- Volume 47, Issue 3, 1997
Volume 47, Issue 3, 1997
- Original Papers Relating To Systematic Bacteriology
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Tsukamurella tyrosinosolvens sp. nov.
AbstractChemotaxonomic and 16S ribosomal DNA sequence analyses of four bacterial isolates from blood cultures from patients with cardiac pacemaker implants and sputa of patients with chronic lung infections clearly demonstrated that these bacteria belong to the genus Tsukamurella. DNA-DNA hybridization data, as well as the physiological characteristics of the isolates, indicate that they are closely related and belong to a single species that differs from previously described members of the genus Tsukamurella. The name Tsukamurella tyrosinosolvens sp. nov. is proposed for these isolates, and the new species is represented by strain IMMIB D-1397T (= DSM 44234T). Strain IMMIB D-1397T exhibits 53.4, 53.5, and 54.7% DNA-DNA relatedness to Tsukamurella paurometabola DSM 20162T, Tsukamurella inchonensis DSM 44067T, and Tsukamurella pulmonis DSM 441 42T, respectively.
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Description of Two New Thermophilic Desulfotomaculum spp., Desulfotomaculum putei sp. nov., from a Deep Terrestrial Subsurface, and Desulfotomaculum luciae sp. nov., from a Hot Spring
AbstractSix strains of thermophilic, endospore-forming, sulfate-reducing bacteria were enriched and isolated from 2.7 km below the earth’s surface in the Taylorsville Triassic Basin in Virginia. The cells of these strains were motile rods that were 1 to 1.1 µm in diameter and 2 to 5 µm long. The cells grew by oxidizing H2, formate, methanol (weakly), lactate (incompletely, to acetate and CO2), or pyruvate (incompletely) while reducing sulfate to sulfide; acetate did not serve as a catabolic substrate. Thiosulfate or sulfite could replace sulfate as an electron acceptor. The results of a phylogenetic analysis of the 16S rRNA gene indicated that these strains belong to the genus Desulfotomaculum, but are distinct from previously described Desulfotomaculum species. Thus, we propose a new species, Desulfotomaculum putei, for them, with strain TH-11 (= SMCC W459) as the type strain. The results of our phylogenetic analysis also indicated that strain SLTT, which was isolated from a hot spring and has been described previously (T. M. Karnauchow, S. F. Koval, and K. F. Jarrell, Syst. Appl. Microbiol. 15:296–310, 1992), is also a member of the genus Desulfotomaculum and is distinct from other species in this genus. We therefore propose the new species Desulfotomaculum luciae for this organism; strain SLT (= SMCC W644) is the type strain of D. luciae.
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Thermococcus hydrothermalis sp. nov., a New Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent
AbstractAn extremely thermophilic archaeon, strain AL662T, was isolated from a deep-sea hydrothermal vent located on the East Pacific Rise at a latitude of 21°N. This strain is a strictly anaerobic coccus, and its cells range from 0.8 to 2 p.m in diameter. The optimum temperature, pH, and Sea Salt concentration for growth are 85°C, 6, and 20 to 40 g/liter, respectively. Strain AL662T grows preferentially on proteolysis products, on a mixture of 20 amino acids, and on maltose in the presence of elemental sulfur. The membrane lipids consist of di- and tetraether glycerol lipids. The DNA G+C content is 58 mol%. Sequencing of the 16S rRNA gene showed that strain AL662T belongs to the genus Thermococcus. On the basis of hybridization results, we propose that this strain should be placed in a new species, Thermococcus hydrothermalis.
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Helicobacter rodentium sp. nov., a Urease-Negative Helicobacter Species Isolated from Laboratory Mice
More LessAbstractA spiral-shaped bacterium with bipolar, single, nonsheathed flagella was isolated from the intestines of laboratory mice. The organism grew at 37 and 42°C under microaerobic and anaerobic conditions, did not hydrolyze urea, was weakly positive for catalase and oxidase, reduced nitrate to nitrite, did not hydrolyze indoxyl acetate or hippurate, and was resistant to cephalothin and nalidixic acid. This is the first urease-negative, murine Helicobacter spp. isolated from intestines. Also, Helicobacter pullorum and this bacterium are unique among the genus Helicobacter in having nonsheathed flagella. The new bacterium appears to be part of the normal intestinal flora; although its pathogenic potential is unknown, this organism was also isolated from scid mice with diarrhea that were co-infected with Helicobacter bilis. On the basis of 16S rRNA gene sequence analysis data and biochemical and phenotypic criteria, the new organism is classified as a novel helicobacter, for which we propose the name Helicobacter rodentium. The type strain is MIT 95-1707 (= ATCC 700285).
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Comparison of the 16S Ribosomal DNA Sequences from the Intracellular Agents of Proliferative Enteritis in a Hamster, Deer, and Ostrich with the Sequence of a Porcine Isolate of Lawsonia intracellularis
More LessAbstractProliferative enteritis is an enteric disease that affects a variety of animals. The causative agent in swine has been determined to be an obligate intracellular bacterium, Lawsonia intracellularis, related to the sulfatereducing bacterium Desulfovibrio desulfuricans. The intracellular agents found in the lesions of different animal species are antigenically similar. In addition, strains from the pig, ferret, and hamster have been shown to be genetically similar. In this study we performed a partial 16S ribosomal DNA sequence analysis on the intracellular agent of proliferative enteritis from a hamster, a deer, and an ostrich and compared these sequences to that of the porcine L. intracellularis isolate. Results of this study indicate that the intracellular agents from these species with proliferative enteritis have high sequence similarity, indicating that they are all in the genus Lawsonia and that they may also be the same species, L. intracellularis.
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Comparison of a New Insertion Element, IS1407, with Established Molecular Markers for the Characterization of Mycobacterium celatum
More LessAbstractGenomic analyses of 18 Mycobacterium celatum strains obtained from different patients in three countries (United States, United Kingdom, and France) were performed; the methods used in this study were restriction fragment length polymorphism (RFLP) analysis, pulsed-field gel electrophoresis (PFGE) analysis, and PCR restriction analysis (PRA) of the hsp-65 gene. A new insertion sequence, IS1407 (GenBank accession no. X97307), belonging to the IS256 family, was identified in M. celatum type 1 strains and was characterized by sequencing. When a probe for Mycobacterium xenopi IS1395-like sequences was used, the RFLP analysis of M. celatum type 1 strains revealed that they contained three or four copies of IS1407 in identical genomic positions, while this element was absent in all M. celatum type 2 strains. PFGE performed with three different endonucleases revealed a unique large restriction fragment (LRF) pattern for M. celatum type 1 strains, whereas the LRF patterns obtained for M. celatum type 2 strains were polymorphic. Moreover, PFGE of nondigested genomic DNA revealed extrachromosomal elements in M. celatum type 2. The type strain of M. celatum type 3 could not be differentiated from M. celatum type 1 strains on the basis of the results of the RFLP analysis, the PFGE analysis, and the PRA of 1S1407. In this study we confirmed that M. celatum types 1 and 2 represent distinct genomic clusters and that the molecular markers in M. celatum type 2 exhibit greater polymorphism than the molecular markers in M. celatum type 1.
