- Volume 48, Issue 1, 1998
Volume 48, Issue 1, 1998
- Systematic Bacteriology
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Revised group classification of the genus Spiroplasma
Significant changes have been made in the systematics of the genus Spiroplasma (class Mollicutes) since it was expanded by revision in 1987 to include 23 groups and eight sub-groups. Since that time, two additional spiroplasmas have been assigned group numbers and species names. More recently, specific epithets have been assigned to nine previously designated groups and three sub-groups. Also, taxonomic descriptions and species names have been published for six previously ungrouped spiroplasmas. These six new organisms are: Spiroplasma alleghenense (strain PLHS-1T) (group XXVI), Spiroplasma lineolae (strain TALS-2T) (group XXVII), Spiroplasma platyhelix (strain PALS-1T) (group XXVIII), Spiroplasma montanense (strain HYOS-1T) (group XXXI), Spiroplasma helicoides (strain TABS-2T) (group XXXII) and Spiroplasma tabanidicola (strain TAUS-1T) (group XXXIII). Also, group XVII, which became vacant when strain DF-1T (Spiroplasma chrysopicola) was transferred to group VIII, has been filled with strain Tab 4c. The discovery of these strains reflects continuing primary search in insect reservoirs, particularly horse flies and deer flies (Diptera:Tabanidae). In the current revision, new group designations for 10 spiroplasma strains, including six recently named organisms, are proposed. Three unnamed but newly grouped spiroplasmas are strain TIUS-1 (group XXIX; ATCC 51751) from a typhiid wasp (Hymenoptera: Tiphiidae), strain BIUS-1 (group XXX; ATCC 51750) from floral surfaces of the tickseed sunflower (Bidens sp.) and strain BARC 1901 (group XXXIV; ATCC 700283). Strain BARC 2649 (ATCC 700284) from Tabanus lineola has been proposed as a new sub-group of group VIII. Strains TIUS-1 and BIUS-1 have unusual morphologies, appearing as helices at only certain stages in culture. In this revision, potentially important intergroup serological relationships observed between strain DW-1 (group II) from a neotropical Drosophila species and certain sub-group representatives of group I spiroplasmas are also reported.
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Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]
More LessMedicago ruthenica [(L.) Ledebour] is native to Inner Mongolia where rhizosphere samples were collected for the isolation of 106 rhizobial cultures. Besides nodulating the original trap host, the isolates formed nitrogen-fixing symbioses with Phaseolus vulgaris. Only half of the isolates nodulated alfalfa (Medicago sativa). but these did not form nitrogen-fixing symbioses. Rhizobium tropici also formed nitrogen-fixing symbioses with Medicago ruthenica. A total of 56 distinctive muitilocus electrophoretic types (ETs) were identified among 94 of the 106 isolates which were analysed for variation in electrophoretic mobility of 12 enzyme loci. One isolate (USDA 1920) possessed a unique ET, while the ETs of the other isolates formed two weakly divergent subgroups approximately equal in size. It was concluded from small subunit rRNA gene sequences of eight isolates of Medicago ruthenica that they belonged to the genus Rhizobium and not to the genus Sinorhizobium which is more commonly associated with Medicago. Genomic similarity, determined from DNA hybridization analysis, between USDA 1920 and the strain representing the remaining isolates (USDA 1844) was lower than 20%. Based upon these observations it was concluded that at least three genomic species of rhizobia form nitrogen-fixing symbioses with Medicago ruthenica. One of these genomic species is R. tropici, another is represented by the single isolate USDA 1920 and the name Rhizobium mongolense is proposed for the third genomic species represented by USDA 1844.
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Thermococcus gorgonarius sp. nov. and Thermococcus pacificus sp. nov.: heterotrophic extremely thermophilic archaea from New Zealand submarine hot vents
Two extremely thermophilic archaea, designated W-12 and P-4, were isolated from a geothermal vent in the tidal zone of Whale Island, New Zealand, and from geothermally heated bottom deposits of the Bay of Plenty, New Zealand, respectively. Cells of isolate W-12 are irregular cocci, 0·3--1·2 pm in diameter, motile with polar flagella. The cell envelope consists of one layer of subunits with a major protein of M r 75000. Cells produce protrusions of different kinds: prostheca-like, chains of bubbles, or network of fimbriae. Cells of isolate P-4 are regular cocci, 0·7--1·0 µm in diameter, motile with polar flagella. The cell envelope consists of two layers of subunits; its major protein has an M r of 56000. Both organisms are obligate anaerobes, fermenting peptides in the case of strain W-12, or peptides and starch in the case of P-4. Elemental sulfur is required for growth and is reduced to hydrogen sulfide. The optimal growth temperature of the new isolates is in the range 80-88 °C. The optimal growth pH is 6·5-7·2. The G+C content of the DNA of strain W-12 is 50·6 mol%, and of strain P-4 is 53·3 mol%. Based on physiological characteristics, 16S rDNA sequence comparison and DNA base composition, the new isolates were considered to be members of the genus Thermococcus. The low level of DNA-DNA hybridization with the type strains of other Thermococcus species confirms the novel species status of the new isolates. The new isolates are described as Thermococcus gorgonarius sp. nov., with type strain W-12 (= DSM 10395T), and Thermococcus pacificus sp. nov., with type strain P-4 (= DSM 10394T).
