- Volume 47, Issue 2, 1997
Volume 47, Issue 2, 1997
- Original Papers Relating To Systematic Bacteriology
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The Phylogeny of the Genera Chryseomonas, Flavimonas, and Pseudomonas Supports Synonymy of These Three Genera
More LessAbstractThe 16S rRNA sequences of Chryseomonas luteola, the type species of the genus Chryseomonas, and Flavimonas oryzihabitans, the type species of the genus Flavimonas, were determined. These sequences were compared with the sequences of 27 representative strains of the genus Pseudomonas. C. luteola and F. oryzihabitans were located in the cluster that contains Pseudomonas aeruginosa, the type species of genus Pseudomonas Migula 1894, and the levels of 16S rRNA sequence homology between P. aeruginosa and the other two species were more than 93.9%. All of the strains of the genus Pseudomonas sensu stricto whose sequences have been determined were included in the P. aeruginosa cluster. These results suggested that Chryseomonas, Flavimonas, and Pseudomonas are synonymous, and we concluded that Chryseomonas and Flavimonas are junior subjective synonyms of Pseudomonas.
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Citrate Synthase Gene Comparison, a New Tool for Phylogenetic Analysis, and Its Application for the Rickettsiae †
More LessAbstractUsing PCR and an automated laser fluorescent DNA sequencer, we amplified and sequenced a 1,234-bp fragment of the citrate synthase-encoding gene (gltA) of 28 bacteria belonging to the genus Rickettsia. Comparative sequence analysis showed that most of the spotted fever group (SFG) rickettsiae belonged to one of two subgroups. The first subgroup included Rickettsia massiliae, strain Bar 29, Rickettsia rhipicephali, “Rickettsia aeschlimanni,” and Rickettsia montana, which have been isolated only from ticks. The second subgroup was larger and included the majority of the human pathogens and also rickettsiae isolated only from ticks; the members of this subgroup were strain S, Rickettsia africae, “Rickettsia mongolotimonae,” Rickettsia sibirica, Rickettsia parken, Rickettsia conorii, Rickettsia rickettsii, the Thai tick typhus rickettsia, the Israeli tick typhus rickettsia, the Astrakhan fever rickettsia, “Rickettsia slovaca,” and Rickettsia japonica. The sequence analysis also showed that the tick-borne organisms Rickettsia helvetica and Rickettsia australis and the mite-borne organism Rickettsia akari were associated with the SFG cluster; that Rickettsia prowazekii and Rickettsia typhi, two representatives of the typhus group, clustered together; and that Rickettsia canada, Rickettsia bellii, and the AB bacterium probably represent three new groups. We compared the phylogenetic trees inferred from citrate synthase gene sequences and from 16S ribosomal DNA (rDNA) sequences. For rickettsial phylogeny, the citrate synthase approach was more suitable, as demonstrated by significant bootstrap values for all of the nodes except those in the larger subgroup defined above. We also compared phylogenetic analysis results obtained in a comparison of the sequences of both genes for all of the representatives of the domain Bacteria for which the gltA sequence was determined. We believe that comparison of gltA sequences could be a complementary approach to 16S rDNA sequencing for inferring bacterial evolution, especially when unstable phylogenetic models are obtained from ribosomal sequences because of high levels of sequence similarity between the bacteria studied.
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“Candidatus Phytoplasma australiense,” a New Phytoplasma Taxon Associated with Australian Grapevine Yellows
More LessAbstractA phytoplasma was detected in naturally diseased ‘Chardonnay’ grapevines exhibiting symptoms of Australian grapevine yellows disease. The use of PCR designed to amplify phytoplasma DNA resulted in detection of phytoplasma DNA in all of the diseased plants examined; no phytoplasma DNA was detected in healthy seedling grapevines. The collective restriction fragment length polymorphism (RFLP) patterns of amplified 16S ribosomal DNA differed from the patterns described previously for other phytoplasmas. On the basis of the RFLP patterns, Australian grapevine yellows phytoplasma was classified as a representative of a new subgroup, designated subgroup 16SrI-J, in phytoplasma 16S rRNA group 16SrI (aster yellows and related phytoplasmas). A phylogenetic analysis in which parsimony of 16S rRNA gene sequences from this and other group 16SrI phytoplasmas was used identified the Australian grapevine yellows phytoplasma as a member of a distinct subclade (subclade xii) in the phytoplasma clade of the class Mollicutes. A phylogenetic tree constructed on the basis of 16S rRNA gene sequences was consistent with the hypothesis that there was divergent evolution of Australian grapevine yellows phytoplasma and its closet known relative, European stolbur phytoplasma (subgroup 16SrI-G), from a common ancestor. The unique properties of the DNA from the Australian grapevine yellows phytoplasma clearly establish that it represents a new taxon, “Candidatus Phytoplasma australiense.”
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Polyamine Distribution in Actinomycetes with Group B Peptidoglycan and Species of the Genera Brevibacterium, Corynebacterium, and Tsukamurella
More LessAbstractPolyamine patterns of 75 strains of actinobacteria belonging to the genera Agrococcus, Agromyces, Aureobacterium, Brevibacterium, Clavibacter, Corynebacterium, Curtobacterium, Microbacterium, Rathayibacter, and Tsukamurella were analyzed in order to investigate the suitability of this approach for differentiation within this group. The results revealed that the overall polyamine contents differ significantly among genera and that various patterns are present in actinobacteria. One characteristic pattern found in the genera Clavibacter, Rathayibacter, and Curtobacterium included a high polyamine concentration, and the polyamines were mainly spermidine and spermine. This feature distinguished the 2,4-diaminobutyric acid-containing genera Rathayibacter, Clavibacter, and Agromyces, which contained low concentrations of polyamines. Strains of the genus Brevibacterium were characterized by the presence of high concentrations of cadavarine and usually high concentrations of putrescine. Members of the genus Corynebacterium had relatively low polyamine contents, and usually spermidine was the major polyamine. A similar polyamine pattern was detected in the species of the genus Tsukamurella. No homogeneous polyamine patterns were detected in representatives of the genera Microbacterium and Aureobacterium, which are phylogenetically intermixed (M. Takeuchi and A. Yokota, FEMS Microbiol. Lett. 124:11–16, 1994). The results of polyamine analyses are in good agreement with the genetic heterogeneity within the actinobacteria and demonstrate that polyamine patterns are suitable for use in classification of actinobacterial taxa.
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Friedmanniella antarctica gen. nov., sp. nov., an LL-Diaminopimelic Acid-Containing Actinomycete from Antarctic Sandstone
More LessAbstractA gram-positive, aerobic, slowly growing actinomycete was isolated from antarctic sandstone. Packets of spherical cells of this organism form clusters. The diagnostic diamino acid of the peptidoglycan is LL-diaminopimelic acid with glycine in position 1 of the peptide subunit. The major menaquinone is MK-9(H4), and the main cellular fatty acids are 12- and 13-methyltetradecanoic acids. Only a few organic compounds are metabolized. The DNA base composition is 73 mol% G + C. A 16S ribosomal DNA sequence comparison showed that this isolate is a phylogenetic neighbor of the Propionibacteria and related taxa. Its closest relative is Microlunatus phosphovorus. Morphological, physiological, and genotypic characteristics support the description of a new genus and new species, Friedmanniella antarctica gen. nov., sp. nov. The type strain is strain AA-1042 (= DSM 11053).
