Showing papers in "International Journal of Systematic and Evolutionary Microbiology in 1989"
TL;DR: High-performance liquid chromatography is a promising alternative for determining the G+C content of bacterial deoxyribonucleic acid (DNA) and may also be more accurate than indirect methods, such as the buoyant density and thermal denaturation methods.
Abstract: High-performance liquid chromatography is a promising alternative for determining the G+C content of bacterial deoxyribonucleic acid (DNA). The method which we evaluated involves enzymatic degradation of the DNA to nucleosides by P1 nuclease and bovine intestinal mucosa alkaline phosphatase, separation of the nucleosides by high-performance liquid chromatography, and calculation of the G+C content from the apparent ratios of deoxyguanosine and thymidine. Because the nucleosides are released from the DNA at different rates, incomplete degradation produces large errors in the apparent G+C content. For partially purified DNA, salts are a major source of interference in degradation. However, when the salts are carefully removed, the preparation and degradation of DNA contribute little error to the determination of G+C content. This method also requires careful selection of the chromatographic conditions to ensure separation of the major nucleosides from the nucleosides of modified bases and precise control of the flow rates. Both of these conditions are achievable with standard equipment and C18 reversed-phase columns. Then the method is precise, and the relative standard deviations of replicate measurements are close to 0.1%. It is also rapid, and a single measurement requires about 15 min. It requires small amounts of sample, and the G+C content can be determined from DNA isolated from a single bacterial colony. It is not affected by contamination with ribonucleic acid. Because this method yields a direct measurement, it may also be more accurate than indirect methods, such as the buoyant density and thermal denaturation methods. In addition, for highly purified DNA, the extent of modification can be determined.
4,685 citations
TL;DR: The results showed that the fluorometric direct binding method in which microdilution wells are used could be an alternative to radioisotope and membrane filter hybridization methods.
Abstract: Fluorometric hybridization in microdilution wells was developed to determine genetic relatedness among microorganisms. Total chromosomal deoxyribonucleic acid (DNA) for hybridization reactions was labeled with photoreactive biotin (photobiotin). The biotinylated DNA was hybridized with single-stranded unlabeled DNAs which had been immobilized on the surfaces of microdilution wells. After hybridization, biotinylated DNA was quantitatively detected with beta-D-galactosidase and a fluorogenic substrate, 4-methylumbelliferyl-beta-D-galactopyranoside. Homology values obtained with this fluorometric direct binding method were compared with values obtained with two membrane filter methods, one in which photobiotin labeling was used and one in which radioisotope labeling was used. The results showed that the fluorometric direct binding method in which microdilution wells are used could be an alternative to radioisotope and membrane filter hybridization methods.
3,310 citations
TL;DR: Five major groups of taxonomic features of the genus Wolinella that differ markedly from those of C. pylori are described, indicating that C. Pylori should be included in the new genus Helicobacter as Helicobacteria mustelae comb.
Abstract: Different types of studies have shown that Campylobacter pylori does not belong in the genus Campylobacter. Ribonucleic acid sequencing has indicated that C. pylori might belong in the genus Wolinella, but we describe five major groups of taxonomic features of the genus Wolinella that differ markedly from those of C. pylori, including ultrastructure and morphology, cellular fatty acids, menaquinones, growth characteristics, and enzyme capabilities, indicating that C. pylori should not be included in the genus Wolinella. Thus, we propose the establishment of a new genus, Helicobacter; C. pylori should be transferred to this genus as Helicobacter pylori comb. nov., and H. pylori NCTC 11637 (= ATCC 43504) is the type strain. The gastric spiral organism from ferrets has been elevated recently from Campylobacter pylori subsp. mustelae to Campylobacter mustelae. We describe the similarities and differences between C. mustelae and C. pylori compared with other campylobacters, and we propose that C. mustelae should be included in the new genus Helicobacter as Helicobacter mustelae comb. nov. (type strain, ATCC 43772).
593 citations
TL;DR: A collection of 151 strains of the viridans type of streptococci, which were isolated mainly from human oral cavities and included several reference strains, are examined in an attempt to revise and improve the taxonomy of this group of bacteria.