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Sulfur-inhibited Thermosphaera aggregans sp. nov., a new genus of hyperthermophilic archaea isolated after its prediction from environmentally derived 16S rRNA sequences
More LessRecently, a new procedure was developed which allowed for the first time the isolation of a hyperthermophilic archaeum tracked by 16S rRNA analysis from a terrestrial hot solfataric spring (‘Obsidian Pool’, Yellowstone National Park, WY, USA). This novel isolate is characterized here. Cells are round cocci with a diameter of 0·2-0·8 µm, occurring singly, in pairs, short chains and in grape-like aggregates. The aggregates exhibit a weak bluish-green fluorescence under UV radiation at 420 nm. The new isolate is an anaerobic obligate heterotroph, using preferentially yeast extract for growth. The metabolic products include CO2, H2, acetate and isovalerate. Growth is observed between 65 and 90 °C (optimum: 85 °C), from pH 5·0 to 7·0 (optimum: 6·5) and up to 0·7% NaCI. The apparent activation energy for growth is about 149 kJ mol−1. Elemental sulfur or hydrogen inhibits growth. The core lipids consist mainly of acyclic and cyclic glycerol diphytanyl tetraethers. The cell envelope contains a cytoplasmic membrane covered by an amorphous layer of unknown composition; there is no evidence for a regularly arrayed surface-layer protein. The G+C content is 46 mol%. On the basis of 16S rRNA sequence comparisons in combination with morphological, physiological and biochemical properties, the isolate represents a new genus within the Desulfurococcaceae, which has been named Thermosphaera. The type species is Thermosphaera aggregans, the type strain is isolate M11TLT (= DSM 11486T).
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Biochemical and genetic characterization of a Prevotella intermedia/nigrescens-like organism
Thirty-three previously non-typable faintly pigmented Gram-negative anaerobic bacterial isolates, biochemically most closely related to Prevotella intermedia and Prevotella nigrescens, were analysed for enzymic reactions, cellular fatty acid (CFA) composition, electrophoretic mobility of malate and glutamate dehydrogenases, hybridization with P. intermedia and P. nigrescens species-specific oligonucleotide probes and, for genetic heterogeneity, by arbitrarily primed PCR (AP-PCR). P. intermedia ATCC 25611T and P. nigrescens ATCC 33563T were run in parallel for comparison. Twenty-nine isolates originated from the normal oral flora of 18 subjects (including five mother-child pairs), and four isolates from various infections. Except for a negative lipase reaction, enzymic profiles of the test isolates were similar to those of P. intermedia and P. nigrescens. Clustering of CFAs, electrophoretic mobility patterns, hybridization with DNA probes for P. intermedia and P. nigrescens, and AP-PCR band patterns of the test isolates differed from those of the type strains of P. intermedia and P. nigrescens, suggesting the existence, in humans, of a new anaerobic species of pigmented, moderately saccharolytic, indole-positive Gram-negative rods.
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Phylogenetic characterization and proposal of a new pigmented species to the genus Prevotella: Prevotella pallens sp. nov.
Complete 16S rRNA gene sequences of three representative strains of anaerobic, Gram-negative, pigmented, moderately saccharolytic, indole-positive bacteria isolated from the oral cavity of humans were determined. According to comparative analyses of the rRNA sequence data, this organism represents a previously unknown species within the genus Prevotella. In addition, 22 representative strains and 21 reference strains (including 11 Prevotella intermedia and 10 Prevotella nigrescens strains) were subjected to multilocus enzyme electrophoretic analysis. The strains were consistently separated into three clearly distinct groups, corresponding to their previous entities. On the basis of the present phylogenetic results that confirmed our biochemical and genetic data, we propose a new species, Prevotella pallens. The type strain is NCTC 13042 (= AHN 10371).
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Saccharopolyspora spinosporotrichia sp. nov., a novel actinomycete from soil
More LessThe generic position of an aerobic, Gram-positive, non-acid-alcohol-fast actinomycete was determined following isolation of the PCR-amplified 16S rRNA genes and alignment of the resultant sequence with corresponding sequences from representatives of the family Pseudonocardiaceae. The assignment of the organism to the genus Saccharopolyspora was strongly supported by chemotaxonomic and morphological data. The strain was distinguished from representatives of validly described Saccharopolyspora species by a number of phenotypic properties. It is proposed that the organism, strain AS4.198T, be classified in the genus Saccharopolyspora as Saccharopolyspora spinosporotrichia sp. nov.
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Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil
More LessFour moderately thermophilic, carboxydotrophic streptomycetes were the subject of a comparative taxonomic investigation designed to establish their taxonomic relationships. Almost complete sequences of the 16S rRNA genes of the test strains were determined following the isolation and direct sequencing of the amplified genes. The resultant nucleotide sequences were aligned with the sequences of previously studied streptomycetes, and phylogenetic trees generated by using the neighbour-joining, Fitch-Margoliash, maximum-likelihood and maximum-parsimony methods. It was evident from the phylogenetic analyses that strains AT50, AT51 and AT52 were most closely related to Streptomyces thermodiastaticus DSM 40573T and strain AT37 to Streptomyces glaucescens DSM 40716 and Streptomyces pseudogriseolus NRRL 3985. Random DNA amplification profiles clearly distinguished strains AT50, AT51 and AT52 from Streptomyces thermodiastaticus and from strain AT37. The molecular systematic evidence, together with phenotypic data derived from this and previous studies, indicate that the test strains merit species status within the genus Streptomyces. The name Streptomyces thermocarboxydovorans sp. nov. is proposed for strains AT50, AT51 and AT52 (type strain) and Streptomyces thermocarboxydus sp. nov. for strain AT37.