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Genotypic and Phenotypic Diversity within Streptococcus anginosus
More LessStreptococcus anginosus is one of the three species currently included in the “anginosus group” of oral or viridans streptococci. In this study 21 strains of S. anginosus were examined in order to determine whether this species, as currently defined, is sufficiently heterogeneous to warrant further subdivision. Phenotypic strain characterization was carried out by performing biochemical tests with a commercial system (Rapid ID32 STREP kit; bioMerieux), by performing tests to determine hyaluronidase production, hemolysis on blood agar, and gliding motility on chocolate agar, by determining Lancefield groups, and by comparing whole-cell polypeptide patterns obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Variations in genotype were determined by studying 16S-23S rRNA intergenic spacer size polymorphisms by PCR amplification, by ribotyping, and by performing DNA-DNA base pairing studies. S. anginosus was found to be heterogeneous at both the species and intraspecies (subspecies) levels. Beta-hemolytic Lancefield group C strains that did not produce hyaluronidase formed a DNA homology group that was separate from the majority of the S. anginosus strains; the members of this group produced a 380-bp intergenic spacer PCR product, exhibited distinct ribotypes, produced an atypical SDS-PAGE pattern, and represented a previously undescribed species in the anginosus group. Two other strains (ATCC 9895 and 1007-77) remained ungrouped as determined by DNA-DNA hybridization and thus represented additional centers of variation at the species level. Hyaluronidase-producing, beta-hemolytic, Lancefield group C strains produced the same atypical SDS-PAGE pattern as beta-hemolytic Lancefield group C strains that did not produce hyaluronidase but differed from the latter organisms by producing a 600-bp intergenic spacer PCR product. In addition, both DNA homology data and ribotyping data suggested that these strains comprise a subspecies of S. anginosus. With the notable exception of the beta-hemolytic Lancefield group C strains that did not produce hyaluronidase, strains ATCC 9895 and 1007-77, and the beta-hemolytic Lancefield group C hyaluronidase-producing strains mentioned above, the strains studied formed a closely related group within which some additional genotypic and phenotypic heterogeneity was observed. The latter group included both strains that fermented mannitol and strains that did not ferment mannitol, as well as strains that exhibited so-called gliding motility. Although no clear-cut division of these organisms was possible, our results indicate that strain NCTC 10713 may not be the most suitable type strain for S. anginosus. We concluded that S. anginosus strains exhibit sufficient heterogeneity to warrant division at both the species and subspecies levels, although insufficient numbers of strains belonging to the putative new taxa have been characterized to allow formal taxonomic proposals to be made.
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Caloramatorproteoclasticus sp. nov., a New Moderately Thermophilic Anaerobic Proteolytic Bacterium
More LessAbstractA new moderately thermophilic proteolytic anaerobe, strain UT, was isolated from mesophilic granular methanogenic sludge. The cells were spore-forming, motile rods that were 0.4 μm wide and 2.4 to 4 μm long and stained gram negative. Electron micrographs of thin sections revealed the presence of an atypical gram-positive cell wall. Optimum growth occurred at 55°C and at pH values between 7.0 and 7.5, with a doubling time of 30 min. The DNA base ratio of guanine plus cytosine was 31 mol%. The bacterium fermented proteins mainly to acetate, hydrogen, formate, and branched-chain fatty acids. Several amino acids, including glutamate, aspartate, arginine, histidine, threonine, methionine, and branched-chain amino acids, were also utilized. Glutamate was degraded to acetate, formate, hydrogen, and alanine. In addition, the strain degraded carbohydrates, including glucose, fructose, mannose, cellobiose, and starch, to acetate, ethanol, formate, lactate, and hydrogen. The results of a 16S rRNA sequence analysis phylogenetically placed strain UT in the low-guanine-plus-cytosine-content subgroup of the gram-positive phylum. We propose to classify the described strain in the genus Caloramator as a new species, Caloramator proteoclasticus. The type strain of C. proteoclasticus, strain U, has been deposited in the Deutsche Sammlung von Mikroorganismen as strain DSM 10124.
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Reclassification of the Crenarchaeal Orders and Families in Accordance with 16S rRNA Sequence Data
More LessAbstractA phylogenetic analysis of all validly published members of the Crenarchaeota, including several new isolates from our laboratory, suggests three orders within this archaeal kingdom. The Thermoproteales consist of both the rod-shaped, hyperthermophilic, neutrophilic representatives of the Thermoproteaceae and the members of the new family Thermofilaceae. The Sulfolobales harbor all thermoacidophilic, coccoid organisms. The neutrophilic, hyperthermophilic cocci are members of a new order tentatively named “Igneococcales.” This order comprises two families, the Desulfurococcaceae, characterized by maximal growth temperatures of up to 100°C, and the new family Pyrodictiaceae, for which optimal growth occurs at temperatures above 100°C.
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Inter- and Intraspecific Genetic Analysis of the Genus Saccharomonospora with 16S to 23S Ribosomal DNA (rDNA) and 23S to 5S rDNA Internally Transcribed Spacer Sequences
More LessIn order to clarify interspecific relationships and to investigate the intraspecific phylogenetic structure of the genus Saccharomonospora, 16S to 23S ribosomal DNA (16S-23S) and 23S to 5S ribosomal DNA (23S-5S) internally transcribed spacers (ITSs) were used for sequence analyses. The 16S-23S and 23S-5S ITSs from 22 Saccharomonospora strains were amplified by PCR and directly sequenced. The average levels of nucleotide similarity of the 16S-23S and 23S-5S ITSs for the four valid species were 87.6% ± 3.9% and 83% ± 2.2%, respectively. For the most part, intraspecific sequence differences were not found in the two ITSs; the only exception was Saccharomonospora glauca K194, which differed from other S. glauca strains by 1 bp in the 23S-5S ITS. The Saccharomonospora viridis strains had a smaller 16S-23S ITS region than the other strains, which may be useful for differentiating these organisms from other Saccharomonospora species. The characteristics of the two ITS regions make them more useful than 16S rRNA sequences as a tool for defining and identifying Saccharomonospora strains. However, Saccharomonospora azurea K161Thad two types of 23S-5S ITSs; rrnB, separated by Xho I digestion, had two additional nucleotides inserted between positions 52 and 55. Most of the 16S-23S and 23S-5S ITS sequences of S. azurea K161Tand strains of “Saccharomonospora caesia” were identical; the only exception was rrnB in S. azurea K161T. The lengths and levels of sequence divergence of the two ITSs of Saccharomonospora sp. strain K180 were different from the lengths and levels of sequence divergence of the ITSs of other species. These findings suggest that a taxonomic revision of the genus Saccharomonospora is necessary. Two trees based on 16S-23S and 23S-5S ITS sequences revealed distinct interspecific relationships in the genus Saccharomonospora.
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Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., Psychrophilic Bacteria Isolated from Antarctic Lacustrine and Sea Ice Habitats
More LessPsychrophilic, yellow-pigmented, seawater-requiring bacteria isolated from the pycnocline of meromictic Burton Lake and from sea ice cores obtained in the Vestfold Hills (68°S, 78°E) in eastern Antarctica were characterized. Phenotypic analysis showed that the strains isolated formed two distinct taxa. The first taxon included nonmotile, nutritionally fastidious strains that were isolated from the pycnocline of Burton Lake. The cells of these strains were morphologically variant, ranging from vibrioid to ring shaped to coiled and filamentous; in addition, the strains were unable to metabolize carbohydrates or polysaccharides and had DNA G+C contents of 27 to 29 mol%. The strains of the second taxon, which were isolated from sea ice cores and from ice algal biomass, were saccharolytic, exhibited rapid gliding motility, were rodlike to filamentous, and had DNA G+C contents of 36 to 38 mol%. A 16S ribosomal DNA (rDNA) sequence analysis revealed that the two Antarctic taxa formed related but distinct lineages within the [Flexibacter] maritimus rRNA branch of the family Flavobacteriaceae. The levels of 16S rDNA sequence similarity between the taxa were 90.5 to 91.3%, while the levels of similarity to other members of the [F.] maritimus rRNA branch were 85 to 90%. The whole-cell lipid profiles of the Antarctic strains were mainly comprised of branched and unbranched monounsaturated C15to C17fatty acids. The presence of significant levels of the lipids a15:1 ω 10c and a17:1 ω 7c appeared to be useful biomarkers for the new Antarctic taxa and for differentiating these organisms from other members of the family Flavobacteriaceae. On the basis of polyphasic taxonomic data we propose that the new taxa are novel bacterial species designated Psychroserpens burtonensis gen. nov., sp. nov. (type strain, ACAM 188) and Gelidibacter algens gen. nov., sp. nov. (type strain, ACAM 536).
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Use of Ribotyping To Distinguish Bordetella bronchiseptica Isolates
More LessA total of 113 Bordetella bronchiseptica strains, isolated from 11 different host species worldwide, were characterized by ribotyping with restriction enzyme Pvu II. Sixteen distinct ribotypes were identified, and each ribotype contained five to seven restriction fragments ranging in size from 1.8 to 5.6 kb. Approximately 88% of the swine isolates were identified as ribotype 3 strains. Isolates from dogs also displayed little variation; 74.1% were found to be ribotype 4 strains. Strains obtained from the remaining nine host species belonged to 15 different ribotypes. There was no association between geographic location and ribotype. The technique which we used may be useful for epidemiologic studies in which the transmission of B. bronchiseptica, both within and between species, is investigated.
