- Volume 43, Issue 4, 1993
Volume 43, Issue 4, 1993
- Original Papers Relating To Systematic Bacteriology
-
-
-
Campylobacter showae sp. nov., Isolated from the Human Oral Cavity
More LessNine Campylobacter-like strains were isolated from human gingival crevices and characterized. These strains were gram-negative, straight rods that were motile by means of multiple unipolar flagella. They were asaccharolytic and preferred an anaerobic atmosphere rather than a microaerophilic atmosphere for growth, and their growth was stimulated by formate and fumarate. These strains were biochemically similar to Campylobacter curvus and Campylobacter rectus, but were clearly distinguishable from these organisms by the number of flagella (two to five flagella at one end of the cell), by being catalase positive, by their whole-cell protein profiles, by their Western blot (immunoblot) patterns, and on the basis of DNA-DNA homology data. They could also be differentiated from the other species of the genus Campylobacter. The nine Campylobacter-like strains were compared with two strains (FDC 286 and VPI 10279) representing a previously described but unnamed Wolinella sp. The nine isolates and strains FDC 286 and VPI 10279 were found to be members of a single species. The 16S rRNA sequences of two strains of the newly identified species were compared with the rRNA sequences of 21 reference Campylobacter, Wolinella, and Helicobacter species in order to generate a phylogenetic tree. We propose the name Campylobacter showae for the newly identified strains; strain SU A4 (= ATCC 51146) is the type strain of this new species.
-
-
-
-
Ureaplasma canigenitalium sp. nov., Isolated from Dogs
More LessUreaplasma strains isolated from dogs (Canis familiaris) were characterized and compared with the type strains of five previously described species of the genus Ureaplasma, Ureaplasma urealyticum(isolated from humans), Ureaplasma diversum(isolated from cattle), Ureaplasma gallorale(isolated from chickens), Ureaplasma cati(isolated from cats), and Ureaplasma felinum(isolated from cats). The canine strains hydrolyzed urea but not arginine or glucose, were membrane bound, lacked a cell wall, passed through 450-nm-pore-size membrane filters, required cholesterol for growth, and formed minute colonies (diameter, 20 to 140 m) on agar medium. These canine ureaplasma strains have been reported to be members of four serovars. The four serovars of canine strains fell into a single group on the basis of their genomic properties, as determined by DNA-DNA hybridization. On the basis of these findings, we propose that ureaplasmas with these characteristics belong to a new species, Ureaplasma canigenitalium, with strain D6P-C (= ATCC 51252) as the type strain.
-
-
-
Classification of Citrobacteria by DNA Hybridization: Designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and Three Unnamed Citrobacter Genomospecies
DNA relatedness studies (hydroxyapatite method) were done on 112 strains of citrobacteria. By using the recommended definition of a genomospecies 11 genomospecies were identified in the genus Citrobacter. These genomospecies were separable by their biochemical profiles. Citrobacter koseri (Citrobacter diversus) and Citrobacter amalonaticus proved to be homogeneous species, as previously described. C. amalonaticus biogroup 1, as described by Farmer et al. (J. Clin. Microbiol. 21:46-76, 1985), was shown to be a separate homogeneous species, which was named Citrobacter farmeri sp. nov. The Citrobacter freundii complex was quite heterogeneous. C. freundii sensu stricto, as represented by the type strain, contained only 9 of 66 strains in this complex. The remaining 57 strains were members of seven genomospecies. Genomospecies 5, containing 21 strains, was named Citrobacter youngae sp. nov. Genomospecies 6, containing 15 strains, was named Citrobacter braakii sp. nov. Genomospecies 7 and 8, each containing six strains, were named Citrobacter werkmanii sp. nov. and Citrobacter sedlakii sp. nov., respectively. Genomospecies 9, 10, and 11, each containing three strains, were not named.
-
-
-
Genetic Relatedness of Bordetella Species as Determined by Macrorestriction Digests Resolved by Pulsed-Field Gel Electrophoresis
More LessThe genetic relatedness of the three medically important Bordetella species was examined by macrorestriction digestion of DNA with the rarely cutting enzyme Xba I and resolution by pulsed-field gel electrophoresis. Our data showed that Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica produced species-specific macrorestriction profiles and that there was some variation between different isolates of the same species. Conserved bands at 130 and 155 kb occurred with B. pertussis(130 isolates tested), but the nine variable bands between 200 and 412 kb distinguished 21 types. The 10 isolates of B. parapertussis tested produced up to 11 bands at 118 to 375 kb, 4 of which were variable, giving three types. The eight B. bronchiseptica isolates examined produced up to 16 bands at 118 to 394 kb, 11 of which were variable, giving three types. The results of this work are compared with the results of previous DNA-DNA hybridization and multilocus enzyme electrophoresis studies which suggested that these three species are closely related and should be considered members of the same species.