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Description of some coryneform bacteria isolated from human clinical specimens as Corynebacterium falsenii sp. nov.
More LessOver a five-year period, four strains of a yellowish-pigmented coryneform bacterium were received for identification by the Culture Collection of the University of Géteborg. All strains had been isolated from normally sterile human body fluids. Initial biochemical characterization revealed that all four isolates were very similar, with weak pyrazinamidase and urease activities, as well as slow fermentative acid production from glucose as the most significant phenotypic features which differentiated the strains from all other presently defined corynebacteria. Chemotaxonomic investigations demonstrated that the strains belonged to the genus Corynebacterium. SDS-PAGE of whole-cell proteins suggested that all four strains were representatives of the same species. Comparative 16S rRNA gene sequence analysis unambiguously demonstrated that the four strains were genealogically related and represent a new subline within the genus Corynebacterium for which the designation Corynebacterium falsenii sp. nov. is proposed. The type strain of Corynebacterium falsenii is CCUG 33651.
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Phylogeny of the family Moraxellaceae by 16S rDNA sequence analysis, with special emphasis on differentiation of Moraxella species
More LessThirty-three strains previously classified into 11 species in the bacterial family Moraxellaceae were subjected to phylogenetic analysis based on 16S rRNA sequences. The family Moraxellaceae formed a distinct clade consisting of four phylogenetic groups as judged from branch lengths, bootstrap values and signature nucleotides. Group I contained the classical moraxellae and strains of the coccal moraxellae, previously known as Branhamella, with 16S rRNA similarity of ≥95%. A further division of group I into five tentative clusters is discussed. Group II consisted of two strains representing Moraxella atlantae and Moraxella osloensis. These strains were only distantly related to each other (93.4%) and also to the other members of the Moraxellaceae (≤93%). Therefore, reasons for reclassification of these species into separate and new genera are discussed. Group III harboured strains of the genus Psychrobacter and strain 752/52 of [Moraxella] phenylpyruvica. This strain of [M.] phenylpyruvica formed an early branch from the group III line of descent. Interestingly, a distant relationship was found between Psychrobacter phenylpyruvicus strain ATCC 23333T (formerly classified as [M.] phenylpyruvica) and [M.] phenylpyruvica strain 752/52, exhibiting less than 96% nucleotide similarity between their 16S rRNA sequences. The establishment of a new genus for [M.] phenylpyruvica strain 752/52 is therefore suggested. Group IV contained only two strains of the genus Acinetobacter. Strategies for the development of diagnostic probes and distinctive sequences for 16S rRNA-based species-specific assays within group I are suggested. Although these findings add to the classificatory placements within the Moraxellaceae, analysis of a more comprehensive selection of strains is still needed to obtain a complete classification system within this family.
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Caldicellulosiruptor owensensis sp. nov., an anaerobic, extremely thermophilic, xylanolytic bacterium
More LessAn anaerobic, extremely thermophilic xylanolytic, non-spore-forming bacterium was isolated from a sediment sample taken from Owens Lake, California, and designated strain OLT (T = type strain). Strain OLT had a Gram-negative reaction and occurred as short rods which sometimes formed long chains containing a few coccoid cells. It grew at 50--80 °C, with an optimum at 75 °C. The pH range for growth was 5·5--9·0 with an optimum at about pH 7·5. When grown on glucose at optimal conditions, its doubling time was 7·3 h. In addition to glucose, the isolate utilized sucrose, xylose, fructose, ribose, xylan, starch, pectin and cellulose. Yeast extract stimulated growth on carbohydrates but was not obligately required. The end products from glucose fermentation were lactate, acetate, ethanol, H2 and CO2. The G+C content of strain OLT was 36·6 mol%. The 16S rDNA sequence analysis indicated that strain OLT was a member of the subdivision containing Gram-positive bacteria with DNA G+C content of less than 55 mol% and clustered with members of the genus Caldicellulosiruptor. Because strain OLT is phylogenetically and phenotypically different from other members of this genus, it is proposed to designate this isolate Caldicellulosiruptor owensensis sp. nov. Strain OLT is the type strain (=ATCC700167T).
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Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus
More LessTwelve strains named Bacillus pantothenticus, at least 29 Bacillus strains representing 16 species belonging to rRNA groups 1 and 2, one Bacillus dipsosauri strain, and 38 strains of Amphibacillus, Aneurinibacillus, Brevibacillus, Halobacillus, Paenibacillus, Sporosarcina and Marinococcus, were characterized genotypically using amplified rDNA restriction analysis (ARDRA), and phenotypically using routine diagnostic characters comprising 61 biochemical tests in the API System and 15 observations of vegetative cell and sporangial morphology. The B. pantothenticus strains were also characterized by fatty acid methyl ester analysis and SDS-PAGE of whole-cell proteins. ARDRA revealed that strains of B. pantothenticus formed a cluster quite separate from other species in rRNA group 1, supporting the recognition of the former as a separate genus, for which the name Virgibacillus is proposed. The polyphasic data also indicate the presence of an as yet undescribed new species within this genus. The species Virgibacillus pantothenticus and related organisms comprising this new genus can be distinguished from members of Bacillus rRNA group 1 (Bacillus sensu stricto), and from members of Paenibacillus and other aerobic endospore-forming bacteria by routine phenotypic tests.