Abstract: We examined a collection of 151 strains of the viridans type of streptococci, which were isolated mainly from human oral cavities and included several reference strains, in an attempt to revise and improve the taxonomy of this group of bacteria. Our examinations included determinations of a high number of biochemical and physiological characteristics and serological reactivity. The resulting data revealed several hitherto unrecognized characters of taxonomic significance, and several of the species can now be more accurately defined. A diagnostic key to the taxa is presented. Strains previously identified as Streptococcus sanguis could be divided into two clearly distinct species, Streptococcus sanguis sensu stricto (type strain, ATCC 10556) and a new species, Streptococcus gordonii (type strain, ATCC 10558). Streptococcus mitis was divided into two biovars, consisting of strains possessing group O antigens and strains possessing group K antigen. The group of strains assigned to Streptococcus anginosus was biochemically and serologically heterogeneous, but the data did not allow natural subdivisions. Based on the results of this study, emended descriptions of the species Streptococcus oralis, S. mitis, and S. sanguis are provided. The classification resulting from this study is in complete agreement with previously published genetic data.
431 citations
TL;DR: A third species, Chlamydia pneumoniae, is proposed for the genusChlamydia, which is a human respiratory pathogen, which has been referred to as the TWAR strain of Chlam Lydia.
Abstract: A third species, Chlamydia pneumoniae, is proposed for the genus Chlamydia. This bacterium is a human respiratory pathogen, which has been referred to as the TWAR strain of Chlamydia. Species identification is based on ultrastructural differences in the elementary bodies, deoxyribonucleic acid analysis, and serology.
394 citations
TL;DR: DNA hybridization group 14589 constitutes a discrete species within the family Enterobacteriaceae and is proposed to unite DNA hybridization groups 14589 and 27155 in a single genus, Pantoea gen. nov.
Abstract: Deoxyribonucleic acid (DNA)-DNA hybridization was performed with 10 strains belonging to the “Erwinia herbicola-Enterobacter agglomerans complex” by using the competition method on nitrocellulose filters. These strains exhibited more than 75% DNA binding to Erwinia herbicola ATCC 14589T (T = type strain) and constitute DNA hybridization group 14589 (including strains ATCC 14589T and CDC 1429-71 from DNA hybridization group III [D. J. Brenner, G. R. Fanning, J. K. Leete Knutson, A. G. Steigerwalt, and M. J. Krichevsky, Int. J. Syst. Bacteriol. 34:45-55, 1984]). The high level of genomic relatedness of these strains was confirmed by the similarities observed in their electrophoretic protein patterns. On the basis of our data, DNA hybridization group 14589 constitutes a discrete species within the family Enterobacteriaceae. Its closest relative is DNA hybridization group 27155 (41 to 53% DNA relatedness), which was previously defined and includes the type strains, among others, of Enterobacter agglomerans, Erwinia herbicola, and Erwinia milletiae (A. Beji, J. Mergaert, F. Gavini, D. Izard. K. Kersters, H. Leclerc, and J. De Ley, Int. J. Syst. Bacteriol. 38:77-88, 1988). We propose to unite DNA hybridization groups 14589 and 27155 in a single genus, Pantoea gen. nov. Pantoea agglomerans (Beijerinck 1888) comb. nov. is proposed to contain most strains of DNA hybridization group 27155 (including DNA hybridization group XIII of Brenner et al.), and its type strain is strain ATCC 27155 (= NCTC 9381 = LMG 1286). Pantoea dispersa sp. nov. is proposed to contain DNA hybridization group 14589, and its type strain is strain ATCC 14589 (= LMG 2603). Descriptions of the genus and its two species are given.
361 citations
TL;DR: Results of deoxyribon nucleic acid (DNA)-ribosomal ribonucleic acid and DNA-DNA hybridizations revealed that nitrogen-fixing bacteria isolated from roots and stems of sugarcane belong to a new species in the genus Acetobacter, for which the name AcetOBacter diazotrophicus sp.
Abstract: Results of deoxyribonucleic acid (DNA)-ribosomal ribonucleic acid and DNA-DNA hybridizations, together with a phenotypic and chemotaxonomic analysis, revealed that nitrogen-fixing bacteria isolated from roots and stems of sugarcane belong to a new species in the genus Acetobacter, for which the name Acetobacter diazotrophicus sp. nov. is proposed. Strain LMG 7603 (= Dobereiner PAI 5 = ATCC 49037) is the type strain.
287 citations
TL;DR: The results show that these five yellow-pigmented hydrogen-oxidizing Pseudomonas species are more closely related to each other than to other taxa belonging to the acidovorans rRNA complex.