-
-
-
Phylogenetic Relationships between Some Members of the Genera Deleya, Halomonas, and Halovibrio
More LessThe genera Halomonas and Deleya, which constitute the family Halomonadaceae, are difficult to differentiate on the basis of phenotypic and chemotaxonomic attributes. DNA-rRNA hybridization studies have indicated that some Halomonas spp. have the same level of relationship to the type species of the genus Deleya as some Deleya spp. A phylogenetic analysis of the 16S rRNA sequences of seven members of the Halomonadaceae indicated that the members of the genera Halomonas and Deleya do not form separate monophyletic subgroups, confirming the lack of any phylogenetic support for retention of these taxa as separate genera. A phylogenetic analysis of the 16S rRNA sequence of Halovibrio variabilis confirmed that this species belongs in the Halomonadaceae. All of the members of the Halomonadaceae examined and Halovibrio variabilis possess a cytosine residue at position 486 (Escherichia coli numbering), which is an extremely rare attribute among the prokaryotes and has been reported in only one other species, Listonella anguillarum. Several other signature characteristics which define this group in the gamma subclass of the Proteobacteria are identified. The Jukes-Cantor distances between members of the family Halomonadaceae, including Halovibrio variabilis, range from 0.086 to 0.000 (the levels of similarity between the 16S rRNA sequences range from 92.6 to 100%). The members of the genera Halomonas, Deleya, and Halovibrio form a monophyletic group and share common chemotaxonomic and phenotypic characteristics. Subgroups containing members of the genera Halomonas, Deleya, and Halovibrio cannot be resolved on the basis of phylogenetic, chemotaxonomic, or phenotypic data. Our data indicate that the members of the genera Halomonas, Deleya, and Halovibrio should be united in a single genus.
-
-
-
Taxonomic Utility of Restriction Endonuclease Fingerprinting of Large DNA Fragments from Streptomyces Strains
More LessUsing a method known as low-frequency restriction fragment analysis (LFRFA) (M. L. Beyazova and M. P. Lechevalier, Int. J. Syst. Bacteriol. 42:422-433, 1992), we determined the molecular weights of Ase I restriction fragments of Streptomyces DNAs by pulsed-field gel electrophoresis. The levels of similarity of fragment patterns among strains were determined by using the simple matching coefficient, and clustering was performed by using the unweighted pair group with mathematical average algorithm. A total of 59 strains representing eight species and the numerically classified taxon Streptomyces cyaneus group A18 (S. T. Williams, M. Goodfellow, G. Alderson, E. M. H. Wellington, P. H. A. Sneath, and M. J. Sackin, J. Gen. Microbiol. 129:1743-1813, 1983) were studied. Forty-two strains (six species) formed eight clusters at levels of similarity of more than 80%; 17 strains (including the entire S. cyaneus group) were unclustered. Cluster 1 contained all of the Streptomyces albus strains studied plus two strains of Streptomyces somaliensis and two strains of Streptomyces lavendulae. Cluster 2 contained 8 of the 12 Streptomyces fradiae strains examined plus one strain each of S. somaliensis and S. lavendulae. Cluster 3 was heterogeneous in terms of species. Cluster 4 contained two S. somaliensis strains; cluster 5 contained three S. fradiae strains; cluster 6 contained three Streptomyces rimosus strains; and clusters 7 and 8 contained seven and three Streptomyces ipomoea strains, respectively. The S. cyaneus group strains exhibited no clustering among themselves or with the other species examined. Some Streptomyces species which exhibited high levels of similarity (85 to 95%) in physiological tests (e.g., S. albus and the S. fradiae strains in cluster 2) exhibited high levels of similarity in the LFRFA (84 and 81%, respectively). Other taxa (S. cyaneus group) which exhibited equally high levels of physiological similarity (90%) appeared to be unrelated as determined by the LFRFA. Species with lower levels of physiological similarity (e.g., S. somaliensis[75%], S. lavendulae[63%], and S. rimosus[68%]) exhibited low levels of LFRFA similarity (75, 64, and 54%, respectively). High levels of DNA-DNA relatedness (<90%) (S. ipomoea) were reflected in high levels of similarity as determined by the LFRFA (75 to 100%); lower levels of DNA-DNA relatedness (ca. 70%) (S. cyaneus group) were reflected in low levels of LFRFA similarity (strains not clustered). We concluded that the presently used physiological tests reflect too small a portion of the genome to be universally useful in streptomycete species characterization. In contrast, high levels of DNA-DNA relatedness (<90%) and high LFRFA similarity values will probably both be valuable in species delineation in actinomycetes.
-
-
-
Characterization of Methanobrevibacter arboriphilicus SA Isolated from a Paddy Field Soil and DNA-DNA Hybridization among M. arboriphilicus strains
More LessWe isolated a methanogenic strain, designated strain SA (= DSM 7056), from an enrichment culture inoculated with a Japanese paddy field soil. Cells of this strain were strictly anaerobic, nonmotile, short rods and stained gram positive. The strain was able to use H2-CO2or formate as a methanogenic substrate. It required vitamins, but not acetate, for growth. Growth was fastest at 35 to 40°C. Methane was produced most rapidly at pH 6.0 to 7.5. The cellular lipid composition of strain SA was similar to that of M. arboriphilicus A2 (= DSM 2462). The G+C content of the DNA was 26.4 mol%. Strain SA had DNA-DNA hybridization values of more than 70% with M. arboriphilicus DH1T(= DSM 1125T). On the basis of phenotypic and genotypic characteristics, we identified strain SA as M. arboriphilicus. In the course of our identification work, the genetic heterogeneity of M. arboriphilicus was revealed by the results of DNA-DNA hybridization experiments. Although strain AZ (= DSM 744) should be classified as a member of a species distinct from the species containing the other four strains studied (DH1T, A2, DC [= DSM 1536], and SA), further phenotypic characterization will be required before a new species can be proposed.
