Showing papers in "International Journal of Systematic and Evolutionary Microbiology in 1992"
TL;DR: Although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.
Abstract: 16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.
1,342 citations
TL;DR: Three DNA relatedness groups were associated with specific rRNA gene restriction patterns, protein electrophoresis patterns, and patterns of reactivity with murine monoclonal antibodies in Borrelia isolates associated with Lyme borreliosis.
Abstract: We studied 48 Borrelia isolates that were associated with Lyme borreliosis or were isolated from ticks and identified three DNA relatedness groups by using the S1 nuclease method. The three DNA groups (genospecies) were associated with specific rRNA gene restriction patterns, protein electrophoresis patterns, and patterns of reactivity with murine monoclonal antibodies. Genospecies I corresponded to Borrelia burgdorferi sensu stricto since it contained the type strain of this species (strain ATCC 35210); this genospecies included 28 isolates from Europe and the United States. Genospecies II was named Borrelia garinii sp. nov. and included 13 isolates from Europe and Japan. Genospecies III (group VS461) included seven isolates from Europe and Japan.
846 citations
TL;DR: It is suggested that this bacterium isolated from Mediterranean seawater near a petroleum refinery be assigned to a new genus, at least temporarily, because of the impossibility of finding a single most closely related species.
Abstract: On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is, however, not excluded. The type strain is M. hydrocarbonoclasticus SP.17 (= ATCC 49840).
573 citations
TL;DR: This phenotype, along with the 16S rRNA sequence data, suggests that these thermoacidophiles are biochemically and genetically unique and supports the proposal that they should be reclassified in the new genus Alicyclobacillus.
Abstract: Comparative 16S rRNA (rDNA) sequence analyses performed on the thermophilic Bacillus species Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus revealed that these organisms are sufficiently different from the traditional Bacillus species to warrant reclassification in a new genus, Alicyclobacillus gen. nov. An analysis of 16S rRNA sequences established that these three thermoacidophiles cluster in a group that differs markedly from both the obligately thermophilic organisms Bacillus stearothermophilus and the facultatively thermophilic organism Bacillus coagulans, as well as many other common mesophilic and thermophilic Bacillus species. The thermoacidophilic Bacillus species B. acidocaldarius, B. acidoterrestris, and B. cycloheptanicus also are unique in that they possess omega-alicylic fatty acid as the major natural membranous lipid component, which is a rare phenotype that has not been found in any other Bacillus species characterized to date. This phenotype, along with the 16S rRNA sequence data, suggests that these thermoacidophiles are biochemically and genetically unique and supports the proposal that they should be reclassified in the new genus Alicyclobacillus.
407 citations
TL;DR: A rapid screening of 77 aerotolerant Arcobacter strains revealed five major groups, which were identified by using DNA-DNA hybridization data as A. butzleri strains and strains belonging to one of the electrophoretic subgroups of A. cryaerophilus had similar fatty acid contents, and an analysis of fatty acid compositions allowed clear-cut differentiation of all of the other groups.
Abstract: The relationships of 77 aerotolerant Arcobacter strains that were originally identified as Campylobacter cryaerophila (now Arcobacter cryaerophilus [P. Vandamme, E. Falsen, R. Rossau, B. Hoste, P. Segers, R. Tytgat, and J. De Ley, Int. J. Syst. Bacteriol. 41:88-103, 1991]) and 6 reference strains belonging to the taxa Arcobacter nitrofigilis, Arcobacter cryaerophilus, and “Campylobacter butzleri” were studied by using a polyphasic approach, in which we performed DNA-rRNA hybridizations, DNA-DNA hybridizations, a numerical analysis of whole-cell protein patterns after sodium dodecyl sulfate-polyacrylamide gel electrophoresis, an analysis of cellular fatty acid compositions, and a phenotypic analysis and determined DNA base ratios. Our results indicate that “C. butzleri” should be transferred to the genus Arcobacter as Arcobacter butzleri comb. nov., as was suggested by Kiehlbauch and coworkers (J. A. Kiehlbauch, D. J. Brenner, M. A. Nicholson, C. N. Baker, C. M. Patton, A. G. Steigerwalt, and I. K. Wachsmuth, J. Clin. Microbiol. 29:376-385, 1991). A rapid screening of all strains in which we used the sodium dodecyl sulfate-polyacrylamide gel electrophoresis technique revealed five major groups, which were identified by using DNA-DNA hybridization data as A. cryaerophilus (two distinct electrophoretic subgroups), A. butzleri, A. nitrofigilis, and a new species, for which we propose the name Arcobacter skirrowii. The phylogenetic position within rRNA superfamily VI was established for each species. A. butzleri strains and strains belonging to one of the electrophoretic subgroups of A. cryaerophilus had similar fatty acid contents. An analysis of fatty acid compositions allowed clear-cut differentiation of all of the other groups. All of the species could be distinguished by using classical phenotypic tests, although erroneous identifications due to a shortage of clear-cut differentiating tests could occur.