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PCR fingerprinting of whole genomes: the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveal a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis
More LessGenomic diversity in 21 strains of Bacillus cereus and 10 strains of Bacillus licheniformis was investigated by random amplified polymorphic DNA (RAPD) analysis, which samples the whole genome, and by two PCR fingerprinting techniques sampling the hypervariable spacers between the conserved 16S and 23S rRNA genes of the rRNA gene operon (ITS-PCR) and regions between tRNA genes (tDNA-PCR). RAPD analysis showed a remarkable diversity among strains of B. cereus that was not observed with the rRNA and tRNA intergenic-spacer-targeted PCR, where all the strains showed practically identical fingerprints. A wide variability among the B. cereus strains was also observed in the plasmid profiles, suggesting that the genetic diversity within B. cereus species can arise from plasmid transfer. One contribution to the diversity detected by RAPD analysis was determined by the presence of large extrachromosomal elements that were amplified during RAPD analysis as shown by Southern hybridization experiments. In contrast to the strains of B. cereus, the 10 strains of B. licheniformis were grouped into two clusters which were the same with all the methods employed. The 16S rRNA genes were identical in all 10 strains when examined using single strand conformation polymorphism analysis after digestion with Alul and Rsal. From these data we hypothesize two different evolutionary schemes for the two species.
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Whole-cell protein electrophoretic analysis of viridans streptococci: evidence for heterogeneity among Streptococcus mitis biovars
More LessOne hundred reference strains representing all species belonging to the different phylogenetic lineages of the viridans streptococci were examined by means of one-dimensional whole-organism protein electrophoresis. For most of the species examined, multiple strains characterized by DNA-DNA hybridization were included and, wherever described, representatives of different biochemical variants were analysed. Most species were clearly differentiated. The data support the viewpoint that members of the Streptococcus anginosus group constitute a single species and indicate that Streptococcus mitis biovar 2 is a heterogeneous taxon comprising strains from several streptococcal species.
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Comparison of PCR-based DNA fingerprinting techniques for the identification of Listeria species and their use for atypical Listeria isolates
Four PCR-based DNA fingerprinting techniques were compared for their ability to identify at the species level a heterogeneous collection of isolates belonging to the six valid Listeria species. 16S rDNA-RFLP analysis identified all species and 16S rDNA-SSCP analysis identified almost all species. Also, isolates with unusual biochemical characteristics and/or unusual antigenic composition could be identified correctly. rRNA-intracistronic length polymorphism analysis suffered from high intraspecific variability, a limited number of fragments per profile, and small length differences between the spacers of different species. tRNA-intergenic length polymorphism analysis resulted in identification of all isolates but one, when fluorescent DNA capillary electrophoresis was used such that fragment length differences of 1 bp could be resolved. The four techniques yielded comparable results relevant to the taxonomy of Listeria. They all indicate a high degree of genetic relatedness between L. innocua and L. welshimeri, homogeneity of L. grayi, distinct but clear relatedness of L. grayi to the other Listeria species, a clear distinction between the two subspecies of L. ivanovii, and a clear distinction between Listeria isolates and isolates from closely related taxa or from species which are phenotypically difficult to distinguish from Listeria. New sequence determination of the 16S rRNA gene was necessary to obtain sequences in accordance with the findings of 16S rDNA-RFLP analysis.
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Two new Rahnella genomospecies that cannot be phenotypically differentiated from Rahnella aquatilis
Fifty-one Rahnella aquatilis and R. aquatilis-like strains from water, snails and human sources were characterized by routine biochemical tests, carbon source utilization tests, DNA relatedness (hydroxyapatite method) and 16S rRNA sequencing. The results of the genetic methods indicated that the strains comprised three closely related species within the genus Rahnella. It was not possible to differentiate R. aquatilis from the two newly recognized species. The new species were therefore given the vernacular names Rahnella genomospecies 2 and Rahnella genomospecies 3.
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New aerobic ammonium-dependent obligately oxalotrophic bacteria: description of Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov.
The genus Ammoniphilus is proposed for aerobic endospore-forming Gram-variable rod-shaped bacteria, which are ammonium-dependent, obligately oxalotrophic and haloalkalitolerant, oxidase- and catalase-positive, mesophilic and motile by peritrichous flagella. Cell wall contained two electron-dense layers. The external layer consists of a chain of electron-dense granules morphologically resembling the cellulosomes of Clostridium thermocellum. Two species are described, Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov. The type strains of these species are strains RAOx-1 (= DSM 11538) and RAOx-FS (= DSM 11537), respectively. Ammoniphilus strains were isolated from the rhizosphere of sorrel (Rumex acetosa) and from decaying wood. The strains require a high concentration of ammonium ions and use oxalate as the sole organic source of carbon and energy for growth; no growth factors were required. Growth occurred at pH 6.8--9.5. The optimum temperature and pH for growth were 28--30 °C and 8.0--8.5. All strains grew in a saturated solution of ammonium oxalate, and tolerated 3% NaCl. Whole-cell hydrolysates contain meso-diaminopimelic acid and glucose. The menaquinone of the strains was MK 7, and the major cellular fatty acids were 12-methyl tetradecanoic, cis-hexadec-9-enoic and hexadecanoic acids. The G+C content of the DNA was 45--46 mol% for A. oxalaticus and 42 mol% for A. oxalivorans. The almost complete 16S rDNA sequence of three strains of the two species of Ammoniphilus shows that the genus falls into the radiation of the Clostridium-Bacillus subphylum of Gram-positive bacteria. The closest phylogenetic neighbour of Ammoniphilus is Oxalophagus oxalicus. The DNA-DNA hybridization value between strains RAOx-1 and RAOx-FS was 39.7%.