-
-
-
Neisseria weaveri sp. nov. (formerly CDC Group M-5), from Dog Bite Wounds of Humans
More LessThe taxonomic relationships of strains belonging to Centers for Disease Control group M-5 were examined. Previous studies of rRNA cistron similarities placed this organism on the Neisseriaceae rRNA branch of rRNA superfamily III; the closest neighbors included the genus Neisseria and groups EF-4a and EF-4b. The group M-5 strains were characterized by a range of phenotypic tests, and their G+C contents and DNA-DNA relatedness levels were determined. In addition, a numerical taxonomic analysis of the whole-cell protein patterns (obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of group M-5 and related taxa was performed. The strains studied included 45 group M-5 strains, the type strains of six Neisseria species or subspecies, three group EF-4a reference strains, and three group EF-4b reference strains plus the type strain of the phenotypically similar organism Oligella urethralis. Our results showed that the group M-5 strains were members of a homogeneous taxon distinct from phylogenetically closely related taxa. The genomic divergence as revealed by levels of rRNA cistron similarity and phenotypic characteristics indicate that group M-5 can be considered a new species of the genus Neisseria. We therefore propose the new species Neisseria weaveri, with NCTC 12742 (= CCUG 4007 = ISL775/91 = LMG 5135) as the type strain. N. weaveri strains are strictly aerobic, gram-negative, nonmotile, rod-shaped organisms which are catalase and oxidase positive, nonsaccha-rolytic, and able to grow on MacConkey agar and do not reduce nitrate but generally reduce nitrite. The guanine-plus-cytosine contents of the DNAs of six representative strains were in the range from 50 to 51 mol%. Almost all 45 group M-5 strains were originally isolated from human wounds following dog bites.
-
-
-
Proposal for Rejection of Agrobacterium tumefaciens and Revised Descriptions for the Genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes
More LessThe 16S rRNA sequences of seven representative Agrobacterium strains, eight representative Rhizobium strains, and the type strains of Azorhizobium caulinodans and Bradyrhizobium japonicum were determined. These strains included the type strains of Agrobacterium tumefaciens, Agrobacterium rhizogenes, Agrobacterium radiobacter, Agrobacterium vitis, Agrobacterium rubi, Rhizobium fredii, Rhizobium galegae, Rhizobium huakuii, Rhizobium leguminosarum, Rhizobium loti, Rhizobium meliloti, and Rhizobium tropici. A phylogenetic analysis showed that the 15 strains of Agrobacterium and Rhizobium species formed a compact phylogenetic cluster clearly separated from the other members of the alpha subclass of the Proteobacteria. However, Agrobacterium species and Rhizobium species are phylogenetically entwined with one another, and the two genera cannot be separated. In the Agrobacterium species, the strains of biovar 1, biovar 2, Agrobacterium rubi, and Agrobacterium vitis were clearly separated. The two biovars exhibited homogeneity in their phenotypic, chemotaxonomic, and phylogenetic characteristics, and two species should be established for the two biovars. We considered the nomenclature of the two biovars, and revised descriptions of Agrobacterium radiobacter(for the biovar 1 strains) and Agrobacterium rhizogenes(for the biovar 2 strains) are proposed. The name Agrobacterium tumefaciens is rejected because the type strain of this species was assigned to Agrobacterium radiobacter, and consequently the description of the genus Agrobacterium is revised.
-
-
-
Hydrogenobacter acidophilus sp. nov., a Thermoacidophilic, Aerobic, Hydrogen-Oxidizing Bacterium Requiring Elemental Sulfur for Growth
More LessA thermoacidophilic, obligately chemolithoautotrophic, aerobic, hydrogen-oxidizing bacterium, strain 3H-1T(T = type strain), was isolated from a solfataric field in Tsumagoi, Japan. This strain is a gram-negative, motile, non-spore-forming rod-shaped organism that requires elemental sulfur for growth by hydrogen oxidation. Type b, c, and o cytochromes are present. Carbon dioxide may be fixed via the reductive tricarboxylic acid cycle. The optimum temperature for growth is 65°C. The optimum pH for growth is 3.0 to 4.0. The guanine-plus-cytosine content of DNA is 35.0 mol%. A straight-chain saturated C18:0acid and straight-chain unsaturated C18:1and C20:1acids are the major components of the cellular fatty acids. 2-Methylthio-3-VI, VII-tetrahydromultiprenyl7-1,4-naphthoquinone (methionaquinone) is the major isoprenoid quinone. This strain is considered a member of a new species of the genus Hydrogenobacter, a genus of obligately chemolithoautotrophic, aerobic, hydrogen-oxidizing bacteria. The name Hydrogenobacter acidophilus sp. nov. is proposed for the organism. The type strain of this species is strain 3H-1 (= JCM 8795).
-
-
-
Polyamine Patterns as Chemotaxonomic Markers for the Genus Xanthomonas
More LessPolyamine profiles of 140 Xanthomonas strains were determined by high-performance liquid chromatography. The results revealed that there are two polyamine profiles within the genus Xanthomonas. The first profile, characterized by spermidine as the major polyamine, was shared by Xanthomonas albilineans, Xanthomonas axonopodis, Xanthomonas campestris, Xanthomonas fragariae, Xanthomonas oryzae, Xanthomonas populi, and some unclassified xanthomonads. The second profile was typical of Xanthomonas maltophilia strains and contained spermidine and cadaverine as the major polyamines.
-
-
-
Amycolatopsis alba sp. nov., Isolated from Soil
More LessA new Amycolatopsis species isolated from soil produces a new glycopeptide antibiotic related to vancomycin. Traditional taxonomic methods and contemporary fatty acid analysis techniques were used to establish the position of this species. The hyphae fragment extensively when the organism is cultured in liquid media. The organism is characterized by white aerial hyphae that bear long chains of cylindrical conidia. The reverse side is yellowish brown; a faint light brown soluble pigment is occasionally produced. The organism has a type IV cell wall (meso-diaminopimelic acid), a type A whole-cell sugar pattern, and a type PII phospholipid pattern. Mycolic acids are not present in whole-cell hydrolysates. The major menaquinone is MK-9(H4); there is also a minor amount of MK-8(H4). The name proposed for this new species is Amycolatopsis alba. The type strain is strain A83850 (= NRRL 18532).