391 citations
TL;DR: The phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas were investigated by using small-subunit ribosomal DNA (rDNA) sequencing and several of the relationships derived from an analysis of the rDNA sequence data were in marked disagreement with the results of chromosomal DNA-DNA pairing experiments.
Abstract: The phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas were investigated by using small-subunit ribosomal DNA (rDNA) sequencing. Members of the genus Aeromonas formed a distinct line within the gamma subclass of the Proteobacteria. Plesiomonas shigelloides also clustered within the confines of the gamma subclass of the Proteobacteria but exhibited a closer association with members of the family Enterobacteriaceae than with members of the family Aeromonadaceae. Species of the genus Aeromonas exhibited very high levels of overall sequence similarity (ca. 98 to 100%) with each other. Several of the relationships derived from an analysis of the rDNA sequence data were in marked disagreement with the results of chromosomal DNA-DNA pairing experiments. Diagnostic rDNA signatures that have possible value for differentiating most Aeromonas species were discerned.
347 citations
TL;DR: A novel intracellular pathogen morphologically similar to the ehrlichiae has been isolated in cell culture and identified as the cause of an epizootic disease of salmonid fish.
Abstract: A novel intracellular pathogen morphologically similar to the ehrlichiae has been isolated in cell culture and identified as the cause of an epizootic disease of salmonid fish. Like the ehrlichiae, the salmonid pathogen, designated strain LF-89, replicates within membrane-bound cytoplasmic vacuoles in host cells. This agent is the first with characteristics of this type to be isolated from a fish. Analysis of the LF-89 16S rRNA indicated that, unlike the ehrlichiae, LF-89 is a gamma proteobacterium distantly related to Coxiella burnetii and perhaps Wolbachia persica. A new genus and species (Piscirickettsia salmonis gen. nov., sp. nov.) are proposed for this organism, with ATCC(R) VR 1361 as the type strain.
248 citations
TL;DR: Biochemical properties and DNA-DNA reassociation studies of Lactobacillus acidophilus strains isolated from humans and animals indicate that these include six genomospecies, and two new species can be differentiated from the established species of the genus LactOBacillus.
Abstract: Biochemical properties and DNA-DNA reassociation studies of Lactobacillus acidophilus strains isolated from humans and animals indicate that these include six genomospecies. Two new species can be differentiated from the established species of the genus Lactobacillus: L. gallinarum sp. nov. (type strain, ATCC 33199) and L. johnsonii sp. nov. (type strain, ATCC 33200). Furthermore, it was clarified that L. acidophilus group A3 (Johnson et al. 1980) is synonymous with L. amylovorus.
236 citations
TL;DR: Using genomic fingerprinting by an arbitrarily primed polymerase chain reaction, a collection of Eurasian and North American isolates of spirochetes that are generally categorized as B. burgdorferi are resolved into three groups.
Abstract: The causative agent of Lyme disease, Borrelia burgdorferi, was first identified by Burgdorfer et al. in 1982 (W. Burgdorfer, A. G. Barbour, S. F. Hayes, J. L. Benach, E. Grunwaldt, and J. P. Davis, Science 216:1317-1319,1982) and was isolated by Barbour et al. in 1983 (A. G. Burbour, W. Burgdorfer, S. E. Hayes, O. Peter, and A. Aeschlimann, Curr. Microbiol. 8:123-126, 1983). Since then, a large number of isolates have been collected, and there have been questions regarding the relationships among the various strains. Using genomic fingerprinting by an arbitrarily primed polymerase chain reaction, we resolved into three groups a collection of Eurasian and North American isolates of spirochetes that are generally categorized as B. burgdorferi. Group I strains have been identified in both North America and Eurasia, while strains belonging to Borrelia groups II and III have been found only in Eurasia. These same three groups have also been delineated by Baranton et al. (G. Baranton, D. Postic, I. Saint Girons, P. Boerlin, J.-C. Piffaretti, M. Assous, and P. A. D. Grimont, Int. J. Syst. Bacteriol. 42:370-375, 1992) by independent methods. Two isolates are distinct from all of the other strains in our collection but are clearly members of the genus Borrelia.