Abstract: The relationships of the yellow-pigmented hydrogen-oxidizing species Pseudomonas flava, Pseudomonas pseudoflava, Pseudomonas palleronii, Pseudomonas taeniospiralis, and “Pseudomonas carboxydoflava,” which are all members of the acidovorans ribosomal ribonucleic acid (rRNA) complex in rRNA superfamily III, were studied by using deoxyribonucleic acid (DNA):rRNA hybridization, immunotyping, numerical analysis of biochemical and auxanographic features, polyacrylamide gel electrophoresis of cellular proteins, numerical analysis of fatty acid patterns, and DNA:DNA hybridization. Our results show that these five yellow-pigmented hydrogen-oxidizing Pseudomonas species are more closely related to each other than to other taxa belonging to the acidovorans rRNA complex. We propose the transfer of these species to a new genus, Hydrogenophaga, with the following four species: Hydrogenophaga flava (formerly Pseudomonas flava), Hydrogenophaga pseudoflava (to accommodate both Pseudomonas pseudoflava and “Pseudomonas carboxydoflava”), Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis), and Hydrogenophaga palleronii (formerly Pseudomonas palleronii). The type species is H. flava, with monotype strain DSM 619 (= LMG 2185 = CCUG 1658). Because H. flava grows slowly and unreliably, but is genotypically and protein electrophoretically very similar to H. pseudoflava, the latter species can be used as an alternative reference taxon for the new genus. The type strains of H. pseudoflava, H. taeniospiralis, and H. palleronii are strains GA3 (= LMG 5945 = CCUG 13799). DSM 2082 (= LMG 7170 = CCUG 15921), and Stanier 362t1 (= LMG 2366t1 = CCUG 20334), respectively.
273 citations
TL;DR: The results indicate that this species as presently constituted is genomically very heterogeneous, and it is suggested that members of L. casei subsp.casei strains be given separate species status, for which the names L. paracasei sp.
Abstract: Deoxyribonucleic acid (DNA)-DNA hybridizations were performed on strains of Lactobacillus casei. Our results indicate that this species as presently constituted is genomically very heterogeneous. The majority of strains designated L. casei subsp. casei, together with members of L. casei subsp. alactosus, L. casei subsp. pseudoplantarum, and L. casei subsp. tolerans, exhibited high levels of DNA relatedness with each other but were distinct from the type strain of L. casei subsp. casei. Strains of L. casei subsp. rhamnosus also formed a genomically homogeneous group unrelated to all members of the other L. casei subspecies examined. On the basis of the present and previous findings we suggest that members of L. casei subsp. alactosus, L. casei subsp. pseudoplantarum, and L. casei subsp. tolerans and the majority of L. casei subsp. casei strains be given separate species status, for which we propose the names L. paracasei sp. nov., L. paracasei subsp. paracasei (type strain, NCDO 151), and L. paracasei subsp. tolerans (type strain ATCC 25599). We also propose that L. casei subsp. rhamnosus be elevated to species status, as L. rhamnosus sp. nov. (type strain, ATCC 7469).
256 citations
TL;DR: Revival of the name Streptomyces scabies is proposed for the predominant species causing common scab of potato and 12 S. scabies strains formed a homogeneous group characterized by smooth grey spores borne in spiral chains, melanin production, and usage of all International Streptomers Project sugars.
Abstract: Revival of the name Streptomyces scabies is proposed for the predominant species causing common scab of potato. Common scab strains from the northeastern United States, Atlantic Canada, and Hungary were differentiated by a phenotypic analysis of 42 criteria from six atypical pathogen strains, three saprophytic streptomycetes isolated from scab lesions, and reference strains of Streptomyces griseus and Streptomyces tendae. The 12 S. scabies strains formed a homogeneous group characterized by smooth grey spores borne in spiral chains, melanin production, and usage of all International Streptomyces Project sugars. Most S. scabies isolates did not degrade xanthine and were susceptible to 25 μg of oleandomycin per ml, 10 IU of penicillin G per ml, 20 μg of streptomycin per ml, 10 μg of thallous acetate per ml, and 0.5 μg of crystal violet per ml. The type strain of S. scabies is strain RL-34 (= ATCC 49173).
235 citations
TL;DR: Studies of root nodule bacteria isolated from Galega orientalis and Galega officinalis are reviewed, and as a result a new species, Rhizobium galegae, is proposed, which forms nitrogen-fixing root nodules on G. Orientalis.
Abstract: Studies of root nodule bacteria isolated from Galega orientalis and Galega officinalis are reviewed, and as a result a new species, Rhizobium galegae, is proposed. The type strain of the species is R. galegae HAMBI 540 (= ATCC 43677), which forms nitrogen-fixing root nodules on G. orientalis. Deoxyribonucleic acid homology distinguishes R. galegae from other rhizobia, whereas nodulation of Galega sp. and sensitivity to phage gal 1/R phenotypically separate the strains currently included in the species from other members of the genus Rhizobium. Other criteria supporting the formation of a new species include ribosomal ribonucleic aciddeoxyribonucleic acid homology data, protein and lipopolysaccharide patterns, serological properties, and numerical taxonomy data.