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Phenotypic Diversity among Ruminai Isolates of Prevotella ruminicola: Proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and Redefinition of Prevotella ruminicola
More LessAbstractSelected phenotypic characteristics of isolates of Prevotella ruminicola (formerly Bacteroides ruminicola) were studied in order to establish whether the characteristics of genotypic strain groups established previously on the basis of 16S ribosomal DNA sequences differed systematically. Among strains formerly considered P. ruminicola subsp. brevis, strains related to strain GA33T (T = type strain) typically failed to produce carboxymethyl cellulase (CMCase) activity detectable by plate assays and failed to ferment xylose, while strains related to strain B14T produced abundant CMCase and fermented xylose. We propose that strains related to GA33T, which have DNA G+C contents between 45 and 51 mol%, should be assigned to a new species, Prevotella brevis, and that strains related to B14T, which have DNA G+C contents between 39 and 43 mol%, should be assigned to another new species, Prevotella bryantii. Most of the isolates formerly classified as P. ruminicola subsp. ruminicola strains produced CMCase and had DNA G+C contents between 45 and 51 mol%, and we propose that these organisms should be placed in the redefined species P. ruminicola. A small group of isolates that have lower G+C contents are assigned to another new species, Prevotella albensis. Most P. brevis and P. bryantii strains produced abundant extracellular DNase activity. Proteinase activities (as determined by [14C] casein hydrolysis) varied widely between strains, and P. brevis strains exhibited the highest mean activity. All strains produced dipeptidyl peptidase activity, but the relative activities against different peptide substrates exhibited by P. bryantii, P. albensis, and P. brevis differed systematically. The phenotypic differences among the newly defined species suggest that they may occupy distinct niches within the rumen ecosystem.
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Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the Genus Paenibacillus and Emended Description of the Genus Paenibacillus
More LessAbstractWe determined the taxonomic status of six Bacillus species (Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus) by using the results of 16S rRNA gene sequence and cellular fatty acid composition analyses. Phylogenetic analysis clustered these species closely with the Paenibacillus species. Like the Paenibacillus species, the six Bacillus species contained anteiso-C15:0 fatty acid as a major cellular fatty acid. The use of a specific PCR primer designed for differentiating the genus Paenibacillus from other members of the Bacillaceae showed that the six Bacillus species had the same amplified 16S rRNA gene fragment as members of the genus Paenibacillus. Based on these observations and other taxonomic characteristics, the six Bacillus species were transferred to the genus Paenibacillus. In addition, we propose emendation of the genus Paenibacillus.
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Emended Description of Paenibacillus amylolyticus and Description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov.
More LessAbstractThe taxonomic position of unidentified group 6 of Bacillus circulons as described by Nakamura and Swezey (L. K. Nakamura and J. Swezey, Int. J. Syst. Bacteriol. 33:46–52, 1983) was determined, and the taxonomy of Paenibacillus amylolyticus was reexamined. The results of PCR amplification of a 16S rRNA gene fragment with a specific primer and comparative analysis of 16S rRNA gene sequences warranted placing the two taxa in the genus Paenibacillus. The levels of DNA reassociation among the strains revealed four groups (designated groups I, II, III, and 6), each with a high level of intragroup relatedness (>72%). Clustering based on pheno-typic characteristics correlated well with DNA relatedness grouping. P. amylolyticus strains were scattered in groups I, II, and III. Strains labeled the type strain of P. amylolyticus from different culture collections appeared in groups I and III. Strains found in group I were identified as P. amylolyticus sensu stricto, and the one strain found in group III was identified as Paenibacillus lautus. Group 6 encompassed strains formerly assigned to B. circulans group 6, and group II contained other strains identified as P. amylolyticus. Groups 6 and II were phenotypically and genetically distinct taxa that were distinguishable from the previously described species. These findings showed that groups 6 and II were new species, for which we propose the names Paenibacillus illinoisensis and Paenibacillus chibensis, respectively.
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Ribotype Delineation and Description of Staphylococcus sciuri Subspecies and Their Potential as Reservoirs of Methicillin Resistance and Staphylolytic Enzyme Genes
AbstractThree subspecies of Staphylococcus sciuri, S. sciuri subsp. sciuri Kloos, Schleifer, and Smith 1976, 23AL emend. Kloos et al. 1996, S. sciuri subsp. carnaticus subsp. nov., and S. sciuri subsp. rodentium subsp. nov., are described on the basis of their ribotype patterns, DNA-DNA liquid hybridization data, and phenotypic characteristics. Normalized ribotyping subdivided the S. sciuri patterns into three blocks of patterns, each corresponding to a subspecies. Each subspecies formed a separate, well-defined DNA similarity group when DNA-DNA hybridizations were conducted under stringent (70°C) reassociation conditions. S. sciuri subsp. sciuri could be distinguished from the other subspecies on the basis of its ability to produce acid from D-cellobiose, alkaline phosphatase activity, and inability to produce either clumping factor or protein A. S. sciuri subsp. carnaticus could be distinguished by its ability to produce acid aerobically from D-xylose and maltose, inability to produce acid from D-melezitose, and smaller colony size on P agar. S. sciuri subsp. rodentium could be distinguished by its positive reaction in the latex agglutination test for clumping factor and/or protein A and generally higher frequencies and levels of oxacillin and methicillin resistance. All 40 strains of S. sciuri tested (including representatives of all three subspecies) hybridized with the mecA gene probe. All strains of S. sciuri subsp. sciuri, 79% of the strains of S. sciuri subsp. carnaticus and 89% of the strains of S. sciuri subsp. rodentium exhibited extracellular, staphylolytic enzyme activity. This activity was associated with an enzyme(s) that immunoblotted with a lysostaphin-specific monoclonal antibody; however, only three strains hybridized with a lysostaphin (end) gene probe. The type strain of S. sciuri subsp. carnaticus is DD 791 (= ATCC 700058), and the type strain of S. sciuri subsp. rodentium is DD 4761 (= ATCC 700061).
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Comparison of 16S Ribosomal DNA Sequences of All Xanthomonas Species
More LessThe phylogenetic relationships of all validly described species of the genus Xanthomonas and the type strain of Stenotrophomonas maltophilia were analyzed by sequencing and comparing 16S ribosomal DNAs (rDNAs). The two genera exhibited a mean sequence similarity value of 96.6%, corresponding to differences at 50 nucleotide positions on average. The species of the genus Xanthomonas exhibited relatively high levels of overall sequence similarity; the mean similarity value was 98.2%, which corresponds to an average of 14 mutual nucleotide differences. Within the genus Xanthomonas, a group containing Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthomonas theicola, and Xanthomonas translucens clustered apart from the main Xanthomonas core, whereas Xanthomonas sacchari formed a third phylogenetic lineage. Due to the very restricted variability in 16S rDNA sequences within the genus Xanthomonas, rDNA signatures that have possible diagnostic value for differentiating the Xanthomonas species could not be determined with certainty. When sequence similarities were compared with DNA-DNA pairing data determined previously, there was only a limited correlation. This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation.
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Pseudoalteromonas antarctica sp. nov., Isolated from an Antarctic Coastal Environment
More LessThe taxonomic characteristics of five bacterial strains which were isolated from Antarctic coastal marine environments were studied. These bacteria were psychrotrophic, aerobic, and gram negative with polar flagella. The G+C contents of the DNAs of these strains were 41 to 42 mol%. The Antarctic strains were phenotypically distinct from the previously described Pseudoalteromonas type species. DNA-DNA hybridization experiments revealed that the new strains were closely related to each other but clearly different from Pseudoalteromonas haloplanktis and Pseudoalteromonas atlantica, which were the most phenotypically similar organisms. None of the bacterial isolates was capable of using dl-malate, d-sorbitol, or m-hydroxybenzoate, and all were capable of gelatin hydrolysis. Strains NF2, NF3T (T = type strain), NF13, NF14, and EN10 had an Na+ requirement but required only 17 mM Na+. Phenotypic, DNA G+C content, DNA-DNA hybridization, 16S rRNA analysis, fatty acid composition, and protein profile data confirmed the identification of the Antarctic strains as members of a Pseudoalteromonas sp. The name Pseudoalteromonas antarctica sp. nov. is proposed for these organisms.
