High Levels Of DNA Relatedness Research Articles

Enterococcus porcinus sp. nov. and Enterococcus ratti sp. nov., associated with enteric disorders in animals.

Recent insights have been brought to the taxonomy of the genus Enterococcus by studies applying whole-cell protein analysis and DNA-DNA reassociation experiments, in addition to conventional physiological tests. Using these techniques, a group of 10 strains resembling the physiological group III of enterococcal species was characterized. Five strains were recovered from pigs and five from rats with enteric disorders. On the basis of the results of conventional physiological tests, the most likely identity of these strains was Enterococcus durans or Enterococcus hirae. Analysis of the electrophoretic whole-cell protein profiles showed two distinct clusters of virtually indistinguishable profiles: one composed of strains isolated from pigs, and one composed of strains isolated from rats. These protein profiles were not similar to the profiles of any previously described Enterococcus species. The results of DNA-DNA relatedness experiments were consistent with the results of the protein-profile analysis. The high levels of DNA relatedness found for pig isolates demonstrated that they belong to a new enterococcal species, for which the designation Enterococcus porcinus sp. nov. is proposed (type strain =DS 1390-83T =ATCC 700913T =CCUG 43229T =NCIMB 13634T). Strains isolated from rats were found to comprise another new species, for which the designation Enterococcus ratti sp. nov. is proposed (type strain =DS 2705-87T =ATCC 700914T =CCUG 43228T =NCIMB 13635T). This report provides data on the phenotypic and genotypic characterization of these two new enterococcal species, which may represent diarrhoeagenic pathogens for animals.

Host Range of Streptomycete Strains Causing Common Scab.

Ten Streptomyces isolates from common scab lesions on carrots (Daucus carota) were characterized. Morphological and physiological characterization of the carrot isolates established that they were closely related to S. scabies. DNA-DNA hybridization studies were carried out between DNA from the carrot isolates and DNA from two potato strains belonging to the two genetic clusters of S. scabies. Most of the carrot isolates exhibited a high level of DNA relatedness (average of 90%) to strain EF-54, which belongs to genetic cluster 1 of S. scabies. Three carrot isolates could not be included in either S. scabies genetic cluster 1 or 2. The pathogenicity of six S. scabies isolates from potato or carrot, two isolates of S. caviscabies, and one isolate of S. acidiscabies was determined on potato, carrot, radish, beet, turnip, and parsnip. All S. scabies isolates were pathogenic on carrot and radish, but pathogenicity on beet, parsnip, turnip, and potato was variable. Even though S. acidiscabies and S. caviscabies until now have been isolated only from potato, we demonstrated that isolates of these species also could infect other crops, such as radish, carrot, parsnip, and turnip.

Phenotypic and genotypic characterization of atypical Lactococcus garvieae strains isolated from water buffalos with subclinical mastitis and confirmation of L. garvieae as a senior subjective synonym of Enterococcus seriolicida.

During a survey of bacterial agents that cause subclinical mastitis in water buffalos, we isolated several strains of gram-positive cocci that appeared to be enterococci except that they grew very slowly at 45 degrees C and grew slowly in broth containing 6.5% NaCl. On the basis of the results of conventional physiologic tests, these strains were identified as Enterococcus durans. However, none of the strains reacted with the AccuProbe Enterococcus genetic probe. The whole-cell protein profiles of these organisms were compared with the profiles of Enterococcus and Lactococcus reference strains. apart from minor quantitative differences, the mastitis isolates had indistinguishable protein profiles that were similar to the profiles of the Lactococcus garvieae and Enterococcus seriolicida type strains. The results of DNA relatedness studies performed by using the hydroxyapatite method at 55 and 70 degrees C indicated that all of the mastitis isolates were related to the type strain of L. garvieae at the species level, despite the fact that they exhibited several uncommon phenotypic characteristics (growth at 45 degrees C, growth in broth containing 6.5% NaCl, and failure to produce acid from mannitol and sucrose). The high levels of DNA relatedness between strains of L. garvieae is a senior synonym of E. seriolicida, L. garvieae should be retained as the species name and strain ATCC 43921 should remain the type strain of this species.