TL;DR: The genus Bacteroides is proposed to be restricted to the B. fragilis group of species, and the description of the genus is emended accordingly.
Abstract: The genus Bacteroides (Castellani and Chalmers) as presently constituted is phenotypically and phylogenetically extremely heterogeneous However, biochemical, chemical, and molecular biological data indicate that Bacteroides fragilis (the type species) and related species form a coherent taxonomic group Therefore, we formally propose that the genus Bacteroides be restricted to the B fragilis group of species, and the description of the genus is emended accordingly
TL;DR: Flexibacter maritimus (three strains) was shown to constitute a DNA relatedness group that is 0 to 8% related to all of the other species tested and can be differentiated by phenotypic tests.
Abstract: Eight unidentified fish pathogens and 10 strains received as “Flexibacter columnaris,” “Cytophaga psychrophila,” and Flexibacter maritimus were compared with the type strains of all previously described species in the genera Cytophaga and Flexibacter and with seven Flavobacterium species by determining levels of deoxyribonucleic acid (DNA) relatedness (S1 nuclease method) and by performing phenotypic tests. The name Flexibacter columnaris sp. nov. is revived for a DNA relatedness group comprising eight strains that are 75 to 100% related to strain TG 39/87 and 0 to 8% related to all of the other species studied. These strains produce flat rhizoid colonies which adhere to agar, show strong gliding movement, absorb Congo red, reduce nitrate to nitrite, and produce H2S. The guanine-plus-cytosine content of the DNA is 32 mol%. The type strain is strain NCMB 2248 (= ATCC 23463). The name Flexibacter psychrophilus sp. nov. is revived for a DNA relatedness group comprising seven strains that are 90 to 100% related to strain NCMB 1947T (T = type strain) and 0 to 5% related to all of the other species studied. These strains produce circular, convex colonies that have regular or spreading margins and do not adhere to agar, show very slow gliding movement, do not absorb Congo red, do not reduce nitrate, and do not produce H2S. The guanine-plus-cytosine content of the DNA is 33 mol%. The type strain is strain NCMB 1947. Both F. columnaris and F. psychrophilus produce the flexirubin type of pigments, are strongly proteolytic, and do not hydrolyze (or produce acid from) any carbohydrate. Flexibacter maritimus (three strains) was shown to constitute a DNA relatedness group that is 0 to 8% related to all of the other species tested. Furthermore, this organism can be differentiated by phenotypic tests. The presence of F. maritimus in Europe is shown for the first time.
TL;DR: The diversity among 43 isolates of the genus Frankia was studied by determining levels of deoxyribonucleic acid relatedness (S1 nuclease method) and DNA base compositions and at least nine genomic species were differentiated.
Abstract: The diversity among 43 isolates of the genus Frankia was studied by determining levels of deoxyribonucleic acid relatedness (S1 nuclease method) and DNA base compositions. The guanine + cytosine contents ranged from 66 to 75 mol%. At least nine genomic species were differentiated, including three genomic species among strains compatible with members of the genus Alnus, five genomic species among strains compatible with members of the family Elaeagnaceae, and one genomic species among strains compatible with members of the genus Casuarina. Genomic species 1, which contained proposed type strain CpI1 and nine strains that were compatible with members of the genus Alnus and were 64 to 97% related to strain ACoN24d, is Frankia alni. Four genomic species contained single strains that were 0 to 30% related to the other genomic species. Typical strains isolated from members of the genus Casuarina were found to be very homogeneous (69 to 100% related to strain ORS020606) and clearly separated from atypical strains. The nine genomic species delineated in this study cannot be named since no phenotypic tests are available for identification.
TL;DR: It is concluded that some pathovars are sufficiently distinct from the type strain of the species X. campestris to be considered as separate species, and that X. citri B/C/D strains and the heterogeneous E strains should be respectively renamed X. Citri group A and X.citri group B.