-
-
-
Mycoplasma imitans sp. nov. Is Related to Mycoplasma gallisepticum and Found in Birds
A mycoplasma designated strain 4229T(T = type strain) was isolated in 1984 from the turbinate of a duck in France, and similar strains were isolated from geese in France and from a partridge in England. All of these strains were originally identified as Mycoplasma gallisepticum by immunofluorescence and growth inhibition tests, but subsequent serological and molecular studies indicated only a partial relationship to this species and DNA-DNA hybridization studies revealed only approximately 40 to 46% genetic homology with M. gallisepticum PG31T. In this study morphological, cultural, and physical investigations were carried out on strain 4229Tand partridge strain B2/85, after we first demonstrated the similarity between these organisms by performing a restriction enzyme analysis of their DNAs. Both strains had phenotypic properties very similar to M. gallisepticum properties, including the presence of an attachment organelle. As a result of these investigations, the organisms were assigned to the class Mollicutes, the order Mycoplasmatales, and the genus Mycoplasma. They fermented glucose, reduced triphenyl tetrazolium chloride aerobically and anaerobically, and exhibited hemadsorption and hemagglutination, but other biochemical tests were negative. Apart from a serological cross-reaction with M. gallisepticum, these organisms exhibited no significant relationship with any previously described Mycoplasma species as determined by growth inhibition or immunofluorescence tests or with a number of additional serovars and unclassified avian strains. This Mycoplasma taxon therefore appears to be a new species, for which we propose the name Mycoplasma imitans. The type strain is strain 4229 (= NCTC 11733 = ATCC 51306). The significance of the organism has not been fully investigated, but preliminary in vitro and in vivo studies have indicated that it may be pathogenic.
-
-
-
Ch2, a Novel Halophilic Archaeon from an Australian Solar Saltern
More LessA novel halophilic archaeon, strain Ch2, was isolated from a marine solar saltern in Geelong, Australia. The fact that this organism had a dam-methylated genome suggested that it is closely related to the taxon that includes Halobacterium saccharovorum, Halobacterium sodomense, and Halobacterium trapanicum. A sequence analysis of the 16S rRNA gene (Ch2 has three copies of this gene) showed that Ch2 is phylogenetically equidistant from the genera Haloarcula and Haloferax and closely related to H. saccharovorum. The susceptibility of both Ch2 and H. saccharovorum to the recently isolated halophage HF2 supported the hypothesis that these two organisms are closely related.
-
-
-
Revised Taxonomy of the Methanotrophs: Description of Methylobacter gen. nov., Emendation of Methylococcus, Validation of Methylosinus and Methylocystis Species, and a Proposal that the Family Methylococcaceae Includes Only the Group I Methanotrophs
More LessNumerical taxonomic, DNA-DNA hybridization, and phospholipid fatty acid composition analyses were performed on an extensive range of methanotrophic strains, including reference strains and environmental isolates obtained from sites throughout eastern Australia. When the results of these studies were related to the results of a study based on genomic physicochemical properties, they clarified group I and II methanotroph genus and species interrelationships. The group I methanotrophs were found to be made up of three broadly phenotypically and genotypically homologous clusters of species. The first group I methanotroph cluster included the carotenoid-containing species Methylomonas methanica, Methylomonas fodinarum, and Methylomonas aurantiaca. These species represent the true members of the genus Methylomonas. The second group I methanotroph cluster was made up of two subclusters of strains. One subcluster included species not capable of producing resting cells and consisted of the species “Methylomonas agile,” “Methylomonas alba,” and Methylomonas pelagica. The other subcluster included species capable of forming desiccation-resistant cysts and included Methylococcus luteus, marine Methylomonas-like strains, and Methylococcus whittenburyi. Strains designated “Methylococcus ucrainicus” and Methylococcus vinelandii were found to be synonyms of Methylococcus whittenburyi, while Methylococcus bovis was a synonym of Methylococcus luteus. It is proposed that these subclusters represent a new genus, Methylobacter gen. nov. The species in the new genus are type species Methylobacter luteus comb. nov., Methylobacter agilis sp. nov., Methylobacter albus sp. nov., nom. rev., Methylobacter marinus sp. nov., Methylobacter pelagicus comb. nov., and Methylobacter whittenburyi comb. nov. The remaining group I methanotrophs included the moderately thermophilic species Methylococcus capsulatus and Methylococcus thermophilus and a group of unnamed strains closely related to Methylococcus capsulatus. It is proposed that these species represent the true members of the genus Methylococcus. The group II methanotrophs consisted of two closely related groups. The first group included budding, exospore-producing strains, while the second group included nonmotile, cyst-forming strains. These groups represent the genera Methylosinus and Methyocystis, which are revived here. The genus Methylosinus gen. nov., nom. rev. includes the species Methylosinus trichosporium sp. nov., nom. rev. and Methylosinus sporium sp. nov., nom. rev., while the genus Methylocystis gen. nov., nom. rev. includes the species Methylocystis parvus sp. nov., nom. rev. and Methylocystis echinoides sp. nov., nom. rev.
