T, contained megaplasmids that were about 200 kbp long. The 16S ribosomal DNA genes of strain A62, a representative of the 10 new isolates, and of P. lemoignei LMG 2207T exhibited more than 0.99 sequence similarity. The DNA-DNA reassociation value for two representative strains was 100%, and the levels of DNA-DNA reassociation between these strains and the type strain were 60 and 61%. The taxonomy of P. lemoignei is briefly discussed.
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Taxonomic Study of Lancefield Streptococcal Groups C, G, and L (Streptococcus dysgalactiae) and Proposal of S. dysgalactiae subsp. equisimilis subsp. nov.
More LessStreptococcus dysgalactiae consists of at least five distinct subgroups on the basis of serogroups, biotypes, and hosts. A chemotaxonomic and phenotypic examination of 80 S. dysgalactiae strains representing the known diversity within this species and 49 reference strains representing all members of the streptococcal pyogenic species group revealed two subpopulations of strains within S. dysgalactiae. The name S. dysgalactiae subsp. dysgalactiae is proposed for strains of animal origin. These strains belong to Lancefield serogroups C and L, are alpha-, beta-, or nonhemolytic, and do not exhibit streptokinase activity on human plasminogen or proteolytic activity on human fibrin. The name S. dysgalactiae subsp. equisimilis is proposed for human isolates. These strains belong to Lancefield serogroups C and G, are beta-hemolytic, and exhibit streptokinase activity on human plasminogen and proteolytic activity on human fibrin.
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Polyphasic Analysis of Strains of the Genus Capnocytophaga and Centers for Disease Control Group DF-3
A polyphasic approach was used to determine the relationships between well-characterized reference strains representing all seven Capnocytophaga species. One Centers for Disease Control (CDC) group DF-3 strain, a presumed relative of the genus Capnocytophaga, and 15 field isolates were included as well. Fourteen isolates were assigned to named Capnocytophaga species, all of which could be differentiated by means of whole-organism protein electrophoresis. A separate position was occupied by the CDC group DF-3 strain and by one field isolate representing a novel Capnocytophaga species. The phylogenetic position of each taxon was determined by means of 16S rRNA sequence analysis. A considerable genotypic heterogeneity within the genus Capnocytophaga was detected in spite of the minimal phenotypic differences. Comparative 16S rRNA sequence analysis revealed that CDC group DF-3 is not a close relative of the capnocytophagas but constitutes a separate genus that clusters together with Bacteroides forsythus and Bacteroides distasonis, two generically misclassified Bacteroides species. The degree of protein similarity correlated with our and published DNA-DNA binding values. Percentage 16S rRNA similarity values of greater than 97% did not guarantee conspecificity. All Capnocytophaga strains had very similar fatty acid contents characterized by significant amounts of 14:0, 15:0 iso (greater than 55%), 16:0, 16:0 30H, and 17:0 iso 30H. PCR-mediated DNA fingerprinting allowed discrimination of most species, although some strains could not be classified efficiently because of DNA polymorphisms.
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Staphylococcus saprophyticus subsp. bovis subsp. nov., Isolated from Bovine Nostrils
More LessA new coagulase-negative subspecies, Staphylococcus saprophyticus subsp. bovis, is described on the basis of a study of five strains isolated from the anterior nares of cows. This subspecies is differentiated from the other novobiocin-resistant staphylococci by its phenotypic properties, cell wall composition, and levels of genetic relatedness. The type strain of the new subspecies is KV 12 (=CCM 4410).
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Spiroplasma syrphidicola sp. nov., from a Syrphid Fly (Diptera: Syrphidae)
Spiroplasma sp. strain EA-1T (T = type strain) (subgroup VIII-1), which was isolated from the syrphid fly Eristalis arbustorum, was serologically distinct from other spiroplasma species, groups, and subgroups. The cells of this strain, as revealed by dark-field light microscopy, were short, helical, and motile. An electron microscopic examination revealed wall-less cells delimited by a single membrane. The unusually short cells passed through 220-nm filter pores with no reduction in titer. The organisms grew well in SM-1, MID, and SP-4 liquid media. Growth also occurred in conventional horse serum medium and 1% serum fraction medium. Strain EA-1T grew at temperatures between 10 and 41°C, and optimuum growth occurred at 32°C. The doubling time at the optimal temperature was 1.0 h. The strain catabolized glucose and hydrolyzed arginine but did not hydrolyze urea. The guanine-plus-cytosine content of the DNA was 30 ± 1 mol%. The genome size was about 1,230 kbp. Strain EA-1 (= ATCC 33826), which represents subgroup VIII-1, is designated the type strain of a new species, Spiroplasma syrphidicola.
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Emended Description of Herbaspirillum; Inccusion of [Pseudomonas] rubrisubalbicans, a Mild Plant Pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and Classification of a Group of Clinical Isolates (EF Group 1) as Herbaspirillum Species 3
[Pseudomonas] rubrisubalbicans. a mild plant pathogen, Herbaspirillum seropedicae, and EF group 1 strains (clustered by an immunological method) were investigated by a polyphasic approach with DNA-rRNA and DNA-DNA hybridizations and auxanography on 147 substrates. Our results show that they all belong to the genus Herbaspirillum. In addition to H. seropedicae, two other species are described: Herbaspirillum rubrisubalbicans and a new unnamed species, Herbaspirillum species 3, containing mainly strains of clinical origin. The three species can be differentiated on the basis of their auxanographic features and DNA-DNA similarities. The type strain of H. rubrisubalbicans is NCPPB 1027 (=LMG 2286): Representative strains of the third Herbaspirillum species are strains CCUG 189 (=LMG 5523), CCUG 10263 (=LMG 5934), and CCUG 11060 (=LMG 5321). It has been confirmed that H. rubrisubalbicans is an endophytic diazotroph. It colonizes the roots, the stems, and predominantly the leaves of sugarcane (Saccharum spp.), while Herbaspirillum seropedicae colonizes in large numbers many different species of the Gramineae. Both diazotrophic Herbaspirillum species could be differentiated with meso-erythritol and N-acetylglucosamine. Oligonucleotide probes based on partial sequences of the 23S rRNA of H. seropedicae and H. rubrisubalbicans (HS and HR probes, respectively), were constructed and used as diagnostic probes.