232 citations
TL;DR: The results support genomic and other data which show that the plant-pathogenic and other pseudomonads tested should be placed in at least six genera.
Abstract: Approximately 500 fatty acid profiles were prepared for 340 strains of plant-pathogenic and other bacteria currently or recently classified in the genus Pseudomonas Migula 1984. Strains representing some infraspecific taxa were included. The fatty acid profiles were stable and reproducible provided that cultural and chemical techniques were standardized. The 2- and 3-hydroxy fatty acids were found to be useful in grouping strains into six major groups, several of which were further differentiated into subgroups. Group 1 contained strains of the following species and subspecies: Pseudomonas aeruginosa, P. agarici, P. asplenii, P. aureofaciens, P. caricapapayae, P. chlororaphis, P. cichorii, P. ficuserectae, P. fluorescens, P. fuscovaginae, “P. gingeri,” P. marginalis, P. meliae, P. putida, “P. reactans,” P. syringae, P. tolaasii, and P. viridiflava (subgroup 1a); P. corrugata (subgroup 1b); P. rubrisubalbicans (subgroup 1c); P. alcaligenes, P. pseudoalcaligenes subsp. Pseudoalcaligenes, and P. stutzeri (subgroup 1d); P. amygdali (subgroup le); and P. cattleyae NCPPB 1874 (subgroup 1f). All group 1 strains contained 10:0 3-OH and 12:0 3-OH, and most group 1 strains also contained 12:0 2-OH. Group 2 contained strains belonging to the following taxa: P. andropogonis, P. caryophylli, P. cepacia, P. gladioli, P. plantarii, and P. glumae (in part) (subgroup 2a); P. glumae (in part) (subgroup 2b); and P. solanacearum, P. syzygii, and the banana blood disease bacterium (subgroup 2c). All of the group 2 strains contained 14:0 3-OH, 16:0 3-OH, and 18:1 2-OH; most also contained 16:1 2-OH and 16:0 2-OH. Group 3 contained strains belonging to the following taxa: Comamonas acidovorans, P. avenae, P. cattleyae NCPPB 961, P. pseudoalcaligenes subsp. citrulli, P. pseudoalcaligenes subsp. konjaci, P. rubrilineans (subgroup 3a); and Comamonas testosteroni (subgroup 3b). All of the group 3 strains contained 10:0 3-OH. The group 4 strains were members of Sphingomonas paucimobilis, and all contained only 14:0 2-OH. The group 5 strains were members of P. ftectens and contained 12:0 2-OH, 14:0 2-OH, and 14:0 3-OH. The group 6 strains were P. betle, P. cissicola, P. hibiscicola, Xanthomonas maltophilia, and Xanthomonas campestris pv. campestris strains, and all contained 12:0 3-OH, 11:0 iso 3-OH, and 13:0 iso 3-OH. Within each group or subgroup, qualitative and quantitative differences in profiles occurred for most species. Differences were also found at the infraspecific level for some taxa. My results support genomic and other data which show that the plant-pathogenic and other pseudomonads tested should be placed in at least six genera.
228 citations
TL;DR: The minimal standards for assignment of a strain to the genus Mycobacterium include acid-alcohol fastness, a DNA G+C content in the range from 61 to 71 mol%, and mycolic acid detection with characterization of C22 to C26 pyrolysis esters.
Abstract: In accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria, which calls for the development of recommended minimal standards for describing new species, we propose minimal standards for describing the genus Mycobacterium and new slowly growing species of this genus. The minimal standards for assignment of a strain to the genus Mycobacterium include acid-alcohol fastness, a DNA G+C content in the range from 61 to 71 mol%, and mycotic acid detection with characterization of C22 to C26 pyrolysis esters. The recommended minimal standards for describing a new slowly growing Mycobacterium species are based on the results of phenotypic and genomic studies and include the results of the following conventional tests: Growth at 25, 30, 33, 37, 42, and 45°C; pigmentation; resistance to isoniazid, thiophene-2-carboxylic acid hydrazide, hydroxylamine, p-nitrobenzoic acid, sodium chloride, thiacetazone, picrate, and oleate; catalase activity; Tween hydrolysis; urease activity; niacin detection; and nitrate reductase, acid phosphatase, arylsulfatase, pyrazinamidase, and α-esterase activities. In addition, a mycolic acid profile should be determined, and DNA-DNA hybridization experiments in which the difference between the denaturation temperature of the homologous reaction and the denaturation temperature of the heterologous reaction is determined should be performed. This proposal has been endorsed by the members of the Subcommittee for Taxonomy of the Mycobacteria of the International Committee on Systematic Bacteriology.