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16S rRNA Gene Sequence of Rubrobacter radiotolerans and Its Phylogenetic Alignment with Members of the Genus Arthrobacter, Gram-Positive Bacteria, and Members of the Family Deinococcaceae
More LessThe nearly complete sequence of the 16S rRNA gene of an extremely highly radiotolerant bacterium, Rubrobacter radiotolerans(reclassified from Arthrobacter radiotolerans based on chemical characteristics), was determined by PCR amplification of the genomic DNA followed by cloning of the amplified gene and sequencing by the dideoxynucleotide method. The sequence was aligned with the sequences of members of the genus Arthrobacter and also with the sequences of representatives of the gram-positive bacteria having high G+C contents and the family Deinococcaceae(radioresistant micrococci and their relatives). The results of our phylogenetic analysis confirmed that R. radiotolerans is not a member of the Arthrobacter group and thus supported the previous reclassification. Moreover, although it is radioresistant and has a high G+C content, R. radiotolerans is more closely related to the gram-positive bacteria with high G+C contents than to the radioresistant members of the Deinococcaceae.
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Actinomyces europaeus sp. nov., Isolated from Human Clinical Specimens
Ten strains of a hitherto undescribed catalase-negative, facultatively anaerobic, coryneform bacterium were isolated or collected by workers at three European clinical bacteriology laboratories or reference centers. These strains were isolated from humans, and most came from abscess material. Biochemical and chemotaxonomic characterization revealed that the strains belonged to the genus Actinomyces. The phenotypic features of the 10 strains were incompatible with the descriptions of the previously established Actinomyces species. A comparative 16S rRNA gene sequence analysis demonstrated that the previously undescribed strains constitute a new line in the genus Actinomyces. The name Actinomyces europaeus sp. nov. is proposed for these clinical isolates. The type strain is CCUG 32789A.
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rRNA Sequences and Evolutionary Relationships among Toxic and Nontoxic Cyanobacteria of the Genus Microcystis
A primary-structure analysis of the 16S rRNA gene was performed with 10 strains representing five described and one unidentified species of the genus Microcystis. The phylogenies determined illustrate the evolutionary affiliations among Microcystis strains, other cyanobacteria, and related plastids and bacteria. A cluster of 10 strains that included hepatotoxic isolates identified as Microcystis aeruginosa formed a monophyletic group. However, the genus Microcystis appeared to be polyphyletic and contained two strains that clustered with unicellular cyanobacteria belonging to the genus Synechococcus. The clustering of related Microcystis strains, including strains involved in the production of the cyclic peptide toxin microcystin, was consistent with cell morphology, gas vacuolation, and the low G+C contents of the genomes. The Microcystis lineage was also distinct from the lineage containing the unicellular genus Synechocystis and the filamentous, heterocyst-forming genus Nostoc. The secondary structure of a Microcystis 16S rRNA molecule was determined, and genus-specific sequence signatures were used to design primers that permitted identification of the potentially toxic cyanobacteria belonging to the genus Microcystis via DNA amplification.
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Discrimination of Members of the Family Pasteurellaceae Based on Polyamine Patterns
More LessIn a study of the classification of members of the family Pasteurellaceae, the polyamine patterns of 101 strains were analyzed. These strains included the type strains of species belonging to the genera Actinobacillus, Haemophilus, and Pasteurella and additional strains of selected species, as well as numerous unnamed strains. Members of the genus Actinobacillus sensu stricto were characterized by the presence of 1,3-diaminopropane as the predominant compound. In the majority of the species of the genus Haemophilus sensu stricto 1,3-diaminopropane was also the major compound in the polyamine pattern. In contrast, Haemophilus intermedius subsp. gazogenes and Haemophilus parainfluenzae were characterized by high levels of 1,3-diaminopropane, cadaverine, and putrescine. These results confirmed the findings of Dewhirst et al. (F. E. Dewhirst, B. J. Paster, I. Olsen, and G. J. Fraser, Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. Abt. 1 Orig. 279:35–44, 1993), who demonstrated that H. parainfluenzae is phylogenetically only distantly related to the type species of the genus Haemophilus, Haemophilus influenzae. The phylogenetic diversity of the genus Pasteurella sensu stricto determined by Dewhirst et al. was also reflected to some extent by different polyamine patterns. The common characteristics found in Pasteurella multocida, Pasteurella canis, Pasteurella dagmatis, Pasteurella stomatis, and Pasteurella sp. strain B were high levels of putrescine and spermidine and the presence of the unusual triamine sym-norspermidine. Pasteurella avium, Pasteurella gallinarum, and Pasteurella volantium contained high concentrations of 1,3-diaminopropane and spermidine. Pasteurella langaa contained only high concentrations of 1,3-diaminopropane, and Pasteurella anatis was characterized by the presence of 1,3-diaminopropane as the predominant compound and high levels of putrescine and spermidine. Our data demonstrate that polyamine patterns are useful for discrimination within the family Pasteurellaceae.
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Spiroplasma lampyridicola sp. nov., from the Firefly Beetle Photuris pennsylvanicus
Spiroplasma strain PUP-1Twas isolated from the gut fluids of a firefly beetle (Photuris pennsylvanicus) collected in Maryland. Cells of the strain were shown by dark-field microscopy to be helical, motile filaments. Ultrastructural examination by electron microscopy revealed filamentous cells bounded by a single cytoplasmic membrane and no evidence of a cell wall. The cells were not sensitive to 500 U of penicillin per ml and grew under aerobic conditions in M1D, SP-4, and M-2 broth formulations, as well as in conventional mycoplasma medium. The doubling times at 15, 20, 25, and 30°C were 83.1, 32.0, 14.9, and 9.8 h, respectively. Suboptimal growth occurred at 37°C, and no growth was apparent in cultures maintained at 10 or 40°C. The organism required cholesterol for growth and produced acid from glucose, fructose, and trehalose; arginine and urea were not hydrolyzed. The results of previous serological analyses of strain PUP-1Tindicated that the organism was not related to the then currently established Spiroplasma species or group representatives, and the organism was classified as the representative of group XIX. Additional testing of strain PUP-1Tagainst recently recognized Spiroplasma species or group representatives by both metabolism inhibition and deformation tests confirmed the unique serological status of the organism. The guanine-plus-cytosine content of the DNA was 26 ± 1 mol%, and the genome size was 1,375 kbp. These values clearly differentiate strain PUP-1Tfrom group XXI strain W115, with which it cross-reacted reciprocally at a low level in deformation and metabolism inhibition tests. We propose that strain PUP-1 (= ATCC 43206) should be recognized as the type strain of a new species, Spiroplasma lampyridicola.
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Spiroplasma chrysopicola sp. nov., Spiroplasma gladiatoris sp. nov., Spiroplasma helicoides sp. nov., and Spiroplasma tabanidicola sp. nov., from Tabanid (Diptera: Tabanidae) Flies
Four spiroplasma strains, DF-1T, TG-1T, TABS-2T, and TAUS-1T, all of which were isolated from deerflies or horseflies (Diptera: Tabanidae), were serologically distinct from previously described spiroplasma species, groups, and subgroups. Strain DF-1Toriginated from a Maryland deerfly (Chrysops sp.); strain TG-1Twas isolated from a Maryland horsefly (Tabanus gladiator); strain TAUS-1Toriginated from a member of the Tabanus abdominalis-limbatinevris complex of horseflies collected in Maryland; and strain TABS-2Twas isolated from a horsefly (Tabanus abactor) collected in Oklahoma. Cells of all of the strains appeared to be helical and motile when they were examined by dark-field microscopy. Cells of strain DF-1Tgrowing in M1D medium were short helices with less than six turns; the helical cells of the other strains were long and usually had six or more turns. The short cells of strain DF-1Tpassed through 450- and 300-nm filter pores with no reduction in titer, but the longer cells of the other strains were partially retained by 450-nm-pore-size filters. Electron microscopic examination of all of the strains revealed wall-less cells surrounded only by a single cytoplasmic membrane. All of the strains grew well in SP-4 liquid media and in conventional mycoplasma or M1D media supplemented with horse or fetal bovine serum. Strains TABS-2T, TAUS-1T, and DF-1Trequired serum or sterol for growth, but strain TG-1Twas able to grow in the absence of serum or sterol. The optimum temperatures for growth of the four strains varied from 30 to 32°C, and growth occurred at 10 to 37°C. All of the strains catabolized glucose but did not hydrolyze urea. Only strain DF-1Thydrolyzed arginine. The guanine-plus-cytosine contents of the DNAs of the strains were: DF-1T, 29 ± 1 mol%; TG-1T, 26 ± 1 mol%; TABS-2T, 27 ± 1 mol%; and TAUS-1T, 26 ± mol%. The genome sizes of strains DF-1Tand TAUS-1Twere 1,270 and 1,375 kbp, respectively. Strain DF-1 (= ATCC 43209), the representative of spiroplasma subgroup VIII-2, is designated the type strain of a new species, Spiroplasma chrysopicola. We also propose that strain TG-1T(= ATCC 43525T), the designated representative of group XXIII, should be placed in a new species, Spiroplasma gladiatoris. In addition, group XXXII spiroplasma strain TABS-2 (= ATCC 51746) is designated the type strain of Spiroplasma helicoides sp. nov., and group XXXIII representative strain TAUS-1 (= ATCC 51747) is designated the type strain of another new species, Spiroplasma tabanidicola.