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NOTES: Sanguibacter inulinus sp. nov.
More LessSix strains of coryneform bacteria were isolated from blood samples obtained from healthy cows. Phenotypic and molecular genetic studies showed that these isolates represent a new species of the genus Sanguibacter, for which the name Sanguibacter inulinus is proposed. The type strain of S. inulinus is strain ST-50 (= NCFB 3024).
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Picrophilus oshimae and Picrophilus torridus fam. nov., gen. nov., sp. nov., Two Species of Hyperacidophilic, Thermophilic, Heterotrophic, Aerobic Archaea
More LessWe describe two species of hyperacidophilic, thermophilic, heterotrophic, aerobic archaea that were isolated from solfataric hydrothermal areas in Hokkaido, Japan. These organisms, Picrophilus oshimae and Picrophilus torridus, represent a novel genus and a novel family, the Picrophilaceae, in the kingdom Euryarchaeota and the order Thermoplasmales. Both of these bacteria are more acidophilic than the genus Thermoplasma since they are able to grow at about pH 0.
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Analysis of 16S rRNA Gene Sequences of Vibrio costicola Strains: Description of Salinivibrio costicola gen. nov., comb. nov.
More LessThe phylogenetic positions of six Vibrio costicola strains were determined by direct sequencing and analysis of their PCR-amplified 16S ribosomal DNAs. A comparative analysis of the sequence data revealed that the moderate halophile V. costicola forms a monophyletic branch that is distinct from other Vibrio species and from moderately halophilic species of other genera. These results complement phenotypic and genotypic data determined previously. The molecular evidence, together with several phenotypic differences, distinguishes V. costicola from species of the genus Vibrio and other species belonging to the gamma subclass of the Proteobacteria and indicates that V. costicola should be placed in a new and separate genus. The name Salinivibrio costicola gen. nov., comb. nov. is proposed for this bacterium. The guanine-plus-cytosine content of the DNA is 49.4 to 50.5 mol%. The type strain of S. costicola is strain NCIMB 701 (= ATCC 33508).
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Polaromonas vacuolata gen. nov., sp. nov., a Psychrophilic, Marine, Gas Vacuolate Bacterium from Antarctica
More LessSeveral strains of a novel heterotrophic gas vacuolate bacterium were isolated from antarctic marine waters. The results of phylogenetic analyses in which 16S ribosomal DNA sequencing was used, coupled with pheno-typic tests, indicated that strain 34-PT (T = type strain) belongs to a new genus and species of the beta subgroup of the Proteobacteria, for which the name Polaromonas vacuolata is proposed. Although the other four strains studied probably belong to this new species, DNA-DNA hybridization tests were not conducted. The closest phylogenetic relatives of P. vacuolata are the photosynthetic nonsulfur purple bacterium Rhodoferax fermentans and the hydrogen autotroph Variovorax paradoxus.
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Phylogenetic Analysis of Genes Coding for 16S rRNA in Mammalian Ureaplasmas
More LessPhylogenetic relationships among species of the genus Ureaplasma were elucidated by analyzing 16S rRNA sequence information. The 16S rRNA genes of six strains of the mammalian Ureaplasma species were amplified by PCR and were sequenced directly by a primer walking method. The phylogenetic tree based on the nucleotide sequence of the 16S rRNA genes corresponded to the evolutionary history of the host animal species.
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- Matters Relating To The International Committee On Systematic Bacteriology
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Subspecies Names Automatically Created by Rule 46
More LessTwo type subspecies names created automatically under Rule 46 are presented.
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Taxonomic Note: A Rule about the Deposition of Type Strains
More LessA rule is proposed to replace Recommendation 30a in the International Code of Nomenclature of Bacteria; this rule makes mandatory the deposition of the type strains of cultivable bacterial species and subspecies in a permanent culture collection so that they are available for study.
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Taxonomic Note: A Proposal for Reviewing the Interpretation of the CAMP Reaction between Listeria monocytogenes and Rhodococcus equi
More LessThe discrepancies between the current description of the CAMP test between Listeria monocytogenes and Rhodococcus equi in the latest edition of Bergey’s Manual of Determinative Bacteriology (L. monocytogenes is described as CAMP test negative with R. equi) and routine findings (positive reactions are usually described in many laboratories) make it advisable to review the current interpretation of the CAMP test to avoid confusion among people working in microbiological laboratories. Overall, 98.4% of the L. monocytogenes strains examined in this study, regardless of their source or the intensity of their hemolytic activity, displayed a synergic hemolytic reaction (CAMP phenomenon) with R. equi, indicating that L. monocytogenes can generally be considered CAMP positive with R. equi. We propose that L. monocytogenes, together with Listeria ivanovii, should be considered CAMP test positive with R. equi (circular or racket and semicircular or shovel shapes, respectively).
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Opinion 68: Designation of Strain B213c (DSM 20284) in Place of Strain NCDO 1859 as the Type Strain of Pediococcus acidilactici Lindner 1887: Judicial Commission of the International Committee on Systematic Bacteriology
The Judicial Commission designated strain B213c (= DSM 20284) as the type strain of Pediococcus acidilactici in place of strain NCDO 1859, which seems to belong in the species Pediococcus pentosaceus.
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- Errata
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