TL;DR: It is confirmed that "Mycobacterium peregrinum" ATCC 14467T (T = type strain) is genetically independent of M. fortuitum ATCC 6841T and the hybridized DNAs maintained stable heteroduplexity at high stringency; thus, it is proposed that "M. pereGRINum" should be revived as an independent species, Mycob bacteria sp.
Abstract: We studied the taxonomic positions of the rapidly growing organism Mycobacterium fortuitum and phenotypically related organisms. We confirmed that “Mycobacterium peregrinum” ATCC 14467T (T = type strain) is genetically independent of M. fortuitum ATCC 6841T by using various DNA hybridization conditions. Strains that were genetically identified as “M. peregrinum” were phenotypically differentiated from M. fortuitum ATCC 6841T. Thus, we propose that “M. peregrinum” should be revived as an independent species, Mycobacterium peregrinum sp. nov., nom. rev. The type strain is strain ATCC 14467. M. fortuitum subsp. acetamidolyticum ATCC 35931T exhibited a high level of DNA relatedness to M. fortuitum ATCC 6841T. The hybridized DNAs maintained stable heteroduplexity at high stringency; thus, we confirmed that M. fortuitum subsp. acetamidolyticum is identical to M. fortuitum ATCC 6841T. We found that A/, chelonae subsp. abscessus ATCC 19977T is genetically different from M. chelonae subsp. chelonae NCTC 946Ton the basis of the results of quantitative hybridization even under optimal conditions. There was no reason to maintain this organism as a subspecies of M. chelonae. Thus, we propose that M. chelonae subsp. abscessus should be elevated to species status as Mycobacterium abscessus (Kubica et al.) comb. nov. The type strain is strain ATCC 19977.
TL;DR: DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups, and it is proposed that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidov orax as Acidovorax avenae and AcidovOrax konjaci.
Abstract: DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenae, Pseudomonas rubrilineans, “Pseudomonas setariae,” Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudomonas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenae. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenae and Acidovorax konjaci. Within Acidovorax avenae we distinguished the following three subspecies: Acidovorax avenae subsp. avenae, Acidovorax avenae subsp. cattleyae, and Acidovorax avenae subsp. citrulli. Emended descriptions of the new taxa are presented.
TL;DR: The C. pecorum strains were distinguished from C. psittaci strains by the results of immunological assays, including an immunofluorescence antibody assay performed with monoclonal antibodies and an immunoblot analysis of the immunological specificity of the major outer membrane protein.
Abstract: Chlamydia pecorum sp. nov. is proposed as the fourth species of the genus Chlamydia on the basis of the results of a genetic analysis of Chlamydia strains that were isolated from cattle and sheep which had various diseases, including sporadic encephalitis, infectious polyarthritis, pneumonia, and diarrhea. The levels of DNA-DNA homology between C. pecorum and strains of C. psittaci, Chlamydia pneumoniae, and Chlamydia trachomatis were less than 10%. Several DNA probes were used to identify C. pecorum. The C. pecorum strains were distinguished from C. psittaci strains by the results of immunological assays, including an immunofluorescence antibody assay performed with monoclonal antibodies and an immunoblot analysis of the immunological specificity of the major outer membrane protein. Species identification was based on results obtained from DNA analyses and serology. The type strain of C. pecorum is strain ATCC VR628.
TL;DR: Using 16S rRNA sequencing, it was found that strain ST1T (T = type strain) was related to previously described Helicobacter species, "Flexispira rappini," and W. succinogenes but could be differentiated from these organisms by their unique cellular ultrastructure.