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Spiroplasma montanense sp. nov., from Hybomitra Horseflies at Northern Latitudes in North America
Spiroplasma strain HYOS-1Twas isolated from a tabanid fly, Hybomitra opaca. The organism was serologically distinct from other spiroplasma species, groups, and subgroups and was recently designated the representative of spiroplasma group XXXI. The cells of strain HYOS-1T, as determined by light microscopy, were long motile helices. Electron microscopic examination revealed wall-less cells delimited by a single membrane. The cells passed through 450- and 300-nm filter pores with a 10-fold reduction in titer, but failed to pass through 100-nm pores. Strain HYOS-1Tgrew very well in most conventional medium formulations for spiro-plasmas or other mollicutes. The organism grew at temperatures ranging from 5 to 41°C, and the optimum temperature was 32°C. The doubling time at the optimum temperature was 0.7 h, one of the shortest values obtained for members of the genus Spiroplasma. The strain catabolized glucose and hydrolyzed arginine but not urea. Growth of the organism was stimulated by cholesterol and serum, but the strain was nevertheless able to grow in the absence of sterols or serum. The guanine-plus-cytosine content of the DNA was about 28 ± 1 mol%, and the genome size was 1,225 kbp. On the basis of the experimental results reported here and previously reported data, group XXXI strain HYOS-1 (= ATCC 51745) is designated the type strain of a new species, Spiroplasma montanense.
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Staphylococcus lutrae sp. nov., a New Coagulase-Positive Species Isolated from Otters
More LessPhenotypic and phylogenetic studies were performed with three strains of a catalase-positive, gram-positive, coccus-shaped bacterium isolated from otters. The results of a 16S rRNA gene sequence analysis demonstrated that these strains represent a hitherto unknown subline within the genus Staphylococcus. Based on the results of the phylogenetic analysis and phenotypic criteria, we propose that these bacteria should be classified as members of a new species, Staphylococcus lutrae. The type strain of S. lutrae is DSM 10244.
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Amaricoccus gen. nov., a Gram-Negative Coccus Occurring in Regular Packages or Tetrads, Isolated from Activated Sludge Biomass, and Descriptions of Amaricoccus veronensis sp. nov., Amaricoccus tamworthensis sp. nov., Amaricoccus macauensis sp. nov., and Amaricoccus kaplicensis sp. nov.
More LessThree isolates of gram-negative bacteria, strains Ben 102T, Ben 103T, and Ben 104T, were obtained in pure culture by micromanipulation from activated sludge biomass from wastewater treatment plants in Italy, Australia, and Macau, respectively. These isolates all had a distinctive morphology; the cells were cocci that usually were arranged in tetrads. Based on this criterion, they resembled other bacteria from activated sludge previously called “G” bacteria. On the basis of phenotypic characteristics and the results of 16S ribosomal DNA sequence analyses, the three isolates were very similar to each other, but were sufficiently different from their closest phylogenetic relatives (namely, the genera Rhodobacter, Rhodovulum, and Paracoccus in the α subdivision of the Proteobacteria) to be placed in a new genus, Amaricoccus gen. nov. Each of the three isolates represents a new species of the genus Amaricoccuś; strains Ben 102T, Ben 103T, and Ben 104Tare named Amaricoccus veronensis, Amaricoccus tamworthensis, and Amaricoccus macauensis, respectively. An isolate designated Ben 101T, which was isolated independently by Cech and Hartman in Kaplice, Czech Republic, was also characterized and belongs to the same genus. We propose that the isolate of Cech and Hartman should be placed in another new species, Amaricoccus kaplicensis.
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Bacillus salexigens sp. nov., a New Moderately Halophilic Bacillus Species
More LessBacillus salexigens sp. nov. is proposed based on the characteristics of six moderately halophilic, gram-positive, rod-shaped strains isolated from salterns and hypersaline soils located in different geographical areas of Spain. These strains were motile, formed endospores, were strictly aerobic, were catalase and oxidase positive, and contained peptidoglycan of the meso-diaminopimelic acid type in their vegetative cell walls. The DNA base compositions of these strains ranged from 36.3 to 39.5 mol%, and these organisms constitute a homology group with levels of DNA-DNA homology ranging from 73 to 100%. The 16S rRNA sequence of strain C-20MoT, which was used as the representative strain of these isolates, groups with the 16S rRNA sequences of members of the genus Bacillus, and the highest level of similarity is 95.4%. The type strain is strain C-20Mo (= ATCC 700290 = DSM 11483 = CCM 4646).
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Mycoplasma crocodyli sp. nov., a New Species from Crocodiles
Organisms with the typical characteristics of mycoplasmas were isolated from joints and lungs of crocodiles. The results of growth inhibition tests and immunobinding assays showed that the 24 mycoplasma strains isolated were identical and distinct from previously described Mycoplasma, Entomoplasma, Mesoplasma, and Acholeplasma species. These organisms represent a new species, for which the name Mycoplasma crocodyli is proposed. M. crocodyli ferments glucose and maltose, does not produce films and spots, does not hydrolyze arginine, esculin, and urea, reduces tetrazolium chloride, and possesses phosphatase activity. It lyses and adsorbs bovine, ovine, and rabbit erythrocytes. Cholesterol or serum is required for growth. The optimum growth temperature is 37°C. The G+C content of the DNA is 27.6 mol%. This organism causes exudative polyarthritis in crocodiles. The type strain of M. crocodyli is strain MP145 (= ATCC 51981).
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Streptomyces stramineus sp. nov., a New Species of the Verticillate Streptomycetes
More LessStrain NRRL 12292T, which produces the bleomycin-like antibiotics LL-BO1208α and LL-BO1208β forms umbels consisting of chains of smooth-surface ovoid spores that are borne on verticils on the aerial mycelia, indicating that it is a member of the verticillate group of the genus Streptomyces formerly classified in the genus Streptoverticillium. This strain was compared morphologically and physiologically to 54 other verticillate Streptomyces strains. The levels of DNA relatedness between strain NRRL 12292Tand 34 other verticillate Streptomyces strains, including strains representing at least 19 genetic species clusters, were also determined. Strain NRRL 12292Tis morphologically and physiologically distinct from the other verticillate strains studied, particularly because of the straw yellow color of its aerial mycelia and spore mass. DNA hybridization data support the uniqueness of this strain, since the levels of DNA relatedness between NRRL 12292Tand the other verticillate strains used in this study were low. Our data support designation of a new species, Streptomyces stramineus, whose type strain is NRRL 12292.
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Desulfuromonas thiophila sp. nov., a New Obligately Sulfur-Reducing Bacterium from Anoxic Freshwater Sediment
More LessA mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27T, was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27T is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27T belongs to the Desulfuromonas cluster in the recently proposed family “Geobacter-aceae” in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27T represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27T in this paper.