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Sporomusa silvacetica sp. nov., an Acetogenic Bacterium Isolated from Aggregated Forest Soil
Sporomusa silvacetica sp. nov. DG-1T (= DSMZ 10669T) (T = type strain) was isolated from well-drained, aggregated forest soil (pH 6.0) in east-central Germany. The cells were obligately anaerobic, slightly curved rods and were motile by means of laterally inserted flagella on the concave side of each cell. Typical cells were approximately 3.5 by 0.7 μm. Cells stained weakly gram positive, but thin sections revealed a complex multilayer cell wall. Spores were spherical and distended the sporangia. Growth and substrate utilization occurred with ferulate, vanillate, fructose, betaine, fumarate, 2,3-butanediol, pyruvate, lactate, glycerol, ethanol, methanol, formate, and H2-CO2. With most substrates, acetate was the primary reduced end product and was produced in stoichiometries indicative of an acetyl-coenzyme A pathway-dependent metabolism. Fumarate was dismutated to succinate and acetate. Methoxyl and acrylate groups of various aromatic compounds were O-demethylated and reduced, respectively. Yeast extract was not required for growth. Cells grew optimally at approximately 30°C and pH 6.8; under these conditions and with fructose as the substrate, the doubling time was approximately 14 h. The lowest temperature that supported growth was between 5 and 10°C. The carbon monoxide dehydrogenase and hydrogenase activities were approximately 9 and 102 μmol min-1 mg of protein-1, respectively. A type b cytochrome was detected in the membrane. The G+C content was approximately 43 mol%. Phylogenetic analysis of the 16S ribosomal DNA indicated that DG-1T was most closely related to members of the genus Sporomusa in the Clostridium subphylum of the gram-positive bacteria.
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Spiroplasma litorale sp. nov., from Tabanid Flies (Tabanidae: Diptera) in the Southeastern United States
Spiroplasma strain TN-1T (T = type strain), a strain serologically distinct from other spiroplasma species, groups, and subgroups, was isolated from the gut of a horsefly (Tabanus nigrovittatus) from a barrier island off the coast of North Carolina. Related strains were isolated from other Tabanus spp., T. atratus, T. americanus, T. gladiator, T. lineola, T. sulcifrons, and T. zythicolor, from coastal Georgia. Cells of strain TN-1T in culture were helical and motile with an average of 5 to 10 helical turns per cell. Electron microscopic studies determined that the cells of strain TN-1T were surrounded by a single cytoplasmic membrane, and there was no evidence of a cell wall. The spiroplasma grew well in MID and SP-4 liquid media. Serum fraction (1%) medium and conventional horse serum medium also supported growth of strain TN-1T. Fried-egg colonies were not produced; instead, the strain produced small diffuse colonies that were surrounded by satellite growth. The optimum temperature for growth was 32°C, but multiplication was observed at temperatures from 10 to 41°C. The doubling time at the optimum temperature (32°C) was 1.6 h. No growth was observed at 5 or 43°C. Spiroplasma strain TN-1T passed through 220-nm filter pores but failed to pass through 100-nm filter pores. Strain TN-1T catabolized glucose but hydrolyzed neither arginine nor urea. The guanine-plus-cytosine content of the DNA was about 25 ± 1 mol%, and the genome size was 1,370 kbp. Based on results from this study and previously published data, strain TN-1T (= ATCC 43211) (group XVIII) is designated the type strain of a new spiroplasma species, Spiroplasma litorale.
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Characterization of Smooth and Rough Morphotypes of Peptostreptococcus micros
More LessIsolation of the smooth (Sm) morphotype of Peptostreptococcus micros, a suspected oral pathogen, is sometimes accompanied by isolation of a rough (Rg) morphotype of P. micros. The Rg type readily changes to a Sm-like variant (RgSm) in broth culture. Sm and Rg isolates and RgSm variants were compared to determine whether these three types are the result of phase variation. The RgSm variants resembled the Sm morphotype in colony morphology; furthermore, the Sm type and the RgSm type did not have the fibrillar surface structures characteristic of the Rg type, and the Sm and RgSm types were more hydrophobic than the Rg type. However, when we compared the sodium dodecyl sulfate-polyacrylamide gel electrophoresis patterns of whole-cell proteins, serotyping data, pyrolysis mass spectrometry data, 16S ribosomal DNA sequences, and hemolytic activities, the RgSm variants and the Rg isolates were very similar and were clearly distinct from the Sm isolates. These results suggest that the Rg and RgSm types form a cluster distinct from the Sm type and thus provide evidence that P. micros can be differentiated into two groups, one consisting of the Sm type and the other consisting of the Rg and RgSm types.
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Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., Two Marine Bacteria from a Lignin-Rich Pulp Mill Waste Enrichment Community
More LessTwo numerically important bacteria in marine pulp mill effluent enrichment cultures were isolated. These organisms were gram-negative, rod-shaped, strictly aerobic bacteria. Isolate IRE-31T (T = type strain) produced hydrolytic enzymes for the breakdown of cellulose, xylan, chitin, gelatin, and Tween 80. It also utilized a variety of monosaccharides, disaccharides, amino acids, and volatile fatty acids for growth. Isolate KW-40T did not utilize natural polymers, but it could grow on a variety of monosaccharides, disaccharides, alcohols, and amino acids. It also utilized methanol and aromatic compounds. The surfaces of both organisms were covered by blebs and vesicles. 16S rRNA analyses placed both organisms in the γ-3 subclass of the phylum Proteobacteria. They were related to Oceanospirillum linum, Marinomonas vaga, Pseudomonas putida, and Halomonas elongata, although a close association with any of these bacteria was not found. The guanine-plus-cytosine contents of strain IRE-31T and KW-40T were 57.6 and 54.9 mol%, respectively. On the basis of 16S rRNA sequence and phenotypic characterizations, these isolates were different enough so that they could be considered members of new genera. Thus, the following two new genera and species are proposed: Microbulbifer hydrolyticus, with type strain IRE-31 (= ATCC 700072), and Marinobacterium georgiense, with type strain KW-40 (= ATCC 700074).
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Phylogenetic Relationships and Uncertain Taxonomy of Pedomicrobium Species
More LessThe phylogenetic relationships among the species of the genus Pedomicrobium were studied by comparing their 16S rRNA sequences. The Pedomicrobium species form a coherent phylogenetic cluster within the genera of the hyphal budding bacteria in the α-Proteobacteria. The sequences of two strains of Pedomicrobium australicum were obtained from DNAs extracted from nonviable freeze-dried cells, which are the only source of material available, and were found to be almost identical (level of similarity, 99.9%). Overall, the Pedomicrobium species are closely related, with sequence similarities ranging from 96.2 to 99.9%. Pedomicrobium manganicum is phylogenetically the most distantly related species and exhibits the lowest similarity (96.2%) with Pedomicrobium americanum. Australian isolate Pedomicrobium sp. strain ACM 3067, P. americanum, and P. australicum are all very highly related, with similarities greater than 99%. Pedomicrobium sp. strain ACM 3067 is most closely related to P. australicum (level of similarity, 99.6%) and P. americanum (99.4%). These manganese-oxidizing species are more closely related to the iron-oxidizing species Pedomicrobium ferrugineum than to the other manganese-oxidizing species, P. manganicum. Taxonomic uncertainties resulting from the loss of the type culture of P. australicum are discussed.