-
-
-
Phylogeny of Twenty Thermus Isolates Constructed from 16S rRNA Gene Sequence Data
The sequences of the 16S rRNA genes of 20 Thermus isolates were determined to a high fidelity by using automated DNA sequencing and fluorescent-dye-labelled primers. The strains tested included members of the three validly named Thermus species and representatives of major taxonomic clusters defined previously for this genus. The parsimony method was used to reconstruct the phylogeny of the strains from the aligned sequences, and a bootstrap analysis revealed a number of well-supported clades. Our results are not consistent with groupings inferred from numerical taxonomy data but support the conjecture that the genus Thermus contains more species than the three currently recognized species.
-
-
-
Genomic Heterogeneity among French Rhizobium Strains Isolated from Phaseolus vulgaris L.
More LessLevels of DNA relatedness between strains isolated from root nodules of Phaseolus vulgaris and reference strains of different Rhizobium species were determined by performing DNA-DNA hybridization experiments (S1 nuclease method). The nine strains examined were members of three genomic groups previously delineated by a restriction fragment length polymorphism analysis among strains isolated from P. vulgaris at different sites in France. In agreement with the results of the restriction fragment length polymorphism analysis, three genomic species were found. We confirmed that one of these species corresponded to Rhizobium leguminosarum since the strain examined was 100% related to the type strain of this species. The other two species were new genomic species which were less than 21% related to reference strains belonging to other Rhizobium species, including Rhizobium etli and Rhizobium tropici, and were 18% related to each other. As determined by an analysis of partial 16S ribosomal DNA sequences, each of the genomic species was found to belong to a lineage independent from the lineages of previously described Rhizobium species. Nevertheless, they were included in the group formed by the fast-growing Rhizobium species. Both genomic species 1 and genomic species 2 contained a majority of strains which were capable of nodulating both P. vulgaris and Leucaena leucocephala, like R. tropici. However, they also contained strains with a nodulation phenotype restricted to P. vulgaris, like R. leguminosarum bv. phaseoli and R. etli bv. phaseoli. Our data are the first evidence that in Europe species other than R. leguminosarum nodulate P. vulgaris.
-
-
-
Riemerella anatipestifer gen. nov., comb. nov., the Causative Agent of Septicemia Anserum Exsudativa, and Its Phylogenetic Affiliation within the Flavobacterium-Cytophaga rRNA Homology Group
More LessThe phylogenetic position of the causative agent of septicemia anserum exsudativa, now most often referred to as [Moraxella] anatipestifer (brackets indicate a generically misnamed taxon) or “[Pasteurella] anatipestifer,” was established by performing rRNA cistron similarity studies. [Moraxella] anatipestifer belongs to rRNA superfamily V, together with the genera Flavobacterium, Cytophaga, Flexibacter, Weeksella, Capnocytophaga, and Sphingobacterium. The detailed structure of rRNA superfamily V, which now contains five major rRNA homology groups, is described. An analysis of various phenotypic parameters, including new data (cellular proteins and fatty acids) and previously published data (respiratory quinones, enzyme activities, and classical phenotypic features), revealed that [Moraxella] anatipestifer differs in many aspects from its closest relatives, Flavobacterium indologenes, Flavobacterium gleum, Flavobacterium indoltheticum, Flavobacterium balustinum, Flavobacterium meningosepticum, and Weeksella zoohelcum. The combined genotypic and phenotypic data indicate that this organism should be placed in a separate genus; the name Riemerella anatipestifer gen. nov., comb. nov. is proposed for this bacterium. The specific epithet anatipestifer is kept in order to avoid nomenclatural confusion. However, it should be emphasized that the illness caused by this organism is a septicemic disease which is not restricted to ducks.
-
-
-
Proposals To Unify the Genera Bartonella and Rochalimaea, with Descriptions of Bartonella quintana comb. nov., Bartonella vinsonii comb. nov., Bartonella henselae comb. nov., and Bartonella elizabethae comb. nov., and To Remove the Family Bartonellaceae from the Order Rickettsiales
More LessDNA hybridization data (hydroxyapatite method, 50 to 70°C) indicate that Rickettsia prowazekii, the type species of the type genus of the family Rickettsiaceae, is substantially less closely related to Rochalimaea species than was previously thought. The levels of relatedness of Rickettsia prowazekii to Rochalimaea species and to Bartonella bacilliformis under optimal conditions for DNA reassociation were 0 to 14%, with 25.5% or greater divergence in related sequences. When stringent reassociation criteria were used, the levels of relatedness were 0 to 2%. The genera Bartonella and Rochalimaea are currently classified in different families (the Bartonellaceae and the Rickettsiaceae) in the order Rickettsiales. On the basis of DNA relatedness data, previous 16S rRNA sequence data, guanine-plus-cytosine contents, and phenotypic characteristics, neither Bartonella bacilliformis nor Rochalimaea species are closely related to other organisms currently classified in the order Rickettsiales. In fact, the closest relative of these organisms is Brucella abortus. It is therefore proposed that the family Bartonellaceae should be removed from the order Rickettsiales. Previous 16S rRNA sequence data and DNA hybridization data revealed high levels of relatedness between Bartonella bacilliformis and the four Rochalimaea species, indicating that these species are members of a single genus. It is proposed that the genus Rochalimaea should be united with the genus Bartonella in the family Bartonellaceae. The name Bartonella is retained as the genus name since it has nomenclatural priority over the name Rochalimaea. This means that new combinations for the Rochalimaea species must be created. Proposals are therefore made for the creation of Bartonella quintana comb. nov., Bartonella vinsonii comb. nov., Bartonella henselae comb. nov., and Bartonella elizabethae comb. nov.