Nocardia pseudobrasiliensis sp. nov., a New Species of Nocardia Which Groups Bacterial Strains Previously Identified as Nocardia brasiliensis and Associated with Invasive Diseases

We studied five strains of a new Nocardia taxon recently identified among Nocardia brasiliensis strains associated with invasive diseases (R. J. Wallace, Jr., B. A. Brown, Z. Blacklock, R. Ulrich, K. Jost, J. M. Brown, M. M. McNeil, G. Onyi, V. A. Steingrube, and J. Gibson, J. Clin. Microbiol. 33:1528-1533, 1995) to determine their taxonomic status. Several characteristics of these organisms, including the presence of chemotype IV cell walls, nocardomycolic acids, a predominant menaquinone similar to that of Nocardia asteroides ATCC 19247T (T = type strain), and G+C contents ranging from 67 to 68 mol%, are characteristics of the genus Nocardia. Phylogenies based on small-subunit ribosomal DNA sequences clearly confirmed that all five strains belong to the genus Nocardia and occur on a single branch that is clearly distinct from N. brasiliensis. This branch forms a clade with Nocardia vaccinii, Nocardia nova, Nocardia otitidiscaviarum, and Nocardia seriolae. The five new strains exhibited high levels of DNA relatedness with each other, as determined by DNA-DNA hybridization experiments (S1 nuclease procedure), but not with N. brasiliensis strains or with strains of the four phylogenetically related Nocardia species mentioned above. The five new strains differ from N. brasiliensis in the following characteristics: mycolic acid pattern, decomposition of adenine, nitrate reduction, and antimicrobial agent susceptibilities. Therefore, we propose that these strains belong to a new species, Nocardia pseudobrasiliensis. The type strain is strain ATCC 51512, which was isolated from a leg abscess on a patient suffering from ulcerative colitis.

Genetic and phenotypic analysis of Borrelia miyamotoi sp. nov., isolated from the ixodid tick Ixodes persulcatus, the vector for Lyme disease in Japan.

The ixodid tick Ixodes persulcatus is the most important vector of Lyme disease in Japan. Most spirochete isolates obtained from I. persulcatus ticks have been classified as Borrelia burgdorferi sensu lato because of their genetic, biological, and immunological characteristics. However, we found that a small number of isolates obtained from I. persulcatus contained a smaller 38-kDa endoflagellar protein and single 23S-5S rRNA gene unit. Representative isolate HT31T (T = type strain) had the same 23S rRNA gene physical map as Borrelia turicatae. The DNA base composition of strain HT31T was 28.6 mol% G+C. DNA-DNA hybridization experiments revealed that strain HT31T exhibited moderate levels of DNA relatedness (24 to 51%) with Borrelia hermsii, B. turicatae, Borrelia parkeri, and Borrelia coriaceae. However, the levels of DNA reassociation with the previously described Lyme disease borreliae (B. burgdorferi, Borrelia garinii, and Borrelia afzelii) were only 8 to 13%. None of the previously described species examined exhibited a high level of DNA relatedness with strain HT31T. In addition, the 16S rRNA gene sequence (length, 1,368 nucleotides) of strain HT31T was determined and aligned with the 16S rRNA sequences of other Borrelia species. Distance matrix analyses were performed, and a phylogenetic tree was constructed. The results showed that isolate HT31T is only distantly related to both previously described Lyme disease borreliae and relapsing fever borreliae. Thus, the spirochetes isolated from I. persulcatus and closely related isolates should be classified as members of a new Borrelia species. We propose the name Borrelia miyamotoi sp. nov. for this spirochete; strain HT31 is the type strain.

Corynebacterium argentoratense sp. nov., from the Human Throat

A new Corynebacterium species, Corynebacterium argentoratense was isolated from the throats of four human patients. It is characterized by the presence of chemotype IV, a cell wall, corynomycolic acids, and a G+C content ranging from 60 to 61 mol%. Strains belonging to this species exhibit high levels of DNA relatedness as determined by DNA-DNA hybridization experiments (S1 nuclease procedure) but no close DNA relatedness with related Corynebacterium species. Phylogenies based on comparative analyses of nearly complete small-subunit rDNA sequences confirmed the inclusion of this new species within the genus Corynebacterium and grouped it in a cluster with C. diphtheriae, C. ulcerans, C. pseudotuberculosis, and C. kutscheri. PCR experiments revealed an absence of the gene coding for diphtheria toxin. This new species can be identified by its mycolic acid pattern, fermentation of sugars, and enzymatic activities. Strain IBS B10697 (CIP 104296) is the type strain of C. argentoratense.

Clarification of the Taxonomy of Bacillus mycoides

Because of the very similar physiological properties and base sequences of the 16S rRNAs of Bacillus cereus, Bacillus mycoides, and Bacillus thuringiensis, some taxonomists question the validity of separating these organisms into distinct species. DNA relatedness studies based on spectrophotometrically measured renaturation rates were carried out to determine the taxonomic relationships of the three species. A study of 58 strains revealed that the levels of relatedness between B. cereus and B. mycoides and between B. cereus and B. thuringiensis ranged from 22 to 44% and from 59 to 69%, respectively. On the basis of the moderately high levels of DNA relatedness which we determined, B. cereus and B. thuringiensis appeared to be genetically related but taxonomically distinct entities. The B. mycoides group was genetically distantly related to the B. cereus group and represented a separate taxon. Furthermore, our data indicated that the B. mycoides group consists of two genetically distinct groups, each of which represents a distinct species. In addition to rhizoidal colonial morphology and lack of motility, the B. mycoides group could be distinguished from B. cereus by differences in fatty acid profiles and acetanilide-producing activities.