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Anaerobiospirillum thomasii sp. nov., an Anaerobic Spiral Bacterium Isolated from the Feces of Cats and Dogs and from Diarrheal Feces of Humans, and Emendation of the Genus Anaerobiospirillum
More LessThirty-seven similar strains isolated from feces of cats and dogs and from human diarrheal feces had characteristics of the genus Anaerobiospirillum. These organisms were distinguished from the only previously described Anaerobiospirillum species, Anaerobiospirillum succiniciproducens, by producing acid from adonitol but not from fructose, raffinose, or sucrose and by the lack of α-glucosidase. The G+C contents of the DNAs of the new strains were 39 to 42 mol%. The results of morphological, physiological, DNA G+C content, and DNA homology studies support the proposal that the description of the genus Anaerobiospirillum should be emended so that a new species can be included in the genus. The new species Anaerobiospirillum thomasii is proposed, with strain A273/88 (= NCTC 12467) as the type strain.
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Xanthobacter tagetidis sp. nov., an Organism Associated with Tagetes Species and Able To Grow on Substituted Thiophenes
More LessMembers of the marigold genus of flowering plants (the genus Tagetes), which synthesize and accumulate thiophene compounds in their roots, were investigated as potential sources of bacteria able to degrade substituted thiophenes. Batch and continuous enrichment cultures inoculated with compost from root balls of Tagetes patula and Tagetes erecta reproducibly produced the same predominant type of bacterium when they were supplied with thiophene-2-carboxylate (T2C) or thiophene-2-acetate (T2A) as a carbon and energy substrate. This organism was a yellow-pigmented, neutrophilic, mesophilic, gram-negative, pleomorphic, rodshaped bacterium, which we classify as a new species of the genus Xanthobacter, Xanthobacter tagetidis; strain TagT2C (= DSM 11105) is the type strain. Strain TagT2CT (T = type strain) grew on simple thiophenes, such as T2C, thiophene-3-carboxylate, and T2A, on analogs of these compounds (pyrrole-2-carboxylate and furan-2-carboxylate), and on the condensed thiophene dibenzothiophene. X. tagetidis was facultatively autotrophic, fixing carbon dioxide by means of ribulose bisphosphate carboxylase, and was able to grow on hydrogen, thiosulfate, or sulfide as an energy substrate. It also grew on a wide range of other heterotrophic, chemolithotrophic, and methylotrophic substrates. Its growth on T2C was optimal at 28 to 31°C and pH 7.6 to 7.8, and the maximum growth rate in batch culture was 0.22 h-1. The DNA base composition of X. tagetidis is 68 mol% G+C. A 16S ribosomal DNA sequence analysis of strain TagT2CT showed that this organism represents a distinct lineage within the Aquabacter-Azorhizobium-Xanthobacter cluster of the alpha-2 subclass of the Proteobacteria. Discrimination of X. tagetidis from the other genera in this group and from other Xanthobacter species is discussed.
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Phylogenetic Evidence for the Taxonomic Heterogeneity of Photorhabdus luminescens
The sequences of the 16S rRNA gene of 40 strains of bacterial symbionts isolated from the nematodes Heterorhabditis spp. and seven bacterial symbionts of the nematodes Steinernema spp. which were isolated from different geographical areas, as well as the type strain of Xenorhabdus japonicus, were determined and compared to each other and to the sequences of several reference strains of members of the Enterobacteriaceae. The data confirmed the separate status of the two genera of symbionts of entomopathogenic rhabditid nematodes. The symbionts of Heterorhabditis spp. clustered with the type strain of Photorhabdus luminescens, while the symbionts of Steinernema spp. grouped with Xenorhabdus species. X. japonicus clustered with the other Xenorhabdus species. Phylogenetic analysis of 15 almost complete 16S ribosomal DNA (rDNA) sequences of the Heterorhabditis symbionts indicated that there were several subclusters. The properties correlated with these subclusters are not yet apparent, although there may be some geographical and ecological correlations. For example, among the nematode-symbiotic bacteria, the members of subclusters I and III are from southeastern and midwestern North America, respectively, while the members of subclusters II and IV are primarily from Europe and Australia, respectively. The nonsymbiotic strains of P. luminescens form a highly homologous subcluster by themselves. The results of DNA-DNA hybridization studies performed with a few selected strains of five of the 16S rDNA subclusters support the existence of several genospecies within P. luminescens.
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Porphyrobacter tepidarius sp. nov., a Moderately Thermophilic Aerobic Photosynthetic Bacterium Isolated from a Hot Spring
A new thermophilic bacterium, strain OT3T (T = type strain), was isolated from a brackish hot spring. Strain OT3T is an obligate aerobe that synthesizes bacteriochlorophyll a and has a photosynthetic apparatus. This isolate is a thermophilic bacterium with an optimal growth temperature of 40 to 48°C. The cells are nonmotile, ovoid to short rods. An analysis of 16S rRNA sequences revealed that the new strain forms a coherent cluster with members of the α-4 group of the α subclass of the Proteobacteria, which contains the genera Erythrobacter, Erythromicrobium, and Porphyrobacter. The closest relative is Porphyrobacter neustonensis with a 16S rRNA sequence similarity of 96.8%. The in vivo absorption spectrum has maxima at 460, 494, 596, 800, and 870 nm. The main carotenoids are OH-β-carotene sulfate derivatives, nostoxanthin, and bacteriorubixanthinal. Growth occurs with glucose, acetate, glutamate, butyrate, Casamino Acids, and yeast extract as sole energy sources. The pigment composition and nutritional profile of the new isolate are similar to the pigment composition and nutritional profile of P. neustonensis. Although there are marked differences in cell morphology between the new isolate and the budding bacterium P. neustonensis, the results of phenotypic and genetic comparisons suggest that the new isolate is closely related to P. neustonensis. Consequently, we assign the new isolate to the genus Porphyrobacter and propose the name Porphyrobacter tepidarius sp. nov. for it; the type strain of P. tepidarius is strain OT3 (= DSM 10595).
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Subspecific Differentiation of Mycobacterium avium Complex Strains by Automated Sequencing of a Region of the Gene (hsp65) Encoding a 65-Kilodalton Heat Shock Protein
To develop a strategy for rapid species assignment and strain differentiation of Mycobacterium avium complex (MAC) organisms, the sequence of a 360-bp region of the gene (hsp65) encoding a 65-kDa heat shock protein was determined for 56 isolates, including 21 patient isolates and 35 reference strains. Eleven hsp65 alleles were identified, and there was no sharing of alleles between strains classified as M. avium and Mycobacterium intracellulare based on serovar and species-specific DNA hybridization probes. Phylogenetic analysis showed that 30 strains had one of two hsp65 alleles which were found in known M. avium organisms, 23 strains had one of six alleles allied with known M. intracellulare organisms, and three MAC isolates had one of three hsp65 alleles that differed substantially from the consensus M. avium and M. intracellulare hsp65 sequences. Estimates of strain relationships based on the sequences of hsp65 and the 16S-23S ribosomal DNA internal transcribed spacer were similar. Automated DNA sequencing of a 360-bp region of the hsp65 gene from MAC organisms provides a rapid and unambiguous marker system for strain differentiation and permits specific assignment of these acid-fast organisms for diagnostic purposes.