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Spiroplasma alleghenense sp. nov., a New Species from the Scorpion Fly Panorpa helena (Mecoptera: Panorpidae)
Spiroplasma strain PLHS-1T from the gut of a common scorpion fly (Panorpa helena) collected in the West Virginia Allegheny Mountains was distinct from other spiroplasma species, groups, and subgroups as determined by reciprocal serological metabolism inhibition and deformation tests. However, when this strain was used as an antigen, it cross-reacted extensively with representatives of other groups. Light microscopy and/or electron microscopy of cells of strain PLHS-1T revealed helical motile cells surrounded by a single cytoplasmic membrane. The strain was resistant to penicillin, which confirmed that it had no cell wall. The organism grew well in M1D and SP-4 liquid media, in 1% serum fraction medium, and in conventional horse serum medium. The optimum temperature for growth was 30°C, at which the doubling time was 6.4 h. Multiplication occurred at temperatures from 10 to 32°C. Strain PLHS-1T catabolized glucose, hydrolyzed arginine but not urea, and required sterol for growth. The guanine-plus-cytosine content of the DNA was 31 ± 1 mol%, and the genome size was 1,465 kbp. Strain PLHS-1 (= ATCC 51752) is designated the type strain of a new species, Spiroplasma alleghenense.
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Spiroplasma platyhelix sp. nov., a New Mollicute with Unusual Morphology and Genome Size from the Dragonfly Pachydiplax longipennis
Spiroplasma strain PALS-1T from the gut of the dragonfly Pachydiplax longipennis was shown to be distinct from other species, groups, and subgroups of the genus Spiroplasma as determined by reciprocal serological metabolism inhibition and deformation tests. However, this strain cross-reacted extensively with representatives of other groups when it was used as an antigen. Electron microscopy of cells of strain PALS-1T revealed cells surrounded by a single cytoplasmic membrane. Light microscopy revealed helical cells that exhibited twisting motility rather than rotatory or flexing motility. Variations in the tightness of coiling were transmitted from one end of the helix to the other. The strain was resistant to penicillin, which confirmed that no cell wall was present. The organism grew well in M1D and SP-4 liquid media under either aerobic or anaerobic conditions. Growth also occurred in 1% serum fraction medium and in conventional horse serum medium. The optimum temperature for growth was 30°C, at which the doubling time was 6.4 h. Multiplication occurred at temperatures from 10 to 32°C. Strain PALS-1T catabolized glucose and hydrolyzed arginine but not urea. The guanine-plus-cytosine content of the DNA was 29 ± 1 mol%. The genome size was 780 kbp, the smallest genome size in the genus Spiroplasma. Strain PALS-1 (= ATCC 51748) is designated the type strain of a new species, Spiroplasma platyhelix.
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Genomic Diversity of Several Corynebacterium Species Identified by Amplification of the 16S–23S rRNA Gene Spacer Regions
More LessIn order to investigate whether 16S–23S ribosomal DNA (rDNA) spacer region length polymorphisms are suitable identification of Corynebacterium strains at the species level, the 16S–23S rDNA intergenic spacer region strains belonging to 11 Corynebacterium species were studied by a PCR-based method. The lengths 16S–23S rDNA spacer regions varied from 394 to 585 bp, fragment lengths which are similar to those described for other genera. A single PCR profile was obtained for each of the following species: Corynebacterium renale, Corynebacterium urealyticum, Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium pseudodiphtheriticum, and Corynebacterium kutscheri. In contrast, two and three PCR patterns were detected for Corynebacterium minutissimum, Corynebacterium striatum, Corynebacterium amycolatum, and Corynebacterium jeikeium, suggesting that genomic heterogeneity occurs in these four species. The 16S–23S rDNA spacer region length polymorphisms allowed us to discriminate among C. minutissimum, C. striatum, and C. amycolatum, three species that are frequently isolated and misidentified in clinical laboratories. Type strain Corynebacterium xerosis ATCC 373, which exhibited a PCR pattern similar to that of C. amycolatum strains classified in PCR group I, could nevertheless be discriminated from PCR group II (C. amycolatum) strains, as Well as minutissimum and C. striatum strains. Type strain C. xerosis ATCC 373 and C. amycolatum strains classified PCR group I could not be distinguished from strains belonging to C. diphtheriae, C. ulcerans, and C. pseudodiphtheriticum. The lipophilic species C. urealyticum and C. jeikeium, which are frequently encountered in clinical specimens, could be clearly distinguished from each other by this method. The use of 16S–23S spacer region length data determined by PCR-mediated amplification is suitable for identification of several Corynebacterium species. This rapid and easy method may be a useful identification tool for clinical microbiologists.
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Sagittula stellata gen. nov., sp. nov., a Lignin-Transforming Bacterium from a Coastal Environment
More LessA numerically important member of marine enrichment cultures prepared with lignin-rich, pulp mill effluent was isolated. This bacterium was gram negative and rod shaped, did not form spores, and was strictly aerobic. The surfaces of its cells were covered by blebs or vesicles and polysaccharide fibrils. Each cell also had a holdfast structure at one pole. The cells formed rosettes and aggregates. During growth in the presence of lignocellulose or cellulose particles, cells attached to the surfaces of the particles. The bacterium utilized a variety of monosaccharides, disaccharides, amino acids, and volatile fatty acids for growth. It hydrolyzed cellulose, and synthetic lignin preparations were partially solubilized and mineralized. As determined by 16S rRNA analysis, the isolate was a member of the α subclass of the phylum Proteobacteria and was related to the genus Roseobacter. A signature secondary structure of the 16S rRNA is proposed. The guanine-plus-cytosine content of the genomic DNA was 65.0 mol%. On the basis of the results of 16S rRNA sequence and phenotypic characterizations, the isolate was sufficiently different to consider it a member of a new genus. Thus, a novel genus and species, Sagittula stellata, are proposed; the type strain is E-37 (= ATCC 700073).
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Description of Three New Species of the Genus Peptostreptococcus from Human Clinical Specimens: Peptostreptococcus harei sp. nov., Peptostreptococcus ivorii sp. nov., and Peptostreptococcus octavius sp. nov.
More LessIn a previous investigation of the laboratory identification of clinical strains of the genus Peptostreptococcus, several isolates were found to be atypical. In this study, we further examined these strains by using both phenotypic and genotypic methods. Based on our findings, we describe the following three new species of the genus Peptostreptococcus from human clinical specimens: Peptostreptococcus harei, whose type strain is DSM 10020 (isolated from a sacral sore); Peptostreptococcus ivorii, whose type strain is DSM 10022 (isolated from a leg ulcer); and Peptostreptococcus octavius, whose type strain is NCTC 9810 (isolated from nasal flora). An analysis of their 16S rRNA gene sequences indicated that all three species are related to Clostridium cluster XIII, which includes most species of the genus Peptostreptococcus. The phenotypic characteristics of the new species are described.
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Bogoriella caseilytica gen. nov., sp. nov., a New Alkaliphilic Actinomycete from a Soda Lake in Africa
More LessA new gram-positive, alkaliphilic, nonsporulating, rod-shaped bacterium is described. The organism was isolated from soda soil (Lake Bogoria, Kenya) and has the following characteristics. It is nonmotile, not acid fast, halotolerant, and microaerophilic, and optimal growth occurs at pH values between 9 and 10. The peptidoglycan type is of type A4α, with lysine as the characteristic diamino acid and glutamic acid as a component of the interpeptide bridge. The major menaquinone is MK-8(H4). The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and an unknown phospholipid. 12-Methyltetradecanoic acid is the predominant fatty acid. The G+C content of the DNA is 70 mol%. The results of 16S ribosomal DNA sequence comparisons revealed that strain HKI 0088T represents a new lineage in the order Actinomycetales. Therefore, we concluded that strain HKI 0088T should be assigned to a new genus and species, for which we propose the name Bogoriella caseilytica gen. nov., sp. nov. The type strain and only strain of this genus and species is HKI 0088 (= DSM 11294).