Abstract: Helical organisms with novel ultrastructural characteristics were isolated from the intestinal mucosa of rats and mice. These bacteria were characterized by the presence of 9 to 11 periplasmic fibers which appeared as concentric helical ridges on the surface of each cell. The cells were motile with a rapid corkscrewlike motion and had bipolar tufts of 10 to 14 sheathed flagella. The bacteria were microaerophilic, nutritionally fastidious, and physiologically similar to Helicobacter species and Wolinella succinogenes but could be differentiated from these organisms by their unique cellular ultrastructure. Using 16S rRNA sequencing, we found that strain ST1T (T = type strain) was related to previously described Helicobacter species, “Flexispira rappini,” and W. succinogenes. The closest relatives of strain ST1T were Helicobacter mustelae and “F. rappini” (average similarity value, 96%). On the basis of phylogenetic data, strain ST1T (= ATCC 49282T) represents a new species of the genus Helicobacter, for which we propose the name Helicobacter muridarum.
TL;DR: It is proposed that a new species, Prevotella nigrescens, should be created for the genetically distinct group of strains that hybridized with strain ATCC 33563T, which is designated the type strain of P. Nigrescens.
Abstract: A total of 31 strains of Prevotella intermedia were subjected to DNA-DNA hybridization and were characterized by performing physiological tests and by performing a multilocus enzyme analysis, using malate dehydrogenase and glutamate dehydrogenase. All of the strains assigned to P. intermedia fermented glucose and sucrose, hydrolyzed starch but not esculin, and produced indole, acetic, isobutyric, isovaleric, and succinic acids as metabolic end products. The results of DNA reassociation experiments performed with the reference probe permitted separation of the strains into two well-defined homology groups. In addition, strains with DNAs that hybridized with DNA from strain ATCC 25611T (T = type strain) had high levels of peptidase activity and cleaved lipid substrates (4-methylumbelliferyl laurate and 4-methylumbellifelyl elaidate). Multilocus enzyme electrophoresis revealed two electromorphic profiles, one characteristic of strain ATCC 25611T and the other characteristic of strain ATCC 33563T. We propose that a new species, Prevotella nigrescens, should be created for the genetically distinct group of strains that hybridized with strain ATCC 33563T. Strain ATCC 33563 is designated the type strain of P. nigrescens.
TL;DR: The results, coupled with previous serologic data, provide conclusive evidence that the canine granulocytic ehrlichiosis agent is a new species of the genus Ehrlichia that is related to, but is distinct from, E. canis and all other species in the genus.
Abstract: The 16S rRNA gene was amplified, cloned, and sequenced from the blood of two dogs that were experimentally infected with the etiologic agent of canine granulocytic ehrlichiosis. The 16S rRNA sequence was found to be unique when it was compared with the sequences of other members of the genus Ehrlichia. The most closely related species were Ehrlichia canis (98.0% related) and the human ehrlichiosis agent (Ehrlichia chaffeensis) (98.1% related); all other species in the genus were found to be phylogenetically much more distant. Our results, coupled with previous serologic data, provide conclusive evidence that the canine granulocytic ehrlichiosis agent is a new species of the genus Ehrlichia that is related to, but is distinct from, E. canis and all other members of the genus. We propose the name Ehrlichia ewingii sp. nov.; the Stillwater strain is the type strain.
TL;DR: A new species is proposed, Leptospira kirschneri, comprising the following serovars: bulgarica, butembo, cynopteri, dania, grippotyphosa, kabura, kambale, ramisi, and tsaratsovo.
Abstract: A total of 66 serovars of potentially pathogenic Leptospira species were examined by slot blot hybridization, and 57 of these serovars were classified in six DNA homology groups. In cases in which common serovars were studied, the results were in general agreement with the results of previous workers, who used different DNA homology methods. However, we propose a new species, Leptospira kirschneri, comprising the following serovars: Bulgarica, butembo, cynopteri, dania, grippotyphosa, kabura, kambale, ramisi, and tsaratsovo. Seven of these serovars have not had their DNAs studied by other workers.
TL;DR: The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives, which confirmed that the genus is a neighboring taxon of the family Enterobacteriaceae.
Abstract: The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives. The results of immunological and 5S rRNA studies were confirmed in that the genus is a neighboring taxon of the family Enterobacteriaceae. With regard to the intrageneric structure, Vibrio alginolyticus, Vibrio campbellii, Vibrio natriegens, Vibrio harveyi, Vibrio proteolyticus, Vibrio parahaemolyticus, and Vibrio vulnificus form the core of the genus, while Vibrio (Listonella) anguillarum, Vibrio diazotrophicus, and Vibrio hollisae are placed on the outskirts of the genus. Variable regions around positions 80, 180, and 450 could be used as target sites for genus- and species-specific oligonucleotide probes and polymerase chain reaction primers to be used in molecular identification.