Abstract: A recent epiphytotic disease on citrus in Florida nurseries was caused by strains of Xanthomonas campestris with different host specificity and lower pathogenic capacities than those of previously described strains of X. campestris pv. citri. The new strains were classified as X. campestris pv. citri because they were isolated from rutaceous hosts and despite the fact that they caused a different disease than strains previously described in that pathovar. Restriction fragment length polymorphism analyses revealed that the Florida strains comprised a heterogeneous (E) group, interrelated with X. campestris pv. alfalfae, X. campestris pv. cyamopsidis, and X. campestris pv. dieffenbachiae. In contrast, the previously described strains of X. campestris pv. citri formed two highly distinct, homogeneous (A and B/C/D) groups. Furthermore, the strains of X. campestris pv. campestris, X. campestris pv. glycines, X. campestris pv. malvacearum, X. campestris pv. phaseoli, X. campestris pv. pisi, and X. campestris pv. vignicola tested were also distinctive and appeared to be only distantly related to one another and to all X. campestris pv. citri strains. We concluded (i) that some pathovars are sufficiently distinct from the type strain of the species X. campestris to be considered as separate species, (ii) that X. campestris pv. citri group A and X. campestris pv. phaseoli (not including X. campestris pv. phaseoli var. fuscans) represent distinctly separate subbranches of the genus and should be respectively reinstated to species as X. citri (ex Hasse) nom. rev. 3213 and X. phaseoli (ex Smith) nom. rev. G27, and (iii) that the X. campestris pv. citri B/C/D strains and the heterogeneous E strains should be respectively renamed X. campestris pv. aurantifolii pv. nov. and X. campestris pv. citrumelo pv. nov.
TL;DR: A new bacterial species is described that causes a scab disease of potatoes which may occur in soils with pH values below 5.2, and the acid scab symptoms caused by this organism are indistinguishable from the symptoms of commn scab caused by Streptomyces scabies.
Abstract: A new bacterial species is described, for which we propose the name Streptomyces acidiscabies. This organism causes a scab disease of potatoes (Solanum tuberosum) which may occur in soils with pH values below 5.2. The acid scab symptoms caused by this organism are indistinguishable from the symptoms of commn scab caused by Streptomyces scabies. In culture, S. acidiscabies is distinct from S. scabies, having flexuous spore chains, a growth medium-dependent spore mass color ranging from white to organish red, and a red or yellow, pH-sensitive diffusible pigment rather than melanin. S. acidiscabies grows on agar media at pH 4.0 (versus pH 5.0 for S. scabies), does not use raffinose as a carbon source, and tolerates higher concentrations of crystal violet (0.5 μg/ml), thallium acetate (10 μg/ml), streptomycin (20 μg/ml), oleandomycin (25 μg/ml), and penicillin G (10 IU/ml) than S. scabies. The type strain of S. acidiscabies is strain RL-110 (= ATCC 49003).
TL;DR: The results strongly suggest that group 2 is a pigmented variant of B. subtilis, but group 1 is a new species, for which the name Bacillus atrophaeus is proposed.
Abstract: The taxonomic position of Bacillus subtilis strains that produce soluble black pigment is unclear. To assess the genetic relatedness between the pigmented and nonpigmented strains, deoxyribonucleic acid (DNA) reassociation was measured spectrophotometrically. Among the 40 pigmented strains examined, two distinct DNA relatedness groups were found. A total of 25 strains (group 1) showed 24 to 34% DNA relatedness and 15 strains (group 2) showed 70 to 100% relatedness to Bacillus subtilis type strain NRRL NRS-744. The intragroup DNA relatedness values for each group ranged from 85 to 100%; the intergroup relatedness values ranged from 20 to 35%. A multilocus enzyme electrophoresis analysis revealed a low level of similarity between group 1 and group 2 or the nonpigmented group. The group 2 strains and the nonpigmented strains clustered in a common group, indicating the close genetic relationship of these organisms. My results strongly suggest that group 2 is a pigmented variant of B. subtilis, but group 1 is a new species, for which the name Bacillus atrophaeus is proposed. The type strain of the new species is strain NRRL NRS-213.
TL;DR: The deoxyribonucleic acid (DNA):ribosomal ribonuclear acid (rRNA) hybridization technique was used to reveal the relationships and taxonomic positions of an additional 83 strains belonging to 43 saprophytic or pathogenic Pseudomonas species and 29 named and unnamed PseUDomonas-like strains.
Abstract: The deoxyribonucleic acid (DNA):ribosomal ribonucleic acid (rRNA) hybridization technique was used to reveal the relationships and taxonomic positions of an additional 83 strains belonging to 43 saprophytic or pathogenic Pseudomonas species and 29 named and unnamed Pseudomonas-like strains. The DNA:rRNA hybrids were characterized by the following two parameters: (i) the temperature at which one-half of the hybrid was eluted and (ii) the percentage of rRNA binding (the amount of rRNA bound per 100 g of filter-fixed DNA). We also used, for a limited number of strains, numerical analysis of carbon assimilation tests to delineate the finer taxonomic relationships of organisms. Of the 83 strains examined, 78 could be definitely assigned either to an rRNA branch or to an rRNA superfamily within the Proteobacteria. Only 25 of our strains belong in the genus Pseudomonas sensu stricto (our Pseudomonas fluorescens rRNA branch). In general, about two-thirds of the named Pseudomonas species have been misclassified and are distributed over at least seven genera all through the Proteobacteria. These organisms need to be reclassified and generically renamed according to their phylogenetic relationships. However, more detailed phenotypic and genotypic studies are necessary before definite nomenclatural proposals can be made. A comprehensive list of the phylogenetic affiliations of the Pseudomonas species is included.