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Cultures of “Clostridium acetobutylicum” from Various Collections Comprise Clostridium acetobutylicum, Clostridium beijerinckii, and Two Other Distinct Types Based on DNA-DNA Reassociation
More LessThe best-known acetone-butanol (solvent)-producing bacterium is the Weizmann organism, Clostridium acetobutylicum, which was used for starch-based industrial fermentation. In the past two decades, cultures of “C, acetobutylicum” from various culture collections have included organisms that were isolated for sugar (molusses)-based industrial solvent production. Recent biochemical and genetic studies have revealed significant differences among some of these “C. acetobutylicum” strains. We used DNA-DNA reassociation to analyze 39 cultures of “C. acetobutylicum” and phenotypically similar organisms from major collections. The results of this study clearly identified four groups with intergroup reassociation values of less than 30%. All of the intragroup values except the value for one strain were 68% or more, which supported species status for each group. The C. acetobutylicum group (with ATCC 824 as the type strain) consisted of 17 cultures and had average reassociation values of 10% with the other three groups. All strains of C. acetobutylicum produced riboflavin in milk, and the cultures were bright yellow, which is useful for differentiating this species from the other three uroups. The Clostridium beijerinckii group (with VPI 5481 [= ATCC 25752] as the type strain) consisted of 16 cultures and included strains NCIMB 8052 and NCP 270. Strains NCP 262 and NRRL B643 constituted the third group, whereas strain N1–4 (“Clostridium saccharoperbutylacetonicum”) and its derivative, strain N1-4081, formed the fourth group. At present, the last two groups are each represented by only one independent strain; difinitive descriptions of these two groups as two new or revived species will require further phenotypic characterization, as well as identification of additional strains. C. beijerinckii NCP 270, Clostridium sp. strain NRRL B643, and “C. saccharoperbutylacetonicum” were used in industrial solvent production from molasses, which confirms that the new organisms used for the sugar-based processes are distinct from C. acetobutylicum.
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Phylogenetic Analysis of the Genus Chlamydia Based on 16S rRNA Gene Sequences
More LessThe phylogenetic relationships among Chlamydia spp. were investigated by comparing 16S rRNA gene sequences. In this analysis we used 14 strains of Chlamydia psittaci, including seven feline isolates, two avian isolates, two human isolates, one bovine isolate, one ovine isolate, and one guinea pig isolate; five strains of Chlamydia pecorum, including three bovine isolates, one ovine isolate, and one koala isolate; and nine strains of Chlamydia trachomatis, including six human isolates, two swine isolates, and one mouse isolate. A phylogenetic analysis of the 16S rRNA gene sequences of these organisms and seven previously published sequences revealed eight genetic groups which formed two clusters. The first cluster was composed of C. pecorum, Chlamydia pneumoniae, and C. psittaci and included three genetic groups (one group containing avian, human, and ovine strains, one group containing feline strains. and one group containing guinea pig strains). The second cluster was composed of C. trachomatis and also included three genetic groups (one group containing human strains, one group containing swine isolates, and one group containing rodent strains). The strains in each genetic group exhibited similar genetic distances. The results of the phylogenetic analysis agreed with the results of previous genomic DNA, ompA gene allele, and biotyping studies. Therefore, the genetic groups based on genetic distances may be considered a criterion for species identification.
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Streptomyces cellulolyticus sp. nov., a New Cellulolytic Member of the Genus Streptomyces
More LessActinomycete strain LXT (T = type strain), which decomposes cellulose, was identified as a member of the genus Streptomyces on the basis of morphological characteristics and the chemotype of the cell wall. The key characteristics of this organism are rectiflexibiles spore chains, a nonfragmenting vegetative mycelium, a warty spore surface, a type I cell wall, white to pink spore masses, and a lack of formation of soluble pigments (including melanin). These results indicate that strain LXT represents a distinct Streptomyces species, for which the name Streptomyces cellulolyticus is proposed. The type strain is strain LX, which has been deposited in the China General Microbiological Culture Collection Center as strain AS. 41332.
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Rickettsia peacockii sp. nov., a New Species Infecting Wood Ticks, Dermacentor andersoni, in Western Montana †
Rickettsia peacockii, a new species of spotted fever group rickettsiae, was identified from Rocky Mountain wood ticks (Dermacentor andersoni) collected in the Sapphire Mountain Range on the eastern side of Bitterroot Valley, Montana. DNA from R. peacockii SkalkahoT (T = type strain) in naturally infected tick tissue was amplified by a PCR assay with primer sets derived from eubacterial 16S ribosomal DNA (rDNA), rickettsial citrate synthase, and 190-kDa surface antigen (rOmpA) genes. Partial 16S rDNA and rOmpA gene sequences exhibited levels of similarity of 99.7 and 93.2%, respectively, with the sequences of the spotted fever agent Rickettsia rickettsii R. By using Giménez staining, fluorescent antibody tests, a PCR assay, and a restriction fragment length polymorphism analysis, 76 of 115 female ticks (minimal field infection rate, 66.1%) collected between 1992 and 1995 were found to be infected. The organism is passed transstadially and transovarially (minimal vertical transmission rate, 73.3%), and infections are localized in ovarial tissues. Attempts to cultivate R. peacockii were unsuccessful.
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The Ribosomal Intergenic Spacer and Domain I of the 23S rRNA Gene Are Phylogenetic Markers for Chlamydia spp.
More LessCurrent methods used to classify Chlamydia strains, including biological, morphological, and DNA hybridization techniques and major outer membrane protein (ompl) gene analysis, can be imprecise or difficult to perform. To facilitate classification, 2.8-kb partial ribosomal DNA (rDNA) segments from a Chlamydia trachomatis strain and a Chlamydia psittaci strain were amplified by PCR and sequenced. Subsequently, a 1, 320-bp region in this segment, including both the 16S/23S intergenic spacer (232 ± 11 bp) and domain I (620 ± 2 bp) of the 23S gene, was sequenced from 41 additional strains and from the chlamydia-like organisms Simkania sp. strains “Z” and “Zl.” When both parsimony and distance analyses were performed, these sequences were found to have variable regions that grouped the isolates into two lineages (C. trachomatis and non-C. trachomatis) and nine distinct genotypic groups. The C. trachomatis lineage included human, swine, and mouse-hamster groups. The non-C. trachomatis lineage included Chlamydia pecorum, Chlamydia pneumoniae, and C. psittaci abortion, avian, feline, and guinea pig groups. These nine groups were essentially equidistant from the genetic root and were congruent with groups identified previously by using DNA-DNA homology, genomic restriction endonuclease analysis, host specificity, tissue specificity, and/or disease production. Phylogenetic trees based on the intergenic spacer or on domain I were congruent with trees previously derived from ompl sequences. DNA sequence analysis of either the intergenic spacer or domain I provides a rapid and reproducible method for identifying, grouping, and classifying chlamydial strains.
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Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an Obligately Psychrophilic Actinomycete To Accommodate “Curtobacterium psychrophilum” Inoue and Komagata 1976
More Less“Curtobacterium psychrophilum,” proposed by Inoue and Komagata in 1976, is a psychrophilic gram-positive irregular rod isolated from Antarctic soil. This organism grew optimally at 9 to 12°C and did not grow at higher than 18°C. Chemotaxonomic characteristics of this organism were the presence of 2,4-diaminobutyric acid in the cell wall and menaquinone-10 as the predominant respiratory quinone. The cellular fatty acid profile, which contained a significant amount of an anteiso-branched monounsaturated acid, 12-methyl tetradecenoic acid, was a distinctive characteristic of this organism and was reasonable for adaptation to low temperature. Phylogenetic analysis based on 16S ribosomal DNA sequences revealed that this organism was positioned at a separate branch in the family Microbacteriaceae, actinomycetes with group B peptidoglycan. We propose the name Cryobacterium psychrophilum gen. nov., sp. nov. for this organism. The type strain is JCM 1463 (=IAM 12024 =ATCC 43563 =IFO 15735 =NCIMB 2068).