TL;DR: P. savastanoi strains belong to a DNA relatedness group that includes strains of P. syringae pv.
Abstract: We found that Pseudomonas syringae subsp. savastanoi strains belong to a DNA relatedness group that includes strains of P. syringae pv. glycinea and P. syringae pv. phaseolicola. This DNA group was distinct from P. syringae pv. syringae (including the type strain of P. syringae). The results of a numerical analysis were in accord with DNA hybridization data. Thus, P. syringae subsp. savastanoi (Janse) 1982 is elevated to species level as Pseudomonas savastanoi sp. nov., which includes P. savastanoi pv. savastanoi, P. savastanoi pv. glycinea, and P. savastanoi pv. phaseolicola.
TL;DR: Two pure cultures of bacteria isolated from soil samples collected in Schirmacher Oasis, Antarctica, conformed to the definition of the genus Sphingobacterium, and were found to be psychrotrophic and 7% homology with S. multivorum and S. spiritivorum.
Abstract: Two pure cultures of bacteria isolated from soil samples collected in Schirmacher Oasis, Antarctica, conformed to the definition of the genus Sphingobacterium. They differed from all of the known species of Sphingobacterium in being psychrotrophic. The G+C contents of the DNA of the two strains were found to be 39.3 and 40.3 mol%, and DNA-DNA hybridization studies indicated 7% homology with S. multivorum and S. spiritivorum. The name Sphingobacterium antarcticus sp. nov. is proposed for the two Antarctic strains. The type strain is 4BY (MTCC 675), and it has been deposited with the Microbial Type Culture Collection, Institute of Microbial Technology, Chandigarh, India.
TL;DR: Two new species of aerobic, gram-negative, peritrichously flagellated or nonmotile marine bacteria usually forming star-shaped aggregates were isolated from northeastern Atlantic Ocean bottom sediments and formed a group of closely related bacteria that could not be excluded from the genus Agrobacteria with certainty.
Abstract: Two new species of aerobic, gram-negative, peritrichously flagellated or nonmotile marine bacteria usually forming star-shaped aggregates were isolated from northeastern Atlantic Ocean bottom sediments. These organisms resembled eight star-shaped-aggregate-forming bacterial species from the Baltic Sea originally ascribed to the genus Agrobacterium but not included on the Approved Lists of Bacterial Names because of their questionable relationships to true agrobacteria. These two sets of star-shaped-aggregate-forming bacteria were compared by means of phenotypic data, DNA base compositions, DNA-DNA relatedness, and one-dimensional electrophoretic analysis of low-molecular-weight RNAs (5S rRNA and tRNA). According to the results of genotyping, the northeastern Atlantic Ocean isolates and three of the Baltic Sea species formed a group of closely related bacteria that could not be excluded from the genus Agrobacterium with certainty. Until more genotypic data are available, these five marine species are regarded as a distinct subdivision of the genus Agrobacterium consisting of Agrobacterium atlanticum sp. nov. (type strain, 1480T = DSM 5823T), A. meteori sp. nov. (type strain, 1513T = DSM 58241), A. ferrugineum sp. nov. nom. rev. emend. (type strain, ATCC 25652T), A. gelatinovorum sp. nov. nom. rev. emend. (type strain, ATCC 25655T), and A. stellulatum sp. nov. nom. rev. emend, (type strain, ATCC 15215T). “A. aggregatum” proved to be a later subjective synonym of A. stellulatum, which had priority. The remaining four Baltic Sea species, “A. agile,” “A. kieliense,” “A. luteum,” and “A. sanguineum,” could not be placed in the new subdivision of Agrobacterium.
TL;DR: This paper identified clinical strains of S. putrefaciens which have a high range of moles percent G+C, as does S. alga, and characterized the reidentified strains and found that the original description of S alga (U. Simidu, Kita-Tsukamoto, T. Yasumoto, and M. Yotsu) is insufficient to identify this strain.
Abstract: Genetic and phenotypic studies on the strains biochemically identified as Shewanella putrefaciens, which had a G+C content ranging from 52 to 54 mol% were conducted. The moles percent G+C of the type strain of S. putrefaciens is 46. Surprisingly, DNA homology experiments revealed that all these strains are genetically related to Shewanella alga (which was reported to produce tetrodotoxin), not to the type strain of S. putrefaciens. In this study, we reidentified clinical strains of S. putrefaciens which have a high range of moles percent G+C, as does S. alga. We also characterized the reidentified strains and found that the original description of S. alga (U. Simidu, K. Kita-Tsukamoto, T. Yasumoto, and M. Yotsu, Int. J. Syst. Bacteriol. 40:331-336, 1990) is insufficient to identify this strain. An emended description of S. alga is given.