TL;DR: A numerical taxonomic study was performed on 52 Leuconostoc spp. strains isolated from chill-stored meats as mentioned in this paper, and three clusters were observed: representative strains from these clusters, together with the type strains of previously described species, were examined by performing a cellular fatty acid analysis and deoxyribonucleic acid (DNA)-DNA hybridization.
Abstract: A numerical taxonomic study was performed on 52 Leuconostoc spp. strains isolated from chill-stored meats. Three clusters were observed: representative strains from these clusters, together with the type strains of previously described species, were examined by performing a cellular fatty acid analysis and deoxyribonucleic acid (DNA)-DNA hybridization. Cluster II contained seven strains, which were assigned to Leuconostoc mesenteroides subsp. mesenteroides on the basis of DNA relatedness and biochemical properties. Clusters I (30 strains) and III (15 strains) were shown to represent two new species, for which the names Leuconostoc gelidum and Leuconostoc carnosum, respectively, are proposed. The type strains of L. gelidum and L. carnosum are strains NCFB 2775 and NCFB 2776, respectively.
TL;DR: Nutritionally variant streptococci formed two deoxyribonucleic acid hybridization groups (as determined by the S1 nuclease method) that were distinct from 39 Streptococcus spp.
Abstract: Nutritionally variant streptococci (12 strains) formed two deoxyribonucleic acid hybridization groups (as determined by the S1 nuclease method) that were distinct from 39 Streptococcus spp. type and reference strains. These two groups differed by their penicillin-binding protein patterns and biochemical properties. Streptococcus defectivus sp. nov. (with type strain SC10) and Streptococcus adjacens sp. nov. (with type strain GaD) are the names proposed for these species.
TL;DR: Phenotypic and chemotaxonomic characteristics of seven moderately halophilic isolates from a mediterranean saltern showed that they were very closely related to “Chromobacterium marismortui,” and it is proposed that they should be placed in a new genus, Chromohalobacter, which includes a single species.
Abstract: Phenotypic and chemotaxonomic characteristics of seven moderately halophilic isolates from a mediterranean saltern showed that they were very closely related to “Chromobacterium marismortui.” This species, which was originally described on the basis of strains isolated from the Dead Sea, was not included on the Approved Lists of Bacterial Names and is not accepted as a member of the genus Chromobacterium since it produces a pigment that is not violacein, does not possess the characteristic flagellar arrangement, and is not genotypically related to this genus as determined by deoxyribonucleic acid-ribosomal ribonucleic acid hybridization experiments. On the basis of the special features of these strains, we propose that they should be placed in a new genus, Chromohalobacter, which includes a single species, Chromohalobacter marismortui comb. nov., nom. rev. The deoxyribonucleic acid base composition is 62.1 to 64.9 mol% guanine plus cytosine. The type strain is strain ATCC 17056 (= CCM 3518).
TL;DR: The phylogenetic interrelationship of members of the genera Nocardioides and Pimelobacter were examined by using reverse transcriptase sequencing of 16S ribosomal ribonucleic acid and it is proposed that PimELobacter tumescens be reclassified in a new genus, Terrabacter, as Terrabacteria tumescen comb.
Abstract: The phylogenetic interrelationship of members of the genera Nocardioides and Pimelobacter were examined by using reverse transcriptase sequencing of 16S ribosomal ribonucleic acid. The sequence studies demonstrated that Nocardioides albus, Nocardioides luteus, Pimelobacter jensenii, and Pimelobacter simplex represent a coherent phylogenetic group at the genus level, whereas Pimelobacter tumescens occupies a separate line of descent. On the basis of sequence data and the chemotaxonomic distinctiveness of the latter organism, we propose that Pimelobacter tumescens be reclassified in a new genus, Terrabacter, as Terrabacter tumescens comb. nov.
TL;DR: The data indicate that the strain representative of the genus Kineosporia shows some similarity to the spore dome actinomycetes described by Willoughby and by Makkar and Cross.