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Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.
More LessA new hierarchic classification structure for the taxa between the taxonomic levels of genus and class is Proposed for the actinomycete line of descent as defined by analysis of small subunit (16S) rRNA and genes coding for this molecule (rDNA). While the traditional circumscription of a genus of the actinomycete subphylum is by and large in accord with the 16S rRNA/rDNA-based phylogenetic clustering of these organisms. most of the higher taxa proposed in the past do not take into account the phylogenetic clustering of genera. The rich chemical, morphological and physiological diversity of phylogenetically closely related genera makes the description of families and higher taxa so broad that they become meaningless for the description of the enclosed taxa. Here we present a classification system in which phylogenetically neighboring taxa at the genus level are clustered into families, suborders, orders, subclasses, and a class irrespective of those phenotypec characteristics on which the delineation of taxa has been based in the past. Rather than being based on a listing of a wide array of chemotaxonomic, morphological, and physiological properties, the delineation is based solely on 16S rDNA/rRNA sequence-based phylogenetic clustering and the presence of taxon-specific 16S rDNA RNA signature nucleotides.
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Streptomyces seoulensis sp. nov.
More LessThe taxonomic position of an actinomycete strain isolated from Korean soil was examined by a polyphasic approach. The isolate, designated IMSNU-1, was clearly assigned to the genus Streptomyces on the basis of morphological and chemotaxonomic data. The test strain was the subject of a probabilistic identification study using the identification matrices generated by Langham et al. (J. Gen. Microbiol. 135:121-133, 1989) and found to be marginally close to clusters 19 and 39. An almost complete 16S rRNA gene (rDNA) sequence was obtained for the test strain and compared with those of representative streptomycetes. 16S rDNA sequence data not only support the strain’s membership in the genus Streptomyces but also provide strong evidence that our isolate is genealogically distant from representatives of clusters 19 and 39, forming a separate phyletic line in a clade encompassed by streptomycetes. It is therefore proposed from the polyphasic evidence that strain IMSNU-1 be classified in the genus Streptomyces as Streptomyces seoulensis sp. nov.
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Proposal of Sporolactobacillus nakayamae subsp. nakayamae sp. nov., subsp. nov., Sporolactobacillus nakayamae subsp. racemicus subsp. nov., Sporolactobacillus terrae sp. nov., Sporolactobacillus kofuensis sp. nov., and Sporolactobacillus lactosus sp. nov.
More LessCatalase-negative spore-forming lactic acid bacteria were isolated from soil samples and fermentation starters for Asian traditional alcoholic beverages. The isolates were characterized by determining morphological, biochemical, physiological, and chemotaxonomic properties and were found to be members of the genus Sporolactobacillus. Twelve isolates and some authentic strains belonging to this genus were used in DNA base composition and DNA relatedness studies, and the results revealed that the strains tested could be divided into six groups which correlated with the phenotypic characteristics. One of the groups corresponded to the previously described species Sporolactobacillus inulinus. In addition, we propose the following four new species and two new subspecies for the remaining five groups: Sporolactobacillus nakayamae subsp. nakayamae sp. nov., subsp. nov. (type strain, M-114 [= JCM 3514]), Sporolactobacillus nakayamae subsp. racemicus subsp. nov. (type strain, M-17 [= JCM 3417]), Sporolactobacillus terrae sp. nov. (type strain, M-116 [= JCM 3516]), Sporolactobacillus kofuensis sp. nov. (type strain, M-19 [= JCM 3419]), and Sporolactobacillus lactosus sp. nov. (type strain, Xl-1 [= JCM 9690]).
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Deferribacter thermophilus gen. nov., sp. nov., a Novel Thermophilic Manganese- and Iron-Reducing Bacterium Isolated from a Petroleum Reservoir
More LessA thermophilic anaerobic bacterium, designated strain BMAT (T = type strain), was isolated from the production water of Beatrice oil field in the North Sea (United Kingdom). The cells were straight to bent rods (1 to 5 by 0.3 to 0.5 μ) which stained gram negative. Strain BMAT obtained energy from the reduction of manganese (IV), iron(III), and nitrate in the presence of yeast extract, peptone, Casamino Acids, tryptone, hydrogen, malate, acetate, citrate, pyruvate, lactate, succinate, and valerate. The isolate grew optimally at 60°C (temperature range for growth, 50 to 65°C) and in the presence of 2% (wt/vol) NaCl (NaCl range for growth, 0 to 5% [wt/vol]). The DNA base composition was 34 mol% G+C. Phylogenetic analyses of the 16S rRNA gene indicated that strain BMAT is a member of the domain Bacteria. The closest known bacterium is the moderate thermophile Flexistipes sinusarabici (similarity value, 88%). Strain BMAT possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, we propose that this isolate should be described as a member of a novel species of a new genus, Deferribacter thermophilus gen. nov., sp. nov.
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Phylogenetic Diversity of the Deinococci as Determined by 16S Ribosomal DNA Sequence Comparison
More Less16S ribosomal DNA (rDNA) sequences were determined for the five species of the genus Deinococcus (Deinococcus erythromyxa, Deinococcus proteolyticus, Deinococcus radiodurans, Deinococcus radiophilus, and Deinococcus radiopugnans) and the single species of the genus Deinobacter (Deinobacter grandis). With the exception of Deinococcus erythromyxa, the deinococci form a coherent phylogenetic cluster which is related to the Thermus-Meiothermus lineage. An analysis of the 16S rDNA sequence of Deinococcus erythromyxa revealed that this organism is an actinomycete and a member of the genus Kocuria. Deinobacter grandis falls within the radiation of the genus Deinococcus and phylogenetically can be considered a member of this genus. The results of the phylogenetic analyses are consistent with chemotaxonomic data. On the basis of our data, Deinobacter grandis is transferred to the genus Deinococcus as Deinococcus grandis comb. nov., the description of the genus Deinococcus is emended accordingly, and Deinococcus erythromyxa is transferred to the genus Kocuria as Kocuria erythromyxa comb. nov. The description of the family Deinococcaceae is emended to include organisms with rod-shaped cells, and a set of 16S rDNA signature nucleotides is designated for this group. On the basis of the distinct phylogenetic position of the Deinococcus lineage and a set of 16S rDNA signature nucleotides, the order Deinococcales ord. nov. is described.
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Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea
More LessSeveral strains of a strictly anaerobic, vibrio-shaped or sigmoid, sulfate-reducing bacterium were isolated from deep marine sediments (depth, 80 and 500 m) obtained from the Japan Sea (Ocean Drilling Program Leg 128, site 798B). This bacterium was identified as a member of the genus Desulfovibrio on the basis of the presence of desulfoviridin and characteristic phospholipid fatty acids (iso 17:1ω7 and iso 15:0), the small number of growth substrates utilized (lactate, pyruvate, and hydrogen), and 16S rRNA gene sequence analysis data. Based on data for 16S rRNA sequences (1,369 bp), all of the Japan Sea strains were identical to each other and were most closely related to Desulfovibrio salexigens and less closely related to Desulfovibrio desulfuricans (levels of similarity, 91 and 89.6%, respectively). There were, however, considerable phenotypic differences (in temperatures, pressures, and salinities tolerated, growth substrates, and electron donors) between the Japan Sea isolates and the type strains of previously described desulfovibrios, as well as important differences among the Japan Sea isolates. The Japan Sea isolates were active (with sulfide production) over a wide temperature range (15 to 65°C) and a wide sodium chloride concentration range (0.2 to 10%) (moderate halophile), and they were barophiles that were active at pressures up to about 40 MPa (400 atm). The optimum pressures for activity corresponded to the calculated pressures at the depths from which the organisms were isolated (for isolates obtained at depths of 80 and 500 m the optimum activities occurred at 10 and 15 MPa, respectively [100 and 150 atm, respectively]). This confirms that the organisms came from deep sediments and indicates that they are well-adapted for deep sediment conditions, which is consistent with other characteristics (utilization of hydrogen, fermentation, and utilization of ferric iron and organic sulfonates as electron acceptors). We propose that Japan Sea isolate 500-1 is the type strain of a new species, Desulfovibrio profundus.