TL;DR: The biologic and genomic characteristics of the organism are essentially the same as those of other pathogenic spotted fever group rickettsiae, although the R. japonica isolates cause a persistent infection in Vero cells for many subcultures.
Abstract: We propose the name Rickettsia japonica sp. nov. (with type strain YH [= ATCC VR-1363]) for a serologically specific species of spotted fever group rickettsiae that are pathogenic for humans (J. Infect. Dis. 159:1122-1126, 1989; J. Clin. Microbiol. 28:1177-1180, 1990). The biologic and genomic characteristics of the organism (G+C content, 31.2 ± 0.7 mol%) are essentially the same as those of other pathogenic spotted fever group rickettsiae, although the R. japonica isolates cause a persistent infection in Vero cells for many subcultures.
TL;DR: The bacterial genus Serpula Stanton et al. 1991 is illegitimate due to the existence of a fungal genus SerPula Pers.
Abstract: The bacterial genus Serpula Stanton et al. 1991 is illegitimate due to the existence of a fungal genus Serpula Pers. ex S. F. Gray. Consequently, a new genus designation, Serpulina, is proposed for this spirochete genus. Serpula hyodysenteriae, the type species, and Serpula innocens Stanton et al. 1991, therefore, become Serpulina hyodysenteriae comb. nov. and Serpulina innocens comb. nov.
TL;DR: F. ovolyticus resembles Flexibacter maritimus, but differs from the latter species in several biochemical and physiological characteristics, and constitutes a new species.
Abstract: A psychrotrophic Flexibacter sp., Flexibacter ovolyticus sp. nov., was isolated from the adherent bacterial epiflora of Atlantic halibut (Hippoglossus hippoglossus L.) eggs and was shown to be an opportunistic pathogen for halibut eggs and larvae. The strains which we isolated had the enzymatic capacity to dissolve both the chorion and the zona radiata of the egg shells. A total of 35 isolates were characterized by using morphological and biochemical tests. These strains were rod shaped, gram negative, Kovacs oxidase positive, and pale yellow and exhibited gliding motility. They did not produce acid from any of the wide range of carbohydrates tested. Our isolates had the ability to degrade gelatin, tyrosine, DNA, and Tween 80. Starch, cellulose, and chitin were not degraded. The strains were catalase and nitrate reductase positive, did not produce H2S, and did not grow under anaerobic conditions. F. ovolyticus resembles Flexibacter maritimus, but differs from the latter species in several biochemical and physiological characteristics. DNAs from F. ovolyticus strains had guanine-plus-cytosine contents which ranged from 30.3 to 32.0 mol% (strains EKC001, EKD002T [T = type strain], and VKB004), and DNA-DNA hybridization studies revealed levels of relatedness between F. ovolyticus EKD002T and F. maritimus NCMB 2154T and NCMB 2153 of 42.7 and 30.0%, respectively. Compared with previously described Cytophaga and Flexibacter spp. with low guanine-plus-cytosine contents, F. ovolyticus constitutes a new species. Strain EKD002 (= NCIMB 13127) is the type strain of the new species.
TL;DR: The phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but the conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses.
Abstract: The 16S rRNAs from nine rapidly growing Mycobacterium species were partially sequenced by using the dideoxynucleotide-terminated, primer extension method with cDNA generated by reverse transcriptase. The sequences were aligned with 47 16S rRNA or DNA sequences that represented 30 previously described and 5 undescribed species of the genus Mycobacterium, and a dendrogram was constructed by using equally weighted distance values. Our results confirmed the phylogenetic separation of the rapidly and slowly growing mycobacteria and showed that the majority of the slowly growing members of the genus represent the most recently evolved organisms. The 24 strains which represented 21 rapidly growing species constituted several sublines, which were defined by the following taxa: (i) Mycobacterium neoaurum and M. diernhoferi, (ii) M. gadium, (iii) the M. chubuense cluster, (iv) the M. fortuitum cluster, (v) M. kommossense, (vi) M. sphagni, (vii) M. fallax and M. chitae, (viii) M. aurum and M. vaccae, (ix) the M. flavescens cluster, and (x) M. chelonae subsp. abscessus. Our phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but our conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses.