Abstract: The description of the genus Kineosporia is amended after chemotaxonomic and morphological studies of the type strain of the type species, Kineosporia aurantiaca JCM 3230. This organism yielded both ll- and meso-diaminopimelic acids, which suggested that the former is present in the mycelium and the latter is present in the spores. There was no characteristic sugar pattern. A diagnostic phospholipid was phosphatidylcholine, and a major menaquinone component was MK-9(H4). No iso/anteiso branched fatty acids and no mycolic acids were observed. Colonies on agar lacked aerial mycelia, formed central projections including spores, and were occasionally accompanied by bunches of spore clusters in the agar. Spores were catenated or were located singly or aggregately at the tips of the vegetative hyphae. Our data indicate that the strain representative of the genus Kineosporia shows some similarity to the spore dome actinomycetes described by Willoughby and by Makkar and Cross.
TL;DR: One of the findings of this study is that Eikenella corrodens is related, as indicated by percentage of sequence homology, to the following organisms: Kingella denitrificans, Simonsiella muelleri, and Chromobacterium fluviatile, which constitute a newly recognized branch of the beta group Proteobacteria.
Abstract: The 16S ribosomal ribonucleic acid sequences of the type strain and three other strains of Eikenella corrodens, the type strains of Alcaligenes faecalis, Alcaligenes xylosoxydans subsp. denitrificans, Chromobacterium fluviatile, Chromobacterium violaceum, Kingella denitrificans, Kingella kingae, and Pseudomonas cepacia, and a strain of Vitreoscilla stercoraria were determined by direct sequencing of bacterial ribosomal ribonucleic acid by a modified Sanger method. These sequences were compared with previously published sequences of Neisseria gonorrhoeae and Pseudomonas testosteroni and unpublished sequences of Nitrosolobus sp., Nitrosomonas europaea, Rhodocyclus gelatinosus, Rhodocyclus purpura, Simonsiella muelleri, and Spirillum volutans. All of the bacteria sequenced in this study were members of the beta group of the class Proteobacteria, formerly called “purple bacteria and their relatives.” A phylogenetic tree was constructed based upon the sequence homologies. One of the findings of this study is that Eikenella corrodens is related, as indicated by percentage of sequence homology, to the following organisms: Kingella denitrificans (97.7%), Simonsiella muelleri (95.7%), Kingella kingae (96.2%), Neisseria gonorrhoeae (95.1%), Vitreoscilla stercoraria (94.4%), Chromobacterium violaceum (91.7%), and Chromobacterium fluviatile (89.8%). These bacteria constitute a newly recognized branch of the beta group Proteobacteria. The remaining species, including Pseudomonas cepacia, Alcaligenes faecalis, and Alcaligenes xylosoxydans subsp. denitrificans, are members of the major cluster of the beta group Proteobacteria. On the basis of our data we propose that the genera Eikenella and Simonsiella be placed in the family Neisseriaceae.
TL;DR: Two new species, Leu Conostoc citreum and Leuconostoc pseudomesenteroides, are proposed for these homology groups of vancomycin-resistant gram-positive cocci isolated from human sources.
Abstract: Deoxyribonucleic acid-deoxyribonucleic acid hybridizations were performed with 31 vancomycin-resistant gram-positive cocci isolated from human sources. A total of 14 human isolates exhibited high levels of homology with Leuconostoc mesenteroides subsp. mesenteroides NCDO 523T (T = type strain), whereas 2 strains were genetically closely related to Leuconostoc lactis NCDO 533T. Nine human isolates formed a tight homology group with an atypical L. mesenteroides strain (strain NCIB 3351), whereas two isolates (together with four strains from food) were found to be highly related to Leuconostoc sp. strain NCDO 768T. Two new species, Leuconostoc citreum and Leuconostoc pseudomesenteroides, are proposed for these homology groups. The type strains of L. citreum and L. pseudomesenteroides are strains NCDO 1837 and NCDO 768, respectively.
TL;DR: A new genus of acidophilic, facultatively methylotrophic bacteria is described, which is gram-negative, nonsporeforming, nonmotile, and rod shaped and grow at pH 2.0 to 5.5, which are unique among the methanol-utilizing bacteria.
Abstract: A new genus of acidophilic, facultatively methylotrophic bacteria is described. These organisms are gram-negative, nonsporeforming, nonmotile, and rod shaped and grow at pH 2.0 to 5.5. These characteristics are unique among the methanol-utilizing bacteria. The deoxyribonucleic acid base composition is 63 to 65 mol% guanine plus cytosine. Acetobacter methanolicus TK 0705T (T = type strain) is a typical strain in this group. These bacteria are distinguished from type and representative strains of Acetobacter, Gluconobacter, Acidiphilium, and Thiobacillus on the basis of deoxyribonucleic acid-deoxyribonucleic acid homology. A new genus, Acidomonas, is proposed to include this group of methylotrophic bacteria. The type species of the genus Acidomonas is Acidomonas methanolica comb, nov., with type strain TK 0705 (= IMET 10945).