-
-
-
Description of Two Morphotypes of Peptostreptococcus micros
More LessPeptostreptococcus micros is often isolated from abscesses in several parts of the human body. The oral cavity is considered the natural habitat for the species, which has been implicated as a periodontal pathogen. In plaque samples from periodontitis patients we observed the presence of a rough morphotype of P. micros in addition to the previously recognized smooth morphotype. The rough morphotype has not been described previously. Both morphotypes are frequently isolated simultaneously from the same patient. In this paper strains of both morphotypes are described. The smooth morphotype, represented by the type strain, grew as small, dome-shaped, bright white, nonhemolytic colonies. The rough morphotype grew as equally white dry colonies which were hemolytic and had wrinkled edges. DNA-DNA reassociation studies revealed homology at the species level between the two morphotypes; in addition, no differences in physiological characteristics were observed when the organisms were tested with API-32A and API-ZYM kits. The rough cells had long, thin fibrillar structures outside the cell envelope when they were stained negatively for electron microscopy. In the smooth morphotype these structures were not present. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of whole-cell extracts were different for the two morphotypes. In xylene-water phase partition studies, the smooth morphotype was found to be hydrophobic, whereas the rough morphotype was found to be relatively hydrophilic. The distinct morphotypes were stable on blood agar; however, the rough morphotype changed to a nonfibrillar type with a smooth colony morphology after repeated subculturing in broth.
-
-
-
Streptomyces bungoensis sp. nov.
More LessTwo actinomycete strains, MS16-10G and MS16-10W, isolated from soil and producing an antibiotic, were examined and assigned to the genus Streptomyces, because they have a gray aerial mass, spiral spore chains, and a spiny spore surface; form a melanoid pigment on tyrosine agar, on peptone-yeast extract-iron agar, and in tryptone-yeast extract broth; and have cell wall chemotype I. The DNA base compositions and DNA-DNA reassociation of the isolates were compared with those of four strains of authentic species of the genus Streptomyces: two synonymous strains of Streptomyces cyaneus(Streptomyces afghaniensis and Streptomyces echinatus) and one strain each of Streptomyces chromofuscus and Streptomyces antibioticus showing similar morphological characteristics. The results indicated that the two isolates differed from the four authentic species and represent a single new species for which the name Streptomyces bungoensis is proposed. The type strain is MS16-10G, which has been deposited in the collection of the Fermentation Research Institute, Agency of Industrial Sciences and Technology, Tsukuba, Japan, with accession no. FERM 8432T.
-
-
-
Growth Characteristics of V Factor-Independent Transformants of Haemophilus influenzae
More LessHaemophilus influenzae is a V factor-dependent species. A plasmid conferring V factor independence in Haemophilus parainfluenzae and Haemophilus ducreyi was transferred to plasmid-free H. influenzae Rd by DNA transformation. The growth characteristics of the transformants in a complex and a chemically defined medium were compared, and the ability of several exogenous pyridine nucleotides and precursors to support growth was examined. Although the transformants appeared to be V factor independent in a complex medium, in a chemically defined medium they exhibited both V factor-dependent and nicotinamide-dependent growth. Because of the inability of the plasmid-free H. influenzae Rd to utilize nicotinamide for growth, it was concluded that the genes conferring this function were plasmid linked. Our results indicate that the V factor requirement, as it is presently defined, is not suitable to serve as a definitive taxonomic criterion for species determination in the family Pasteurellaceae.
-
-
-
Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a New Genus of the Order Actinomycetales
More LessThirteen strains of motile arthrospore-bearing actinomycetes were isolated from soils in Japan, India, and Nepal. These organisms underwent differentiation into aerial and substrate mycelia in their growth cycles and produced motile spores arranged in chains on their aerial mycelia. Sporangia were not observed. The cell walls contained L-lysine, serine, glycine, D-glutamic acid, and D-alanine (cell wall type VI). Mycolic acids were absent; the major menaquinones were MK-9(H8) and MK-10(H8); the phospholipid type was type PIII. The taxonomic characteristics of these isolates are different from those of the previously described motile actinomycetes. The name Catenuloplanes japonicus gen. nov., sp. nov., nom. rev. is proposed for these organisms. The type strain is strain N381-16, which has been deposited in the Institute for Fermentation, Osaka as strain IFO 14176 and in the American Type Culture Collection as strain ATCC 31637.
-
-
-
Micrococci Demonstrate a Phosphatase Activity Which Is Repressed by Phosphates and Which Can Be Differentiated from That of Staphylococci
More LessThe phosphatase activities of 114 micrococcal strains belonging to seven different species and of an additional 150 unspeciated micrococcal strains were evaluated on solid media at various pHs containing or not containing phosphates. In the presence of phosphates, only nine strains (five unspeciated strains, one Micrococcus luteus strain, and three Micrococcus varians strains) yielded a positive reaction on plates at pH 8. In media (at pH 8) deprived of phosphates, in contrast, all but 15 strains demonstrated clear-cut phosphatase activity. Acid phosphatase could not be evaluated on solid media since none of the strains grew satisfactorily on plates at pH 5. The phosphatase activities of seven (one or two for each species, which included phosphatase-negative strains) of the strains whose colonies proved phosphatase negative at pH 8 and of 18 (two or three strains per species) of those with phosphatase-positive colonies were evaluated at pH 5 and 8.5 in toluene-treated cells which had been grown in liquid media at pH 7 containing or not containing phosphates. All strains demonstrated distinct phosphatase activity at both pHs when grown in media not containing phosphates. In contrast, when strains were grown in the presence of such substances, virtually no activity was observed at pH 8.5, and, generally, a much reduced activity was observed at pH 5. The phosphatase activity of micrococci of the various species (three to eight strains per species) was also compared with that of staphylococci of different species (5 to 10 strains per species) by the methyl green-phenolphthalein diphosphate method, the sensitivity of which can be varied by using different enzyme substrates. By using phenolphthalein diphosphate as an enzyme substrate, it was found that virtually all the different species of staphylococci yielded a positive reaction on plates not containing phosphates while almost all micrococci proved phosphatase negative with the methyl green-phenolphthalein diphosphate method. This indicates that the phosphatase activity of micrococci can easily be differentiated from that of staphylococci.