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Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov.
More LessSixteen heparinase-producing isolates, related to Sphingobacterium heparinum, were grouped into three major clusters by SDS-PAGE and DNA-rRNA hybridizations. Based on a polyphasic approach, it was shown that isolates of two of these clusters and S. heparinum species belong to a new genus for which the name Pedobacter is proposed. The genus consists of Pedobacter heparinus comb. nov. (formerly Sphingobacterium heparinum), which is the type species, Pedobacter piscium comb. nov. (formerly Sphingobacterium piscium), Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. and four as-yet-unnamed DNA hybridization groups. All the previously named taxa can be discriminated by phenotypic features, but have strong overall similarities with representatives of the genus Sphingobacterium and the misclassified species [Flexibacter] canadensis. All these organisms constitute a separate rRNA branch in rRNA superfamily V for which the family Sphingobacteriaceae fam. nov. is proposed.
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Reclassification of Shewanella putrefaciens Owen’s genomic group II as Shewanella baltica sp. nov.
More LessThe taxonomic relationship between several Shewanella putrefaciens isolates from the Baltic Sea and reference strains of this species is presented in this study. Results from DNA-DNA hybridization using a newly developed nonradioactive detection system and from 165 rRNA gene sequencing demonstrated that S. putrefaciens is a heterogeneous species containing more than a single genomic group. The genomic group II was phylogenetically, genotypically and phenotypically distant enough from the species type strain to be classified as a single species within the genus Shewanella. Therefore, we propose to reclassify Owen’s genomic group II as Shewanella baltica sp. nov. with the type strain NCTC 10735.
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Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences
More LessThe 16S rDNAs from 38 strains of the genus Nocardioides, two Aeromicrobium species and Terrabacter tumescens were directly sequenced and then analysed. The mean nucleotide similarity value between the type strains of validly described Nocardioides species was 96.1±3.0%. The mean nucleotide similarity value between the type strains of validly described Nocardioides species and the two Aeromicrobium species was 93.7±1.4%. T. tumescens was distantly related to the genera Nocardioides and Aeromicrobium. The mean intraspecific nucleotide similarity value of 16S rDNA sequences from Nocardioides albus was 99.5±0.5%. The mean intraspecific nucleotide similarity of 16S rDNA sequences from Nocardioides simplex was 100%, except for N. simplex strains ATCC 13260, ATCC 19565 and ATCC 19566, which were shown not to be members of the genus Nocardioides. ‘Nocardioides flavus’ strains IFO 14396T and IFO 14397, and ‘Nocardioides fulvus’ JCM 3335T showed a 16S rDNA similarity value of 100% with Nocardioides luteus KCTC 9575T and Nocardioides albus JCM 5854. ‘N. fulvus’ IFO 14399 shared its highest 16S rDNA similarity with Nocardioides sp. ATCC 39419 at 99%. ‘N. fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 formed a phylogenetic lineage distinct from the genera Nocardioides and Aeromicrobium. ‘Nocardioides thermolilacinus’ strains IFO 14335T and IFO 14336 displayed a close relationship to the genus Streptomyces. From 16S rDNA sequence analyses, it is considered that some strains that have been attributed to the genus Nocardioides should be taxonomically re-evaluated.
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Emended description of Campylobacter sputorum and revision of its infrasubspecific (biovar) divisions, including C. sputorum biovar paraureolyticus, a urease-producing variant from cattle and humans
More LessA polyphasic taxonomic study of 15 bovine and human strains assigned to the catalase-negative, urease-positive campylobacter (CNUPC) group identified these bacteria as a novel, ureolytic biovar of Campylobacter sputorum for which we propose the name C. sputorum bv. paraureolyticus: suitable reference strains are LMG 11764 (human isolate) and LMG 17590 (=CCUG 37579, bovine isolate). The present study confirmed previous findings showing that the salient biochemical tests used to differentiate C. sputorum bv. sputorum from C. sputorum bv. bubulus are not reproducible; and that the absolute validity of source-specific biovars of the species is questionable. A correlation between the results of numerical analysis of protein profiles and the reaction of strains in certain enzyme tests was, however, noted. Therefore, it is proposed that the infrasubspecific (biovar) divisions of C. sputorum should be revised to include bv. sputorum for catalase-negative strains; bv. fecalis for catalase-positive strains; and bv. paraureolyticus for urease-positive strains. Strains classified previously as bv. bubulus should be reclassified as bv. sputorum. The species description of C. sputorum is revised accordingly.
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A new leptospiral serovar, ngavi, in the Tarassovi serogroup isolated from Zimbabwe oxen
More LessTwo strains of the genus Leptospira, belonging to serogroup Tarassovi, were isolated from kidneys of apparently healthy oxen slaughtered at an abattoir in Zimbabwe. Both strains belonged to the same serovar but could not be assigned to previously known serovars using the cross-agglutinin absorption test. The name ngavi is proposed for the new serovar containing these two strains; strain SBF 16 is the reference strain. The Zimbabwe isolates showed some antigenic similarity to serovar gatuni when analyses were carried out using eight monoclonal antibodies, and had restriction patterns similar to those of serovars tarassovi, tunis, moldaviae and guidae when their chromosomal DNAs were analysed using RFLP analysis. The restriction patterns of the two strains could be distinguished from each other and from those of the four serovars when their Southern blots were hybridized with a probe synthesized from a repetitive sequence element cloned from serovar hardjo strain Hardjo-bovis.