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Composition of Mycolic Acid Molecular Species as a Criterion in Nocardial Classification
More LessBy using gas chromatography and gas chromatography-mass spectrometry, we analyzed the mycolic acid compositions of 18 strains of Nocardia asteroides, 17 strains of Nocardia farcinica, and 17 strains of Nocardia nova classified by numerical taxonomy. These organisms had characteristic mycolic acid compositions. We calculated the peak areas of the molecular species of mycolic acids on gas chromatograms and determined the average total carbon number in each strain. The strains of N. asteroides were divided into five groups, and the type strain belonged to group C54. The strains of N. farcinica were divided into three groups, and the type strain was in group C53. On the other hand, the strains of N. nova differed distinctly from the other two species and belonged mainly to groups C56 and C57. Our detailed analysis of mycolic acids was simple and precise. Therefore, the use of this method should be encouraged more for nocardial classification in combination with DNA or RNA analysis.
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Characterization of Bordetella Strains and Related Bacteria by Amplified Ribosomal DNA Restriction Analysis and Randomly and Repetitive Element-Primed PCR
More LessAmplified ribosomal DNA restriction analysis (ARDRA) in which the almost complete 16S rRNA gene was used as the target of the PCR assay and randomly and repetitive element-primed PCR were used to characterize 67 strains belonging to the family Alcaligenaceae. Particular emphasis was placed on strains of Bordetella pertussis (13 strains), Bordetella parapertussis (10 strains), and Bordetella bronchiseptica (10 strains) (these organisms were referred to as the B. bronchiseptica group), as well as Bordetella avium (19 strains). Our data indicate that strains belonging to the B. bronchiseptica group behave as a single species comparable to strains of B. avium. ARDRA allowed us to differentiate among all other species as well but was not useful for infraspecific typing. Randomly and repetitive element-primed PCR could be used to distinguish several infraspecific types within B. avium and the B. bronchiseptica group and allowed us to differentiate these two taxa.
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A Polyphasic Reassessment of the Genus Aneurinibacillus, Reclassification of Bacillus thermoaerophilus (Meier-Stauffer et al. 1996) as Aneurinibacillus thermoaerophilus comb, nov., and Emended Descriptions of A. aneurinilyticus corrig., A. migulanus, and A. thermoaerophilus
Fifty-three strains representing 25 species of aerobic endospore-forming bacteria, of which 11 (37 strains) belong to the genera Aneurinibacillus and Brevibacillus (Bacillus rRNA group 4 of Ash et al. [Lett. Appl. Microbiol. 13:202–206, 1991]), were characterized genotypically by amplified ribosomal DNA restriction analysis (ARDRA) and/or phenotypically by fatty acid methyl ester analysis, sodium dodecylsulfate-polyacrylamide gel electrophoresis of whole-cell proteins, pyrolysis mass spectrometry, 99 API Biotype 100 assimilation tests, and 16 other routine phenotypic tests. ARDRA revealed that Aneurinibacillus aneurinilyticus, Aneurinibacillus migulanus, and Bacillus thermoaerophilus formed a cluster quite separate from Brevibacillus species, supporting the distinction of both genera and the transfer of B. thermoaerophilus to the genus Aneurinibacillus. Two of the species, A. aneurinilyticus (the type species) and A. migulanus, are phenotypically and genotypically quite similar but can be distinguished from each other by several phenotypic characters. Phenotypic differentiation at the generic level is also described.
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Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a New Anaerobic, Slightly Halophilic, Thiosulfate-Reducing Bacterium from Corroding Offshore Oil Wells
A strictly anaerobic thiosulfate-reducing bacterium was isolated from a corroding offshore oil well in Congo and was designated strain SEBR 4207T. Pure culture of the strain induced a very active pitting corrosion of mild steel, with penetration rates of up to 4 mm per year. This constitutes the first experimental evidence of the involvement of thiosulfate reduction in microbial corrosion of steel. Strain SEBR 4207T cells were vibrios (3 to 5 by 1 µm), stained gram negative, and possessed lateral flagella. Spores were not detected. Optimum growth occurred in the presence of 3% NaCl at pH 7.0 and 42°C. Strain SEBR 4207T utilized peptides and amino acids, but not sugars or fatty acids. It fermented serine, histidine, and Casamino Acids, whereas arginine, glutamate, leucine, isoleucine, alanine, valine, methionine, and asparagine were only used in the presence of thiosulfate. Peptides were fermented to acetate, isobutyrate, isovalerate, 2-methylbutyrate, H2, and CO2. The addition of either thiosulfate or sulfur but not sulfate increased peptide utilization, growth rate, and biomass; during growth, H2S was produced and a concomitant decrease in H2 was observed. The addition of either thiosulfate or sulfur also reversed H2 inhibition. 16S rRNA sequence analysis indicates that strain SEBR 4207T is distantly related to members of the genus Thermoanaerobacter (83% similarity). Because the phenotypic and phylogenetic characteristics cannot be assigned to any described genus, strain SEBR 4207T is designated as a new species of a new genus, Dethiosulfovibrio peptidovorans gen. nov., sp. nov. Strain SEBR 4207T has been deposited in the Deutsche Sammlung von Mikroorganismen und zellkulturen GmbH (= DSM 11002).
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Propionibacterium cyclohexanicum sp. nov., a New Acid-Tolerant ω-Cyclohexyl Fatty Acid-Containing Propionibacterium Isolated from Spoiled Orange Juice
More LessA non-spore-forming, coryneform bacterium, strain TA-12T, was isolated from spoiled off-flavor orange juice. Growth of this organism occurs at pH 3.2 to 7.5, and optimum growth occurs at pH values between 5.5 and 6.5. This organism produces lactic acid, propionic acid, and acetic acid from glucose. It is catalase negative. The cells are heat resistant and can withstand a temperature of 90°C for 10 min. The DNA G+C content is 66.8 mol%. This strain has an MK-9(H4) respiratory quinone system and contains meso-diaminopimelic acid in its cell wall, and ω-cyclohexyl undecanoic acid is the major cellular fatty acid. The results of a phylogenetic analysis of the 16S rRNA gene of this organism indicated that its highest level of homology is its level of homology with the representative of the classical propionibacteria, Propionibacterium freudenreichii (97.1%). Strain TA-12T is phenotypically similar to P. freudenreichii, but it produces a large amount of lactic acid and has a distinct fatty acid composition, acid tolerance, and heat resistance, which differentiate it from P. freudenreichii and other propionic acid-producing bacteria. On the basis of these findings we propose the name Propionibacterium cyclohexanicum sp. nov. for this organism. The type strain is TA-12 (= IAM 14535 = NRIC 0247).
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Tetragenococcus muriaticus sp. nov., a New Moderately Halophilic Lactic Acid Bacterium Isolated from Fermented Squid Liver Sauce
More LessA total of 11 strains of moderately halophilic histamine-producing bacteria isolated from fermented squid liver sauce were studied phenotypically, genotypically, and phylogenetically. These strains are considered members of the genus Tetragenococcus based on their physiological, morphological, and chemotaxonomic characteristics. A16S rRNA gene sequence analysis showed that these strains clustered with, but were separate from, Tetragenococcus halophilus. The results of DNA-DNA hybridization experiments indicated that the new isolates represent a new Tetragenococcus species, for which we propose the name Tetragenococcus muriaticus; strain X-1 (= JCM 10006) is the type strain of this species.
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Phylogenetic Relationship of the Twenty-One DNA Groups of the Genus Acinetobacter as Revealed by 16S Ribosomal DNA Sequence Analysis
More LessThe inter- and intrageneric relationships of members of the genus Acinetobacter were investigated by performing a comparative sequence analysis of PCR-amplified 16S ribosomal DNAs (rDNAs) from 21 strains representing all of the DNA groups that have been described. Phylogenetic treeing confirmed that Acinetobacter spp. form a coherent cluster within the gamma subdivision of the class Proteobacteria that includes strains with overall levels of 16S rDNA sequence similarity of more than 94%. The analysis of intrageneric relationships suggested that the majority of the strains cluster in five clearly distinguishable clusters, and this conclusion was supported by the results obtained with the different methods used for phylogenetic analysis (i.e., the maximum-likelihood, parsimony, and distance matrix methods). The first cluster contains the representatives of DNA groups 2 (Acinetobacter baumannii) and TU13, whereas the second cluster comprises representatives of DNA groups 3, “Close To TU13,” and “between 1 and 3.” The representatives of closely related Acinetobacter DNA groups 8 (Acinetobacter lwoffii) and 9 belong to the third cluster, which includes the representative of DNA group 6 as well. The fourth cluster is formed by DNA groups BJ15, BJ16, and BJ17, and the fifth cluster comprises DNA groups 1 (Acinetobacter calcoaceticus), BJ14,10, and 11. Within the fifth cluster the 16S rDNA sequences of DNA group 10 and 11 strains are nearly identical. The representatives of DNA groups 4 (Acinetobacter haemolyticus), 5 (Acinetobacter junii), 7 (Acinetobacter johnsonii), 12 (Acinetobacter radioresistens), TU14, and TU15 form individual branches that are not significantly affiliated with any of the five clusters identified. Apart from the clustering of the most closely related DNA groups, the general topology of the distance dendrogram revealed some discrepancy with previous DNA-DNA hybridization data, which may point to the inadequacy of comparative 16S rDNA sequence analysis for reflecting true evolutionary relationships of closely related bacterial taxa. Important, however, was the presence of unique sequence motifs in each of the 21 different DNA groups studied, which may be useful for rapid differentiation of DNA groups of the genus Acinetobacter.