-
-
-
Fusobacterium pseudonecrophorum Is a Synonym for Fusobacterium varium
More LessDNA-DNA hybridization studies (with the S1 nuclease method [J. L. Johnson, Methods Microbiol. 18:33-74, 1985]) were performed on members of the genus Fusobacterium. Fusobacterium varium ATCC 8501Tshowed 88 and 79% DNA homology with F. pseudonecrophorum JCM 3722Tand JCM 3723, respectively, while F. pseudonecrophorum JCM 3722Tshowed 81 and 82% DNA homology with F. varium ATCC 8501Tand F. pseudonecrophorum JCM 3723, respectively. These genetic data and their similar phenotypic characteristics suggest that F. varium(Eggerth and Gagnon 1933) Moore and Holdeman 1969 and F. pseudonecrophorum(ex Prévot 1940) Shinjo et al. 1990 belong to a single species. We propose, therefore, that strains JCM 3722 and JCM 3723 of F. pseudonecrophorum be transferred to the species F. varium.
-
-
-
DNA Relatedness among Strains of the Streptomyces lavendulae Phenotypic Cluster Group
More LessDNA relatedness was evaluated among the type strains of Streptomyces lavendulae and the 11 species which were designated as subjective synonyms in volume 4 of Bergey’s Manual of Systematic Bacteriology. Three S. lavendulae subspecies, five putative strains of S. lavendulae, and the type strain of “S. majorciensis” were also included in the present study. The 21 strains studied segregated into 14 clusters (average linkage) when grouped at >70% DNA relatedness, including 10 single-member clusters. S. lavendulae, S. lavendulae subsp. avirens, S. lavendulae subsp. grasserius, and S. columbiensis were found to be synonymous at >79% DNA relatedness. The other clusters, on the basis of their relatively low DNA relatedness to S. lavendulae, appear to be valid species rather than subjective synonyms of S. lavendulae.
-
-
-
Molecular Systematics of the Genus Zoogloea and Emendation of the Genus
More LessPhylogenetic relationships among strains of Zoogloea and related taxa were determined by 16S rDNA sequencing and genomic DNA hybridization techniques. The 16S rRNA gene was amplified by the polymerase chain reaction with a pair of eubacterial consensus primers and sequenced directly by using an automated fluorescent DNA sequencer. Sequence comparisons and distance matrix tree analysis revealed that Zoogloea ramigera IAM 12136 (= N. C. Dondero 106, type strain) and Zoogloea sp. ATCC 19324 formed a lineage with Rhodocyclus purpureus in the β subclass of Proteobacteria. Z. ramigera IAM 12670 (= P. R. Dugan 115) was shown to belong to another cluster with Alcaligenes eutrophus and Pseudomonas cepacia in the β subclass. In contrast, Z. ramigera IAM 12669 (= K. Crabtree I-16-M) proved to be a member of the ± subclass of the Proteobacteria, closely related to Agrobacterium tumefaciens. Genomic DNA hybridization studies also showed that there is genetic diversity among the strains currently designated Z. ramigera, but typical Zoogloea strains, characterized by their production of rhodoquinones, are highly related to each other and can be regarded as a single species. On the basis of the molecular data, together with the early phenotypic and chemotaxonomic information, we have emended the generic description of Zoogloea.
-
-
-
Phylogenetic Relationship of Gemella morbillorum to Gemella haemolysans
More LessPartial 16S rRNA gene sequences (16S rDNA) of Gemella morbillorum and Gemella haemolysans were determined by sequencing polymerase chain reaction-amplified DNA. A phylogenetic analysis of 53 eubacterial 16S rRNA sequences grouped the gemellae on a distinct branch separate from the 18 members of the genus Streptococcus. DNA-DNA hybridization results indicate that the two gemellae are related at the genus level but are not a single species.
-
-
-
NOTES: Rickettsia massiliae sp. nov., a New Spotted Fever Group Rickettsia
More LessWe propose the name Rickettsia massiliae sp. nov. (type strain, Mtul in the Collection of the World Health Organization Collaborative Center for Rickettsial Reference, Marseille, France) for a spotted fever group rickettsia determined to be distinct from previously recognized species by the serotyping method (L. Beati, J.-P. Finidori, B. Gilot, and D. Raoult, J. Clin. Microbiol. 30:1922-1930, 1992). This rickettsia has biological characteristics similar to those of the other spotted fever group rickettsiae. In addition, a sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein analysis, a polymerase chain reaction followed by a restriction fragment length polymorphism analysis of DNA fragments, and pulsed-field electrophoresis of the genome of R. massiliae revealed unique migration patterns distinct from those of all previously recognized spotted fever group rickettsiae. These additional characteristics (Beati et al., J. Clin. Microbiol. 30:1922-1930, 1992), together with the data usually considered sufficient for description of rickettsiae, are crucial to the proposal of this new species and should be helpful in species identification.