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Fermentative degradation of 3-hydroxybenzoate in pure culture by a novel strictly anaerobic bacterium, Sporotomaculum hydroxybenzoicum gen. nov., sp. nov.
More LessA strictly anaerobic bacterium, strain BT, from termite hindgut homogenates, was isolated in pure culture and grew on 3-hydroxybenzoate as sole source of carbon and energy. No other substrate tested was degraded, sulfate, sulfite, thiosulfate, nitrate, ferric iron, oxygen or fumarate were not reduced, and no electron transfer to partner organisms was observed. 3-Hydroxybenzoate was fermented to butyrate, acetate and CO2. Benzoate was detected in the culture supernatant as an intermediate. The isolate was a slightly motile, endospore- forming Gram-positive rod; 16S rDNA sequence analysis revealed a high similarity to members of the genus Desulfotomaculum. The G+C content of the DNA was 48 mol %. Strain BT differs from the members of the genus Desulfotomaculum significantly due to its lack of dissimilatory sulfate reduction, and is therefore described as the type strain of a new genus and species, Sporotomaculum hydroxybenzoicum gen. nov., sp. nov.
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Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of ‘Flectobacillus glomeratus’ as Polaribacter glomeratus comb. nov.
More LessSeveral psychrophilic, gas vacuolate strains of the Cytophage-Flavobacterium-Bacteroides (CFB) phylogenetic group were isolated from sea ice and water from the Arctic and the Antarctic. The closest taxonomically defined species by 16S rRNA sequence analysis is ‘Flectobacillus glomeratus’. However, ‘FIc. glomeratus’ is phylogenetically distant from the Flectobacillus type species, FIc. major. On the basis of phenotypic, genotypic and 16S rRNA sequence analyses we propose a new genus, Polaribacter, with three new species, Polaribacter irgensii strain 23-P (ATCC 700398), Polaribacter franzmannii strain 301 (ATCC 700399) and Polaribacter filamentus strain 215 (ATCC 700397). P. filamentus is the type species of the genus. None of these species exhibits a cosmopolitan or bipolar distribution. This is the first taxonomic description of gas vacuolate bacteria in the CFB group. Additionally, we propose that ‘FIc. glomeratus’ be reclassified to the genus Polaribacter as P. glomeratus, comb. nov.
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Nocardia crassostreae sp. nov., the causal agent of nocardiosis in Pacific oysters
Seven strains of bacteria were isolated from Pacific oysters, Crassostrea gigas, with a focal or systemic disease. The strains were aerobic, Gram-positive, acid-fast, produced a mycelium which fragmented into irregular rod-like elements, had a peptidoglycan containing meso-diaminopimelic acid, arabinose and galactose as major sugars, mycolic acids with 46-58 carbon atoms and G+C-rich DNA. All of these properties are consistent with the classification of the organisms in the genus Nocardia. A partial sequence of the 165 rRNA gene of isolate NB4H was determined following isolation and cloning of the PCR-amplified gene. The sequence was aligned with those of representative mycolic-acid-containing taxa and a phylogenetic tree was generated using the neighbour-joining method. It was evident from the phylogenetic tree that the three strains tested, RB1, OB3P and NB4H, were identical and belonged to the Nocardia otitidiscaviarum rRNA sub-group. The biochemical, chemical, morphological and physiological properties of the isolates were also essentially identical and served to distinguish them from representative nocardiae. It is, therefore, proposed that the strains isolated from the diseased Pacific oysters be assigned to a new species, Nocardia crassostreae. The type strain is NB4H (= ATCC 700418).
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Phenotypic diversity of Pseudoalteromonas citrea from different marine habitats and emendation of the description
Four strains of marine, aerobic, agar-decomposing bacteria with one polar flagellum and with DNA G+C contents of 38.9-40.2 mol% were isolated from the Far-Eastern mussels Crenomytilus grayanus and Patinopecten yessoensis. These four strains were identified as Pseudoalteromon as; however, they were phenotypically different from species described previously according to carbon compound utilization tests and the BIOLOG identification system. High agar-decomposing activity was found in two strains, in one of which agarase, α-galactosidase, pustulanase and laminarinase had been detected. The level of DNA homology of three of the strains was 70-100%. The fourth isolate was genetically less related to the others (67 % DNA relatedness) and phenotypically was more distant from other members of this group; however, all four strains were assigned to a single species genotypically. DNA from the strains isolated from mussels showed 40-45% genetic relatedness with the DNA of Alteromonas atlantica, 8-36% with DNA of Pseudoalteromonas haloplanktis subsp. haloplanktis, Pseudoalteromon as haloplanktis subsp. tetraodonis, Pseudoalteromon as undina, Pseudoalteromon as nigrifaciens and Pseudoalteromon as carrageenovora, 53% with Pseudoalteromon as elyakovii, 32-48% with marine P. nigrifaciens from mussels and 14-16% with Alteromonas macleodii. The DNA-DNA hybridization data revealed that the levels of relatedness between the strains isolated and the type strains of Pseudoalteromon as citrea and Pseudoalteromon as fuliginea described recently were significant (95-85 %). These results were confirmed by serological data employing polyclonal antibodies to cell surface antigens. The strains isolated from mussels were identified as P. citrea. The hybridization data showed that the name P. fuliginea Romanenko et al. 1994 should be recognized as a junior subjective synonym of P. citrea Gauthier 1977. A notable phenotypic diversity of P. citrea which might be a reflection of their ecological habitats is discussed.