Small-Subunit rRNA Sequences and Whole DNA Relatedness Concur for the Reassignment of Pasteurella piscicida (Snieszko et al.) Janssen and Surgalla to the Genus Photobacterium as Photobacterium damsela subsp. piscicida comb. nov.

The taxonomic status of Pasteurella piscicida (strain NCIMB 2058T [T = type strain] and a strain isolated from the environment) was investigated by performing phylogenetic analyses of small-subunit rRNA sequences, DNA-DNA hybridization analyses, and biochemical characterization analyses. The results of the phylogenetic analyses and the levels of DNA-DNA complementarity demonstrated conclusively that Pasteurella piscicida is extremely closely related to Photobacterium damsela ATCC 33539T. Since the two taxa exhibited a level of DNA-DNA relatedness of 80%, they are members of the same species. The high level of DNA relatedness and the presence of specific morphological and biochemical characteristics support the hypothesis that two subspecies should be recognized. On the basis of its phylogenetic position, we concluded that Pasteurella piscicida should be renamed Photobacterium damsela subsp. piscicida comb. nov.

Genetic Relationships among Eubacterium Species

The genetic relationships among Eubacterium species were assessed by using DNAs from American Type Culture Collection type strains of 10 species and two subspecies of the genus Eubacterium, i.e., Eubacterium aerofaciens, E. alactolyticum, E. brachy, E. lentum, E. limosum, E. nodatum, E. rectale, E. saburreum, E. timidum, E. yurii subsp. yurii, and E. yurii subsp. margaretiae. The DNA base compositions (determined by high-performance liquid chromatography) of these species varied widely, from 38 to 62 mol% G+C. Seven Eubacterium species showed significant differences (nearly 10%) in G+C content compared with E. limosum, the type species of the genus. DNA-DNA hybridization (by the membrane filter method) showed that two subspecies, E. yurii subsp. yurii and E. yurii subsp. margaretiae, and two strains of E. timidum exhibited high levels of DNA relatedness. However, the DNA reassociations among the 10 Eubacterium species studied were 1 to 16%. None of the species examined shared a high level of DNA reassociation with the type species of the genus Eubacterium. The protein profile patterns (determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of whole bacterial cells from these Eubacterium species were distinct, and no major peptide bands were shared among the 10 Eubacterium species. Therefore, the Eubacterium species we tested must be considered genetically distinct from each other.

Characterization of Pediococcus pentosaceus and Pediococcus acidilactici Strains and Replacement of the Type Strain of P. acidilactici with the Proposed Neotype DSM 20284: Request for an Opinion

Levels 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).

Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov.

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 M. chelonae subsp. abscessus ATCC 19977T is genetically different from M. chelonae subsp. chelonae NCTC 946T on 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.

DNA Relatedness among Species of Sterigmatomyces and Fellomyces

Species assigned to the anamorphic yeast genera Sterigmatomyces, Fellomyces, Tsuchiyaea, and Kurtzmanomyces were compared for extent of nuclear DNA complementarity. The following organisms show little relatedness and are recognized as genetically distinct species: Sterigmatomyces halophilus, Sterigmatomyces elviae, Fellomyces fuzhouensis, Fellomyces penicillatus, Fellomyces polyborus, Tsuchiyaea wingfieldii, Kurtzmanomyces nectairii, and Sterigmatosporidium polymorphum. Sterigmatomyces indicus exhibited a high level of DNA relatedness with Sterigmatomyces halophilus and is considered a synonym of the latter species despite the difference in nitrate assimilation that led to the initial taxonomic separation of these taxa. The three taxa Sterigmatomyces aphidis, Trichosporon oryzae, and Sporobolomyces antarcticus showed moderate to high levels of DNA relatedness and are considered synonyms of Vanrija antarctica.

A cooperative taxonomic study of mycobacteria isolated from armadillos infected with Mycobacterium leprae.

Seventeen strains of mycobacteria, recovered from six armadillos experimentally infected with Mycobacterium leprae, were examined in ten different laboratories. This collaborative study included use of conventional bacteriological tests, lipid analyses, determination of mycobactins and peptidoglycans, characterization by Py-MS, and immunological, metabolic, pathological and DNA studies. These armadillo-derived mycobacteria (ADM) formed five homogeneous groups (numbered ADM 1 to 5) on the basis of phenetic analyses. However, DNA studies revealed only four homogeneous groups since group ADM 1 and one of the two strains in group ADM 3 showed a high level of DNA relatedness. The phenetic and DNA studies confirmed that the ADM strains differed from all other known mycobacteria. Cultural, biochemical, metabolic and pathogenic properties as well as DNA-DNA hybridizations clearly differentiated these ADM from M. leprae.