TL;DR: A thorough taxonomic study of the genera Saccharopolyspora and Faenia showed that both of these taxa can be included in one genus and a new Saccharpolyspora species is presented.
Abstract: A thorough taxonomic study of the genera Saccharopolyspora and Faenia showed that both of these taxa can be included in one genus. We propose that Faenia rectivirgula be transferred to the genus Saccharopolyspora Lacey and Goodfellow 1975 as Saccharopolyspora rectivirgula (Kurup and Agre 1983) comb. nov. A description of the new Saccharopolyspora species is presented. The type strain is strain DSM 43 747 (= ATCC 33 515). In addition, we propose that Saccharopolyspora hirsuta subsp. taberi Labeda 1987 strain NRRL B-16 173T (T = type strain) be given species status as Saccharopolyspora taberi sp. nov.
TL;DR: Emendation of the description of the order Prochlorales Florenzano, Balloni, and Materassi 1986 is proposed since the original definition of this taxon would exclude the genus Prochlorothrix, and the family Prochlorotrichaceae fam.
Abstract: The genus Prochlorothrix gen., with one species, Prochlorothrix hollandica sp. nov., is proposed for filamentous oxygenic photoautotrophic procaryotes containing chlorophylls a and b. The cylindrical cells are arranged in trichomes which lack sheaths, are not motile, and do not possess differentiated cells. P. hollandica grows in liquid media or on solid mineral media and is incapable of dinitrogen fixation. Optimum growth occurs between 20 and 30°C and at pH 8.4. The deoxyribonucleic acid base composition of this organism is 53 mol% guanine plus cytosine. Emendation of the description of the order Prochlorales Florenzano, Balloni, and Materassi 1986 is proposed since the original definition of this taxon would exclude the genus Prochlorothrix. To accommodate the filamentous genera in the order Prochlorales. we propose the family Prochlorotrichaceae fam. nov.
TL;DR: The results obtained with this technique confirmed and expanded previous observations on the low levels of deoxyribonucleic acid similarity among species of the Pseudomonas genus as determined by membrane competition experiments.
Abstract: Deoxyribonucleic acid similarity experiments in which the S1 nuclease methodology was used were performed on strains of Pseudomonas species, including some that had not been previously subjected to similarity measurements. The results obtained with this technique confirmed and expanded previous observations on the low levels of deoxyribonucleic acid similarity among species of the genus as determined by membrane competition experiments. A general discussion of the results and nomenclatural status of some of the species is included.
TL;DR: It is proposed that this large cluster represents the emended family Neisseriaceae containing the following genera and groups: Neisseria, Kingella (not the generically misnamed Kingella indologenes), Eikenella, Simonsiella, Alysiella (not some misnamed strains), and Centers for Disease Control groups EF-4 and M-5.
Abstract: We detected distinct taxonomic relationships among the true Neisseria species, Kingella kingae, Kingella denitrificans, Eikenella corrodens, all Simonsiella species, the type strain of Alysiella filiformis, and members of Centers for Disease Control groups EF-4 and M-5. All these taxa constitute one large separate cluster having high levels of ribosomal ribonucleic acid cistron similarity (thermal denaturation temperature range, 74 to 81°C) in ribosomal ribonucleic acid superfamily III. There are at least four subbranches. We found high deoxyribonucleic acid (DNA)-DNA homology values between Neisseria gonorrhoeae and some other true Neisseria species and within the following species: Simonsiella muelleri, Simonsiella crassa, Simonsiella steedae, Kingella denitrificans, and Eikenella corrodens. All of the members of this large cluster have genome base compositions in the range from 42.8 to 57.7 mol% guanine plus cytosine. The molecular complexities of the genomic DNAs are 2.2 x 109 to 2.7 x 109 for Simonsiella and Alysiella species and 1.4 x 109 to 1.8 x 109 for the other members of this large cluster. We formally propose that this large cluster represents the emended family Neisseriaceae containing the following genera and groups: Neisseria, Kingella (not the generically misnamed Kingella indologenes), Eikenella, Simonsiella, Alysiella (not some misnamed strains), and Centers for Disease Control groups EF-4 and M-5. The genera and subgenera Acinetobacter, Moraxella, Branhamella, Psychrobacter, the false neisseriae, and Kingella indologenes should be removed from the Neisseriaceae, as they belong to superfamilies I and II.