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Treponema amylovorum sp. nov., a Saccharolytic Spirochete of Medium Size Isolated from an Advanced Human Periodontal Lesion †
More LessA highly motile, medium-size, saccharolytic spirochete was isolated from an advanced human periodontal lesion in medium OMIZ-Pat supplemented with 1% human serum. The growth of this organism is dependent on either glucose, maltose, starch, or glycogen. The cells contain six endoflagella, three per pole, which overlap in the central region of the cell body. On the basis of its cell morphology and enzyme activities, as well as its sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein and antigen profiles, this organism is clearly distinct from all previously cultured spirochetes. The presence of a novel species is supported by the 16S rRNA sequence of this organism, which places it in phylotype 19 of Choi et al. (B. K. Choi, B. J. Paster, F. E. Dewhirst, and U. B. Göbel, Infect. Immun. 62:1889–1895, 1994). The only isolate, strain HA2P, is designated the type strain of a novel species, for which we propose the name Treponema amylovorum.
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Pseudomonas monteilii sp. nov., Isolated from Clinical Specimens
More LessWe propose the name Pseudomonas monteilii for a new species of gram-negative, rod-shaped, motile bacteria that were nonhemolytic on blood agar and were isolated from clinical sources. The 10 strains of P. monteilii were incapable of liquefing gelatin. They grew at 10°C but not at 41°C, produced fluorescent pigments, catalase, and cytochrome oxidase, and possessed the arginine dihydrolase system. They were capable of respiratory but not fermentative metabolism. They did not hydrolyze esculin or starch and were able to use benzylamine, α-aminobutyrate, d-ribose, l-arabinose, butyrate, valerate, isovalerate, isobutyrate, inositol, phenylacetate, d-ala-nine, and amylamine. They possessed l-phenylalanine arylamidase, l-lysine arylamidase, l-alanine arylamidase, γ-glutamyl-transferase, glycyl-phenylalanine arylamidase, l-tryptophan arylamidase, glycyl-l-alanine arylamidase, esterase C4, esterase C6, esterase C8, esterase C9, esterase C10, and esterase C18. DNA relatedness studies revealed that P. monteilii strains formed a homogeneous DNA hybridization group. A total of 57 strains representing previously described or partially characterized taxa belonging to the genus Pseudomonas were 6 to 54% related to P. monteilii. The highest hybridization values were obtained with strains belonging to or related to Pseudomonas putida biovar A. The average G+C content of the DNA was 60.5 ± 0.5 mol% for four of the P. monteilii strains studied. The type strain of P. monteilii is CFML 90-60 (= CIP 104883); it was isolated from bronchial aspirate and has a G+C content of 60 mol%. The clinical significance of these organisms is not known.
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Diversity of Alkaliphilic Halobacteria: Proposals for Transfer of Natronobacterium vacuolatum, Natronobacterium magadii, and Natronobacterium pharaonis to Halorubrum, Natrialba, and Natronomonas gen. nov., Respectively, as Halorubrum vacuolatum comb. nov., Natrialba magadii comb. nov., and Natronomonas pharaonis comb. nov., Respectively
More LessThe 16S rRNA genes of three species of the genus Natronobacterium (Natronobacterium gregoryi, Natronobacterium pharaonis, and Natronobacterium vacuolatum) were sequenced and compared to that of the previously sequenced species Natronobacterium magadii. The sequences revealed that Natronobacterium pharaonis was phylogenetically distinct from the other members of the genus and also from other recognized genera of the family Halobacteriaceae. However, Natronobacterium vacuolatum and Natronobacterium magadii were found to be most closely related to the genera Halorubrum and Natrialba, respectively. An unidentified haloalkaliphile, strain SSL1, was also closely related to Natronobacterium magadii and Natrialba asiatica. On the basis of phylogenetic tree reconstructions, signature bases specific for individual genera, and sequences of spacer regions between 16 and 23S rRNA genes, we propose the following changes: Natronobacterium pharaonis to be transferred to Natronomonas gen. nov. as Natronomonas pharaonis gen. nov., comb. nov.; Natronobacterium vacuolatum to be transferred to the genus Halorubrum as Halorubrum vacuolatum comb. nov.; and Natronobacterium magadii to be transferred to the genus Natrialba as Natrialba magadii.
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Rearrangements in the Genomes of Vibrio cholerae Strains Belonging to Different Serovars and Biovars
The intron-encoded enzyme I-CeuI provides an excellent tool for rapidly examining the organization of genomes of related species of bacteria. Vibrio cholerae strains belonging to serovars O1 and O139 have 9 I-CeuI sites in their genomes, and V. cholerae strains belonging to serovars non-Ol and non-O139 have 10 I-CeuI sites in their genomes. This information can be used as a criterion to differentiate O1 strains from non-O1 and non-O139 strains. To our knowledge, intraspecies variation in the number of rrn operons has not been reported in any other organism. Our data revealed extensive restriction fragment length polymorphism based on a comparison of the I-CeuI digestion profiles of strains belonging to different serovars and biovars. From the analysis of partial digestion products, I-CeuI macrorestriction maps of several classical, E1 Tor, and O139 strains were constructed. While the linkage maps are conserved within biovars, linkage maps vary substantially between biovars.
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Inter- and Intraspecies Comparison of the 16S-23S rRNA Operon Intergenic Spacer Regions of Six Listeria spp.
More LessThe 16S-23S rRNA intergenic spacer (IGS) regions found in six Listeria species were characterized. PCR amplification of the 16S-23S IGS with a “generic primer” set generated products of about 340 bp (small) and 550 to 590 bp (large) with DNA from all Listeria strains tested. Seven Listeria monocytogenes serotype 4b strains and one L. monocytogenes serotype 4d strain also had an additional PCR product of ca. 360 bp. The 360-bp PCR product from one of these L. monocytogenes serotype 4b strains was identical in nucleotide sequence to the small 340-bp IGS, except that it contained an 18-bp tandem repeat. The small rRNA IGSs of L. innocua, L. ivanovii, L. seeligeri, L. welshimeri, and L. grayi were 83 to 99% homologous to that of L. monocytogenes. The large rRNA IGS of L. monocytogenes was 81 to 96% homologous to those of the other Listeria species and agreed with current taxonomic division among these species. The nucleotide sequences of the central 274 bp of the large rRNA IGS of strains from seven different L. monocytogenes serotypes were highly homologous; however, serotype-specific differences were noted, and four groups were identified within L. monocytogenes based on this analysis.
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Rhizobium hainanense sp. nov., Isolated from Tropical Legumes
More LessA fast-growing rhizobial group isolated from leguminous plants in Hainan Province, a tropical region of China, is proposed as a new Rhizobium species on the basis of 16S rRNA gene sequencing, DNA-DNA hybridization, and phenotypic characterization. This new species belongs to the phylogenetic branch which includes Rhizobium leguminosarum. We propose the name Rhizobium hainanense sp. nov. for this species. The strain CCBAU 57015 (166) is the type strain; it has been deposited in the culture collection of Beijing Agricultural University, People’s Republic of China.