-
-
-
Mycobacterium genavense sp. nov.
More LessStrains of a suggested novel type of mycobacterium have been repeatedly isolated from patients with AIDS. We summarize the results of tests performed to determine enzymatic activities and metabolic properties, the results of fatty acid analyses, and the results of a comparative 16S rRNA sequence determination. We propose formally that this organism represents a new species, Mycobacterium genavense. The type strain is strain 2289, a culture of which has been deposited in the American Type Culture Collection as strain ATCC 51234.
-
-
-
Characteristics of DNA and Multiple rpoD Homologs of Microcystis(Synechocystis) Strains
The base compositions of DNAs from nine Microcystis strains, as determined by high-performance liquid chromatography, were 41 to 42 mol% G+C. Chromosomal DNAs derived from these strains were found to be extremely resistant to many restriction endonucleases, and a restriction analysis revealed the presence of a dam-like methylase or both dam- and dcm-like methylases in all of the strains examined. Genomic Southern hybridization in which a synthetic oligonucleotide probe (rpoD probe) was used showed that members of the genus Microcystis might have multiple rpoD homologs, and the hybridization signal patterns observed with the DNAs of Microcystis aeruginosa strains were different from each other.
-
-
-
Pursuit of the Corynebacterium striatum Type Strain
More LessThe description of Corynebacterium striatum(Chester 1901) Eberson 1918ALin Bergey's Manual of Systematic Bacteriology has many inconsistencies with the identification scheme from the Centers for Disease Control and Prevention. We have studied the four C. striatum reference strains available from the American Type Culture Collection and the National Collection of Type Cultures and found that they fit the Centers for Disease Control and Prevention description of this species. However, it appears that the wrong strains were deposited for this species, because none of the reference strains fits the descriptions in the original publications. This is a substantial case for declaring it a nomen dubium, but the name could be rescued if a careful search reveals a strain that was used in making the original description. It is hoped that some readers may have the missing strains labeled with the early names Bacillus striatus, Bacillus flavidus, or Corynebacterium flavidum.
-
-
-
Taxonomic Relationship between Pseudomonas perfectomarina ZoBell and Pseudomonas stutzeri
More LessWe clarified the taxonomic position of Pseudomonas perfectomarina ZoBell in the species Pseudomonas stutzeri. Both genotypic and phenotypic observations led us to conclude that this strain belongs to genomovar 2 of P. stutzeri, for which strain ATCC 17591 is the reference strain. The uncertainty about the motility of strain ZoBell was also clarified. We found that strain ZoBell is motile by means of one polarly inserted flagellum.
-
-
-
Aeromonas enteropelogenes and Aeromonas ichthiosmia Are Identical to Aeromonas trota and Aeromonas veronii, Respectively, as Revealed by Small-Subunit rRNA Sequence Analysis
More LessThe 16S rRNA gene sequences of the type strains of Aeromonas enteropelogenes and Aeromonas ichthiosmia were determined by polymerase chain reaction direct sequencing in order to clarify their interrelationships with other aeromonad species. On the basis of 16S rRNA gene sequence analysis, A. enteropelogenes and A. ichthiosmia were found to be identical to Aeromonas trota and Aeromonas veronii, respectively.
-
-
-
Transfer of the Type Species of the Genus Thermobacteroides to the Genus Thermoanaerobacter as Thermoanaerobacter acetoethylicus(Ben-Bassat and Zeikus 1981) comb. nov., Description of Coprothermobacter gen. nov., and Reclassification of Thermobacteroides proteolyticus as Coprothermobacter proteolyticus(Ollivier et al. 1985) comb. nov.
More LessPhylogenetic and phenotypic evidence demonstrates the taxonomic heterogeneity of the genus Thermobacteroides and indicates a close relationship between Thermobacteroides acetoethylicus and members of the genus Thermoanaerobacter. Since T. acetoethylicus is the type species of Thermobacteroides, its removal invalidates the genus. As a consequence, the remaining species Thermobacteroides proteolyticus is proposed as the type species of the new genus Coprothermobacter gen. nov., as Coprothermobacter proteolyticus comb. nov.
-
- Matters Relating To The International Committee On Systematic Bacteriology
-
-
-
Characterization of Pediococcus pentosaceus and Pediococcus acidilactici Strains and Replacement of the Type Strain of P. acidilactici with the Proposed Neotype DSM 20284
More LessLevels of DNA relatedness were determined for 16 strains of Pediococcus pentosaceus and Pediococcus acidilactici, and two distinct groups were recognized. The DNA base compositions of the members of one group ranged from 37.4 to 38.7 mol% guanine plus cytosine and the DNA base compositions of the members of the other group ranged from 42.7 to 43.5 mol% guanine plus cytosine. The phenotypic characteristics after growth at 50°C and acid production from maltose correlated with the levels of DNA relatedness and DNA base compositions. Strains in the first group exhibited high levels of DNA relatedness to the type strain of P. pentosaceus and were identified as P. pentosaceus strains. Strains in the second group exhibited high levels of DNA relatedness to authentic reference strains of P. acidilactici but did not exhibit relatedness to P. acidilactici JCM 5885T(= NCDO 1859T) (T = type strain). The taxonomic standing of the type strain of P. acidilactici was examined, and strains in the second group were identified as P. acidilactici. In addition, we request the replacement of the type strain P. acidilactici with the proposed neotype DSM 20284 (= JCM 8797 = NRIC 0115).
-
-
- Author's Correction
-
- Errata
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)