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Phylogenetic characterization of the bacterium-like organism associated with marginal chlorosis of strawberry and proposition of a Candidates taxon for the organism, ‘ Candidates Phlomobacter f ragariae '
More LessMarginal chlorosis is a new disease of strawberry which was first seen in France in 1988. A phloem-restricted bacterium-like organism was found associated with the disease. Even though the organism could not be cultured, and resembles in this way most other phloem-restricted pathogens, characterization was achieved from the sequence of its PCR-generated 16S rDNA, and comparison with other organisms. From these studies, the strawberry agent was found to be a new bacterium within group 3 of the gamma subclass of Proteobacteria, a group of Gram-negative bacteria including, in particular, insect symbionts or parasites as well as enterobacteria. Its closest relative, Arsenophonus nasoniae, is the causal agent of the son- killer trait in wasps. The two bacteria share 92% 16S rDNA sequence identity. We propose a Candidates taxon for the marginal-chlorosis-associated bacterium, ‘Candidates Phlomobacter fragariae'.
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Sequences of the 16S rRNA genes and phylogeny of the goat mycoplasmas Mycoplasma adleri, Mycoplasma auris, Mycoplasma cottewii and Mycoplasma yeatsii
More LessThe nucleotide sequences of the 16S rRNA genes from the type strains of four goat mycoplasmas, Mycoplasma adleri, Mycoplasma auris, Mycoplasma cottewii and Mycoplasma yeatsii, were determined by direct solid-phase DNA sequencing. Polymorphisms were found in two of the 16S rRNA gene sequences, showing the existence of two different rRNA operons. Three polymorphisms were found in M. adleri, and one was found in M. yeatsii. The sequence information was used for the construction of phylogenetic trees. M. adleri was included in the Mycoplasma lipophilum cluster within the hominis group. M. auris was comprised in the Mycoplasma hominis cluster of the hominis group. M. cottewii and M. yeatsii were found to be very closely related with only four nucleotide differences, and they grouped with Mycoplasma putrefaciens in the Mycoplasma mycoides cluster within the spiroplasma group. Sequencing of two field isolates of M. cottewii and M. yeatsii, geographically distant from the type strains, showed that the 16S rRNA gene from the field isolate of M. cottewii was identical to the one from the type strain. The field isolate of M. yeatsii had only two nucleotide differences to the type strain and these were present in only one of the two rRNA operons. Sequencing of the 16S rRNA genes from two unidentified mycoplasma isolates from Nepal indicated that they should both be regarded as M. auris strains.
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Classification of new phytoplasmas associated with diseases of strawberry in Florida, based on analysis of 16S rRNA and ribosomal protein gene operon sequences
More LessStrawberry plants exhibiting symptoms of stunting and abnormally small leaves were observed in production fields in central Florida, USA. Since the symptoms were suggestive of phytoplasma infection, plants were assayed for presence of phytoplasma by PCR amplification of 16S rDNA and ribosomal protein (rp) gene sequences. Amplification of phytoplasma-specific DNA sequences by PCR indicated infection of the diseased strawberry plants by phytoplasmas. RFLP analyses of amplified 16S rDNA revealed that the plants were infected by two mutually distinct phytoplasmas that differed from strawberry green petal phytoplasma (group 16Srl-C). Both phytoplasmas were members of 16S rRNA gene group I (16Srl). Based on RFLP analysis of amplified 16S rDNA and rp gene sequences, one was classified in group 16Srl subgroup I and new rp subgroup 16Srl-l(rp); its 16S rRNA-rp subgroup was designated 16Srl-K(rr-rp). The second phytoplasma represented a previously undescribed subgroup, designated K, in 16S rRNA group I but belonged to rp subgroup 16Srl-J(rp); this phytoplasma's 16S rRNA-rp subgroup was designated 16Srl- J(rr-rp). Results of RFLP analyses agreed with putative restriction site maps based on nucleotide sequences determined for the amplified 16S rDNAs and rp gene operon DNAs. Further evidence indicated that the 16Srl-K(rr-rp) strawberry phytoplasma, Mexican periwinkle virescence phytoplasma and stolbur phytoplasma shared sequence homologies that enabled amplification of DNA from all three by PCR using primers previously designed as stolbur- specific.
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Note
More LessThe nucleotide sequence of the 16S rRNA genes of four rare human mycoplasma species. Mycoplasma faucium, M. buccale, M. primatum and M. spermatophilum, were partially sequenced and compared to published rRNA genes of mycoplasmas to determine their position in the Mollicutes phylogenetic tree. Nucleotide sequence motif and overall similarities allowed positioning of these mycoplasmas in the hominis phylogenetic group, as defined by Weisburg et al. [Weisburg, W. G., Tully, J. G., Rose, D. L. & 9 other authors (1989). J Bacteriol 171, 6455-6467]. Furthermore, these mycoplasmas could be clustered into two different subdivisions of the hominis group: (i) M. faucium and M. buccale were found to be included in the M. fermentans subdivision, and (ii) M. primatum and M. spermatophilum were included in the M. hominis one. Variable regions of the 16S rRNA genes were used to determine specific PCR primers to detect and identify M. faucium.