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Phylogenetic and Genetic Relationships of Mesorhizobium tianshanense and Related Rhizobia
More LessThe genetic and phylogenetic relationships for strains of Mesorhizobium tianshanense and its relatives were compared by an analysis of the results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins, DNA-DNA hybridization, and full 16S rRNA gene sequencing. The strains of M. tianshanense formed a cluster which was distinct from those of other rhizobium species in the clustering analysis of SDS-PAGE. DNA-DNA relatedness between A-1BS (type strain of M. tianshanense) and the type or reference strains for Mesorhizobium loti, M. huakuii, M. ciceri, M. mediterraneum, and cluster U, an unnamed rhizobial group, ranged from 4.4 to 43.8%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that M. tianshanense was closely related to the Mesorhizobium phylogenetic branch and could be distinguished from the other four species in this branch. These results further confirmed that these bacteria constitute a distinct rhizobial species.
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Phenotypic and Phylogenetic Characterization of Some Globicatella-Like Organisms from Human Sources: Description of Facklamia hominis gen. nov., sp. nov.
AbstractSix strains of a hitherto undescribed gram-positive, catalase-negative, facultatively anaerobic coccus from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically homogeneous and constitute a new line closely related to, but distinct from, the genus Globicatella. The unknown bacterium was readily distinguished from Globicatella sanguis, the type species of the genus Globicatella, by the results of biochemical tests and an electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, we propose that the unknown bacterium be classified as Facklamia hominis gen. nov., sp. nov. The type strain of Facklamia hominis is CCUG 36813.
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Identification of Rickettsiae Isolated in Japan as Coxiella burnetii by 16S rRNA Sequencing
AbstractThe 16S rRNA genes of Japanese Coxiella isolates obtained from various sources and geographical areas were directly sequenced by dideoxynucleotide chain termination methods in which Taq DNA polymerase was used. The levels of sequence similarity among Japanese, European, and American isolates were more than 99%, and the Japanese isolates were identified as Coxiella burnetii. C. burnetii strains isolated worldwide, including Japan, were found to be very similar.
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Actinomyces graevenitzii sp. nov., Isolated from Human Clinical Specimens
AbstractFour strains of a previously unknown, catalase-negative, facultatively anaerobic, gram-positive, rod-shaped organism originating from humans were characterized by biochemical, chemical, and molecular taxonomic methods. The four strains phenotypically closely resembled one another, and although they possessed characteristics consistent with membership in the genus Actinomyces, they differed from all previously recognized species of this genus. The results of comparative 16S rRNA gene sequencing studies demonstrated that the unknown human bacterium was phylogenetically a member of the genus Actinomyces. Within the genus Actinomyces, the unidentified bacterium formed a loose, but statistically significant, association with a subgroup which included Actinomyces bovis, the type species of the genus. 16S rRNA sequence divergence values of >6%, however, unequivocally demonstrated that the unidentified bacterium represents a new subline of the genus Actinomyces. A new species, Actinomyces graevenitzii, is proposed for the four new isolates. The type strain of A. graevenitzii is CCUG 27294.
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Reclassification of Desulfovibrio desulfuricans Norway 4 as Desulfomicrobium norvegicum comb. nov. and Confirmation of Desulfomicrobium escambiense (corrig., Formerly “escambium” ) as a New Species in the Genus Desulfomicrobium
More LessAbstractDesulfomicrobium escambiense, Desulfomicrobium baculatum, Desulfomicrobium apsheronum, and Desulfovibrio desulfuricans Norway 4 are closely related as determined by a 16S rRNA comparison (levels of relatedness, 0.976 to 0.997) and are distinct on the basis of levels of DNA-DNA similarity (11.1 to 27.4%), genomic restriction fragment length polymorphism patterns, and certain phenotypic characteristics. We proposed that Desulfovibrio desulfuricans Norway 4 be renamed Desulfomicrobium norvegicum comb. nov.
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The Tannin-Degrading Species Streptococcus gallolyticus and Streptococcus caprinus Are Subjective Synonyms
More LessAbstractThe tannin-degrading species Streptococcus gallolyticus and Streptococcus caprinus have been shown to be subjective synonyms on the basis of their levels of 16S rRNA sequence similarity (98.3%) and DNA-DNA homology (>70%) and the phenotypes of their type strains. S. gallolyticus has nomenclatural priority according to Rule 24b(2) of the International Code of Nomenclature of Bacteria.
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Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov.
AbstractReasons are advanced for removal of Rhizobium ciceri, Rhizobium huakuii, Rhizobium loti, Rhizobium mediterraneum, and Rhizobium tianshanense from the genus Rhizobium and for establishment of Mesorhizobium gen. nov. for these species. A description of the genus Mesorhizobium and amended descriptions of Mesorhizobium ciceri, Mesorhizobium huakuii, Mesorhizobium loti, Mesorhizobium mediterraneum, and Mezorhizobium tianshanense are provided.
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Characterization of Some Actinomyces-Like Isolates from Human Clinical Specimens: Reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and Description of Actinobaculum schaalii sp. nov.
More LessAbstractFive strains of a hitherto unknown Actinomyces-like bacterium were isolated from human clinical sources, including blood cultures. Biochemical and chemotaxonomic characterization indicated that the strains were distinct from previously described Actinomyces and Arcanobacterium species. A comparative 16S rRNA gene sequence analysis demonstrated that the undescribed strains constitute a new subline within the Actinomyces-Arcanobacterium species complex. The closest known relative of the isolates was found to be Actinomyces suis, although a 16S rRNA sequence divergence value of approximately 6% clearly demonstrated that the unknown bacterium represents a distinct species. Based on the results of the present and earlier phylogenetic investigations, it is proposed that Actinomyces suis should be reclassified in a new genus, the genus Actinobaculum, as Actinobaculum suis comb. nov. In addition, a new species, Actinobaculum schaalii, is proposed for the Actinomyces-like bacterium from human sources. The type strain of Actinobaculum schaalii is CCUG 27420.
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- Matters Relating To The International Committee On Systematic Bacteriology
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Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis
More LessAbstractOur phylogenetic analysis based on 16S ribosomal DNA (rDNA) sequences and chemotaxonomic analyses showed that Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 are more closely related to the genus Rhodococcus, especially Rhodococcus erythropolis, than to the genus Nocardioides. N. simplex ATCC 13260 and N. simplex ATCC 19565 and ATCC 19566 exhibited levels of 16S rDNA similarity of 99.4 and 100%, respectively, to R. erythropolis DSM 43066T. Strains ATCC 13260, ATCC 19565, and ATCC 19566 had meso-diaminopimelic acid in their peptidoglycan and MK-8(H2) as their predominant menaquinone. These three strains produced cellular fatty acid patterns similar to those of R. erythropolis strains rather than those of Nocardioides species. Therefore, N. simplex ATCC 13260, ATCC 19565, and ATCC 19566 should be reclassified as strains of R. erythropolis Gray and Thornton 1928.
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Taxonomic Note: Necessary Correction of Specific Epithets Formed as Substantives (Nouns) “in Apposition”
More LessAbstractForming Latin species names (specific epithets) as “nominative nouns in apposition” (according to Rule 12c of the International Code of Nomenclature of Bacteria) has often been misunderstood or posed problems. Here, this grammatical construction is explained, and 24 cases that did not meet the requirements for this type of construction are corrected to a genitive noun or adjectival form in agreement with Rule 12c.
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Rejection of Lactobacillus panis (Wiese et al. 1996) Request for an Opinion
More LessAbstractLactobacillus panis (Wiese et al. 1996) has not been validly published because type strain DSM 6035 is not available from any culture collection. The lack of an available type strain is not consistent with Principle 1 of the International Code of Nomenclature of Bacteria: Bacteriological Code and may cause confusion if taxonomists are not able to compare new Lactobacillus isolates with an L. panis type strain. We request an opinion which indicates whether the name L. panis should be rejected. In addition, on behalf of the Subcommittee on Taxonomy of Bifidobacterium, Lactobacillus, and Related Organisms, we strongly support an emendation of Rule 30 of the Bacteriological Code proposed by the Judicial Commission of the International Committee on Systematic Bacteriology in Jerusalem in 1996. This emendation would make mandatory the availability of a type strain of a new species from a culture collection and thus would prevent descriptions of invalidly published species.
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- Errata
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