TL;DR: Comparisons of the SAY-MLO 16S rRNA nucleotide sequence with16S r RNA sequences of other organisms indicated that the SAY -MLO is phylogenetically related most closely to other plant-pathogenic mycoplasmalike organisms, followed by Anaeroplasma species, Acholeplasma Species, and some Mycoplasma Species.
Abstract: Restriction fragments containing the 16S rRNA gene of the western aster yellows mycoplasmalike organism (SAY-MLO) were identified in Southern blots probed with cloned fragments of the western X-disease mycoplasmalike organism 16S rRNA gene. Two fragments which contained the entire SAY-MLO 16S rRNA gene and flanking DNA were cloned in M13 and sequenced. The SAY-MLO 16S rRNA gene is approximately 1,535 bp long, has a G+C content of 47 mol%, and has an overall secondary structure similar to that proposed for Escherichia coli. Putative rRNA promoter sequences and sequences involved in processing of the primary rRNA transcript were similar in the SAY-MLO, two Mycoplasma species, and Bacillus subtilis, suggesting that these prokaryotes and the mycoplasmalike organisms may have similar transcriptional and processing enzymes. We identified two tRNA genes, a tRNATyr (GTA) gene upstream from the 16S rRNA gene and a tRNAIle (GAT) gene in the spacer region between the 16S and 23S rRNA genes. Comparisons of the SAY-MLO 16S rRNA nucleotide sequence with 16S rRNA sequences of other organisms indicated that the SAY-MLO is phylogenetically related most closely to other plant-pathogenic mycoplasmalike organisms, followed by Anaeroplasma species, Acholeplasma species, and some Mycoplasma species.
TL;DR: An unusual mycoplasma, which was isolated from the urine of a human immunodeficiency virus-positive male homosexual patient, has an elongated flask shape and two unique sharply divided internal compartments, and it is proposed that this new mollicute species should be named MyCoplasma penetrans sp.
Abstract: An unusual mycoplasma, which was isolated from the urine of a human immunodeficiency virus-positive male homosexual patient, has an elongated flask shape and two unique sharply divided internal compartments. The tiplike compartment is densely packed with fine granules, and the body compartment is loosely filled with coarse granules consistent with ribosomal structures. The organism has properties of adherence, hemadsorption, and cytadsorption and invades many different types of mammalian cells. Adhesion and penetration apparently involve the terminally located tiplike structure. Cholesterol is required for growth, and the mycoplasma ferments glucose and hydrolyzes arginine, but does not hydrolyze urea. The results of DNA homology studies revealed that this organism is not genetically related to previously described mycoplasma species that have the same biochemical properties. The results of serologic studies demonstrated that this organism is antigenically distinct from all previously described mycoplasmas. We propose that this new mollicute species should be named Mycoplasma penetrans sp. nov. The type strain is strain GTU-54-6A1 (= ATCC 55252).
TL;DR: The results confirm that the genus Erysipelothrix contains two main genomic species, E. rhusiopathiae and E. tonsillarum, which can be differentiated into serovars.
Abstract: The levels of relatedness among strains of Erysipelothrix rhusiopathiae (serovars 1 through 23 and type N) were estimated by performing DNA-DNA hybridization experiments with the type strains of E. rhusiopathiae and Erysipelothrix tonsillarum, which are the two Erysipelothrix species that have been described. Two distinct DNA relatedness groups were identified. The group 1 strains, representing serovars 1, 2, 4 through 6, 8, 9, 11, 12, 15 through 17, 19, and 21 and type N, exhibited more than 73% hybridization with the type strain of E. rhusiopathiae but less than 24% hybridization with the type strain of E. tonsillarum. Group 2 included serovar 3, 7, 10, 14, 20, 22, and 23 strains, and these strains exhibited more than 66% hybridization with the type strain of E. tonsillarum but less than 27% hybridization with the type strain of E. rhusiopathiae. Strains representing serovars 13 and 18 exhibited low levels of hybridization (16 to 47%) with both of the type strains, indicating that these serovars may be members of a new genomic species. The members of the E. rhusiopathiae and E. tonsillarum groups resembled each other in many phenotypic characteristics, but differed in their ability to produce acid from saccharose and in their pathogenicity for swine. Our results confirm that the genus Erysipelothrix contains two main genomic species, E. rhusiopathiae and E. tonsillarum, which can be differentiated into serovars.