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Note
More LessA sulfate-reducing bacterium, strain Aspo-2, was isolated from granitic groundwater sampled at a depth of 600 m. This and other strains of SRB frequently occur in the deep granitic rock aquifers studied. On the basis of its morphological, physiological and genotypical properties, and its unique habitat, we propose strain Aspo-2 as a new species of the genus Desulfovibrio, Desulfovibrio aespoeensis (DSM 10631T).
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Note
More LessThe presence of a Burkholderia pseudomallei-like species based upon the significant genotypic and phenotypic dissimilarities exhibited between these organisms and true B. pseudomallei strains has been reported previously. In this study, a comprehensive 16S rDNA-based phylogenetic analysis further supports the existence of this newly described Burkholderia species for which the name Burkholderia thailandensis sp. nov. is proposed.
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More LessSpiroplasma group XIV strain EC-1T and other isolates from the lampyrid beetle Ellychnia corrusca form a serogroup with tabanid spiroplasma strains (TC-1 and TS-1). It was hypothesized that similarities among these strains reflect a transmission cycle in which lampyrid beetles serve as overwintering hosts and tabanid adults become infected and transmit a homogeneous population of spiroplasma strains during spring, summer and autumn. In the present study, variations in restriction fragment length patterns suggest the presence of multiple genovars. Genotypic analysis may therefore be a companion to serology in elucidating spiroplasma diversity, and may provide clues to strain host range.
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- Systematics Of Yeasts
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Differentiation and species identification of yeasts using PCR
More LessA PCR-based method has been developed that permits both intraspecies differentiation and species identification of yeast isolates. Oligonucleotide primers that are complementary to intron splice sites were used to produce PCR fingerprints that display polymorphisms between different species of indigenous wine yeasts. Although polymorphisms existed between isolates of the same species, the banding patterns shared several amplification products that allowed species identification. Importantly, the method was able to distinguish between species of the closely related Saccharomyces sensu stricto yeasts. In two cases where isolates could not be positively identified there was discrepancy between the phenetic and phylogenetic species concept. The method has applications in yeast ecological studies, enabling the rapid grouping of isolates with related genomes and the investigation of population dynamics of strains of the same species.
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Fellomyces ogasawarensis sp. nov. and Fellomyces distylii sp. nov., yeasts isolated from a plant in Japan
More LessFellomyces ogasawarensis and Fellomyces distylii, new yeast species isolated from a dead leaf of a plant (Distylium lepidotum Nakai, family Hamamelidaceae) collected in the Ogasawara Islands, isolated islands in the Pacific Ocean about 1000 km south of Japan, are described. The phylogenetic relationship of F. ogasawarensis and F. distylii with other members of the genus Fellomyces was estimated from 18S rRNA gene sequence analysis. The type strain of F. ogasawarensis is strain OK-81 (= JCM 9861) and that of F. distylii is strain OK-83 (= JCM 9862).
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Phylogenetic analysis of the Saccharomyces cerevisiae group based on polymorphisms of rDNA spacer sequences
More LessThe phylogenetic relationships between species of yeasts assigned to the Saccharomyces sensu stricto group, which includes Saccharomyces cerevisiae and Saccharomyces bay anus, were studied together with Saccharomyces pastorianus and Saccharomyces paradoxus. The experimental approaches used were RFLP analysis of the PCR-amplified rDNA internal transcribed spacer (ITS) and intergenic spacer, and total ITS sequence analysis. Both RFLP and sequence analyses gave fairly similar results. The gene trees generated with either of the two data sets showed the distribution of the yeasts into two major, well- separated, phylogenetic clusters called 'cerevisiae' and 'bayanus'. The 'cerevisiae' cluster included the S. cerevisiae type strain, together with most of the species (16 out of 23), whereas the 'bayanus' cluster included the remaining seven type strains. Therefore, analysis of rDNA sequences confirmed 5. cerevisiae and S. bayanus as two well-defined taxa. However, 5. pastorianus and 5. paradoxus, the two other usually accepted taxa of the now- defined Saccharomyces sensu stricto complex, could not be clearly separated from 5. bayanus and S. cerevisiae, respectively. However, in both PCR-RFLP and ITS sequence analyses, 5. paradoxus had the outermost position in the 'cerevisiae' cluster. PCR-RFLP analysis of the ribosomal spacer sequences was also carried out on 26 Saccharomyces strains isolated in various wine-growing regions of France in an attempt to clarify their positions in the Saccharomyces phylogenetic tree. Compared to the diversity of the Saccharomyces type strains, less genetic diversity was detected among these yeasts and several of them exhibited identical RFLP patterns. Most of the wine yeast strains (16 out of 26) were closely related to each other and were found within the 'cerevisiae' cluster. The remaining 10 wine yeast strains branched within the 'bayanus' cluster. PCR-RFLP analysis of ribosomal spacer sequences thus appears to be a useful and appropriate method for the correct characterization of Saccharomyces yeast strains used in food processing.
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- International Committee On Systematic Bacteriology
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Paenibacillus azotofixans (Seldin et al. 1984) Ash et al. 1995 does not have priority over Paenibacillus durum (Smith and Cato 1974) Collins et al. 1994: request for an opinion
More LessWe propose that the organism described by Seldin et al. (1984), which is based on the type strain ATCC 35681, should continue to be called Paenibacillus azotofixans although, with the reclassification of Paenibacillus durum as a member of Paenibacillus azotofixans, the epithet durum has priority.
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- Errata
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Volumes and issues
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Volume 74 (2024)
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