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Phylogeny of Thiobacillus cuprinus and Other Mixotrophic Thiobacilli: Proposal for Thiomonas gen. nov.
More LessThe complete 5S and 16S ribosomal DNA (rDNA) sequences of the facultatively chemolithotrophic bacterium Thiobacillus cuprinus and results of a comparison of these sequences with homologous sequences from several proteobacterial species supported affiliation of T. cuprinus with the β subgroup of the Proteobacteria. T. cuprinus, Thiobacillus intermedius, Thiobacillus perometabolis, and Thiobacillus thermosulfatus form a phylogenetic cluster that comprises some of the thiobacilli capable of mixotrophic growth. This cluster is related to some pseudomonads and Alcaligenes species belonging to the β subclass. In addition, a low-frequency restriction fragment analysis (LFRFA) of some mixotrophic thiobacilli and some related species was carried out by using pulsed-field gel electrophoresis (PFGE) to determine the Spe I and Xba I macrorestriction patterns and genome sizes of these organisms. The correlation of the LFRFA results and the 16S rDNA analysis results and the usefulness of the two analyses are discussed. The PFGE fingerprints suggested that Thiobacillus sp. strain ATCC 27793 is related to T. intermedius rather than to T. perometabolis, as described previously. The distinctive characteristics of the mixotrophic species analyzed in this work, their phylogenetic relatedness, and their physiological differences from other groups belonging to the Proteobacteria, including other thiobacilli, suggest that these organisms should be transferred to a new genus, the genus Thiomonas gen. nov.
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Janibacter limosus gen. nov., sp. nov., a New Actinomycete with meso-Diaminopimelic Acid in the Cell Wall
More LessNew gram-positive bacteria were isolated from 1-year-old sludge from a wastewater treatment plant. The isolates are coccoid to rod-shaped, nonmotile aerobes that form neither spores nor mycelia. They are characterized by a peptidoglycan with directly cross-linked meso-diaminopimelic acid (type A1-γ), by the presence of menaquinone MK-8(H4). and by the lack of mycolic acids. The strains have complex fatty acid patterns with i-C16:0 and straight-chain saturated and unsaturated fatty acids as major components. The G+C content of the DNA is 70 mol%. The results of chemotaxonomic studies and a 16S ribosomal DNA sequence comparison support our proposal to assign these bacteria to a new genus, the genus Janibacter gen. nov.; the type species is Janibactor limosus sp. nov, and the type strain of J. limosus is strain HKI 83 (= DSM 11140).
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Mycobacterium mageritense sp. nov. †
More LessStrains of a new species of rapidly growing, nonphotochromogenic mycobacteria, Mycobacterium mageritense, were isolated from human sputum. The growth characteristics, acid fastness, and mycolic acids of the isolates were consistent with those of Mycobacterium species. The isolates were identified as members of a new species by performing a biochemical analysis and DNA-DNA hybridization experiments, and by comparing the sequences of several conserved genes, such as the 16S rRNA, hsp65, and sodA genes. A phylogenetic analysis in which 16S rRNA and sodA sequences were used identified M. mageritense as a novel distinct species and placed M. mageritense between members of the Mycobacterium fortuitum complex and the thermotolerant rapidly growing group. Our results demonstrate that the taxonomic value of sodA sequence analysis in the genus Mycobacterium is similar to the well-established value of 16S rRNA sequence analysis.
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Thermoterrabacterium ferrireducens gen. nov., sp. nov., a Thermophilic Anaerobic Dissimilatory Fe(III)-Reducing Bacterium from a Continental Hot Spring
More LessA strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7T; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 μm, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74°C with an optimum at 65°C. The pH range for growth at 65°C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO2, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H2 was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO2, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type-positive Bacillus-Clostridium subphylum.
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Rickettsia aeschlimannii sp. nov., a New Spotted Fever Group Rickettsia Associated with Hyalomma marginatum Ticks
More LessWe formally propose the name Rickettsia aeschlimannii sp. nov. for a new spotted fever group (SFG) rickettsia, strain MC16T, isolated from Hyalomma marginatum marginatum ticks collected in Morocco. This organism shows a typical rickettsial morphology when analyzed by electron microscopy. After characterization by serotyping, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Western immunoblotting, PCR-restriction fragment length polymorphism (RFLP), pulsed-field gel electrophoresis, and 16S rDNA sequencing, this organism was found to be different from all of the recognized SFG rickettsiae. Identical PCR-RFLP profiles have, however, been found in H. marginatum marginatum from Portugal and H. marginatum rufipes from Zimbabwe, which suggests that the distribution of this rickettsia reaches from the Mediterranean to southern Africa.
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Evaluation of Arbitrarily Primed PCR Analysis and Pulsed-Field Gel Electrophoresis of Large Genomic DNA Fragments for Identification of Enterococci Important in Human Medicine
More LessThe increasing problems encountered with enterococcal nosocomial infections and the intrinsic and acquired resistance of the enterococci to different antimicrobial compounds highlight the need for a rapid identification technique. Enterococcus faecalis is readily identified by biochemical tests, but species differentiation within the Enterococcus faecium and Enterococcus gallinarum species groups is less well established. In the present study, 66 strains representing the most prevalent human enterococci were used to develop a PCR-based species-specific identification protocol. Whole-cell protein analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used as a reference method for species identification. In addition, the genomic Sma I macro-restriction fragment distribution of all of the strains was examined by pulsed-field gel electrophoresis (PFGE). Oligonucleotide D11344-primed PCR was as discriminative as whole-cell protein analysis and resulted in more easily interpreted band patterns. This PCR-based technique allowed identification of clinical isolates by visual examination of the DNA profiles obtained. The inability of both methods to discriminate between Enterococcus casseliflavus and Enterococcus flavescens brought into question the species status of E. flavescens. PFGE did not result in species-discriminative DNA bands or band patterns, but proved to be superior for interpretation of interstrain relationships.
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Phylogenetic Position of Riemerella anatipestifer Based on 16S rRNA Gene Sequences
More LessRiemerella anatipestifer, the causative agent of septicemia anserum exsudativa (also called new duckling disease), belongs to the family Flavobacteriaceae of gram-negative bacteria. We determined the DNA sequences of the rrs genes encoding the 16S rRNAs of four R. anatipestifer strains by directly sequencing PCR-amplified rrs genes. A sequence similarity analysis confirmed the phylogenetic position of R. anatipestifer in the family Flavobacteriaceae in rRNA superfamily V and allowed fine mapping of R. anatipestifer on a separate rRNA branch comprising the most closely related species, Bergeyella zoohelcum, as well as Chryseobacterium balustinum, Chryseobacterium indologenes, and Chryseobacterium gleum. The sequences of the rrs genes of the four R. anatipestifer strains varied between 0.5 and 1.0%, but all of the strains occupied the same position on the phylogenetic tree. In general, differences in rrs genes were observed among R. anatipestifer strains, even within a given serotype, as shown by restriction fragment length polymorphism of PCR-amplified rrs genes.
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Transfer of Blastobacter natatorius (Sly 1985) to the Genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov.
More LessThe budding bacterium Blastobacter natatorius belongs to the alpha-4 group of the Proteobacteria and clusters phylogenetically on a deep branch with Sphingomonas capsulata, with which it shares 93.9% 16S rRNA sequence similarity. On phylogenetic, phenotypic, and chemotaxonomic grounds a proposal is made to transfer B. natatorius to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov.
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Reclassification of Paenibacillus durum (Formerly Clostridium durum Smith and Cato 1974) Collins et al. 1994 as a Member of the Species P. azotofixans (Formerly Bacillus azotofixans Seldin et al. 1984) Ash et al. 1994
More LessPhenotypic studies, as well as the reaction of Paenibacillus durum genomic DNA with a 16S ribosomal DNA (sequence of variable regions V1 to V4)-based Paenibacillus azotofixans-specific PCR system and oligonucleotide probe, the presence of sequences homologous to Klebsiella pneumoniae nifKDH in both P. durum and P. azotofixans, and the results of DNA-DNA hybridization experiments performed with the P. durum and P. azotofixans type strains and one additional P. durum strain, showed that these two species form a homogeneous group. In addition, evidence was found for the presence of nif genes in P. durum, and P. durum was shown to fix atmospheric nitrogen. Therefore, the names P. durum and P. azotofixans should be considered synonyms. As P. durum was capable of fixing nitrogen and fixation without inhibition by nitrate is a major characteristic of the group, we propose that P. durum be included in the species P. azotofixans.
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Streptomyces spitsbergensis Wieczorek et al. 1993 Is a Later Subjective Synonym of Streptomyces baldaccii (Farina and Locci 1966) Witt and Stackebrandt 1991
More LessReexamination of the morphological, cultural, and physiological characteristics of Streptomyces spitsbergensis Wieczorek et al. 1993 revealed that this organism belongs to the whorl-forming streptomycetes, and DNA-DNA hybridization data confirmed that S. spitsbergensis is a later subjective synonym of Streptomyces baldaccii (Farina and Locci 1966) Witt and Stackebrandt 1991.
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Characterization of Leptospiral Serovars by Randomly Amplified Polymorphic DNA Fingerprinting
More LessRandomly amplified polymorphic DNA (RAPD) fingerprinting of 14 laboratory strains of leptospiral serovars (serovars australis, autumnalis, ballum, bataviae, canicola, grippotyphosa, hardjoprajitno, hebdomadis, icterohaemorrhagiae, javanica, pomona, pyrogenes, panama, and tarassovi) was carried out by using a pair of primers. Each serovar had a unique and distinct fingerprint pattern. DNAs of other bacterial species, including Escherichia coli, Pasteurella multocida, Salmonella spp., Pseudomonas spp., and Klebsiella spp., did not show any amplification. RAPD fingerprinting was found to be a rapid and sensitive method for serovar identification when it was compared to DNA restriction enzyme analysis, which produced a larger number of bands that made it more difficult to compare serovars.
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Classification of “Pseudomonas azotocolligans” Anderson 1955, 132, in the Genus Sphingomonas as Sphingomonas trueperi sp. nov.
More Less“Pseudomonas azotocolligans” ATCC 12417T (T = type strain), which was described as a diazotrophic bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this strain clusters phylogenetically with species of the genus Sphingomonas and represents a new species. The results of investigations of the fatty acid patterns, polar lipid profiles, and quinone system supported this placement. The substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of any previously described species of the genus Sphingomonas. The new name Sphingomonas trueperi is proposed on the basis of these results and previously published data for the G+C content of the genomic DNA and the polyamine pattern.
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Etymology of the Genus Name Nostoc (Cyanobacteria)
More LessThe word Nostoch was invented by the 15th century scientist, philosopher, and alchemist Aureolus Philippus Theophrastus Bombastus von Hohenheim (Paracelsus) to describe the gelatinous colonies of the ubiquitous terrestrial cyanobacterium Nostoc commune. It is proposed that Nostoch is a play on two words, an Old English word and a German word, which both describe that part of the human anatomy intimately associated with extracellular polysaccharide; Nost hryl and Nasenloch = Nostoch.
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Revised Nomenclature of Specific or Subspecific Epithets That Do Not Agree in Gender with Generic Names That End in -bacter
More LessThe names Acetobacter xylinum, Acetobacter xylinum subsp. sucrofermentans, Acetobacter xylinum subsp. xylinum. Caedibacter caryophila, Campylobacter cryaerophila, Fibrobacter succinogenes subsp. elongata, Iodobacter fluviatile, and Rhodobacter blastica are revised in accordance with Rule 12c or Rule 13b of the International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 revision.
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Genomic Relationship of Five Species of the Genus Chromatium by Analysis of Large Restriction Fragments (Macrorestriction Analysis) Using Pulsed-Field Gel Electrophoresis
More LessLarge restriction fragment (macrorestriction) patterns resolved by pulsed-field gel electrophoresis (PFGE) were used to calculate the genomic similarity within and among five members of the genus Chromatium with closely related phenotypes: C. minutissimum, C. vinosum, C. gracile, C. salexigens, and C. tepidum. PFGE allowed the study of the genomic organizations of these organisms. The results reveal a high level of homogeneity among the strains of C. vinosum analyzed. Moreover, there seems to be a close genetic relationship between C. vinosum and C. minutissimum.
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- Original Papers Relating To The Systematics Of Yeasts
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Dipodascus starmeri sp. nov., a New Species of Yeast Occurring in Cactus Necroses
More LessAbstractIn a previous publication describing the geographic distribution of yeasts associated with cactus necroses (W. T. Starmer, M.-A. Lachance, H. J. Phaff, and W. B. Heed, Evol. Biol. 24:253–296, 1990), 127 isolates were identified as strains of Candida ingens van der Walt et van Kerken on the basis of morphology and certain phenotypic characteristics. Here we show by using DNA hybridization and additional phenotypic properties that these strains were misidentified and that they represent a minimum of three separate species that can be differentiated from C. ingens and from each other by utilization of 2-propanol or acetone, sensitivity to digitonin, utilization of L-lysine as a sole nitrogen source, vitamin dependence, NaCl tolerance, lipolytic activity, and habitat. One of the new species is haploid and heterothallic, and its teleomorph represents the genus Dipodascus. We describe Dipodascus starmeri sp. nov. The phylogenetic relationship of D. starmeri with other members of the genus Dipodascus and its anamorph, the genus Geotrichum, was estimated from ribosomal DNA nucleotide sequence divergence. The type strain, a heterothallic haploid isolate, is UCD-FST 72-316 (= CBS 780.96 = ATCC 200546 = NRRL Υ-17816). The complementary mating type is UCD-FST 81-513.3 (= CBS 781.96 = ATCC 200547 = NRRL Υ-17817).
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Rhodotorula cresolica sp. nov., a Cresol-Assimilating Yeast Species Isolated from Soil
More LessAbstractA cresol-assimilating yeast strain of a previously undescribed species belonging to the genus Rhodotorula was isolated from soil. The new strain differs from the previously described species of the genus in its pattern of assimilation of carbon and nitrogen compounds, G+C content, and low levels of DNA-DNA-homology. The new species Rhodotorula cresolica is described. The type strain is CBS 7998.
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