- Volume 48, Issue 3, 1998
Volume 48, Issue 3, 1998
- Systematic Bacteriology
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Phylogenetic analysis and intrageneric structure of the genus Hyphomicrobium and the related genus Filomicrobium
More LessAlmost complete 16S rDNA sequences from the type strains of seven species of the genus Hyphomicrobium and of Filomicrobium fusiforme have been determined. The Hyphomicrobium species form two phylogenetic clusters that are only moderately related to each other. While cluster I contains the type species Hyphomicrobium vulgare, Hyphomicrobium aestuarii, Hyphomicrobium hollandicum and Hyphomicrobium zavarzinii, cluster II comprises Hyphomicrobium facilis, Hyphomicrobium denitrificans and Hyphomicrobium methylovorum. Within the two species clusters, the species are highly related. Phylogenetically, Filomicrobium fusiforme clusters moderately with Hyphomicrobium species. The lack of distinguishing phenotypical properties presently excludes the possibility of describing cluster II as a new genus.
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Genetic analyses of the genus Nocardioides and related taxa based on 16S-23S rDNA internally transcribed spacer sequences
More LessThe 16S-23S internally transcribed spacer (ITS) sequences were analysed to clarify inter-and intraspecific relationships among strains of the genus Nocardioides and the relationship between two Aeromicrobium species. The 16S-23S ITS regions from 33 Nocardioides strains, two Aeromicrobium species and Terrabacter tumescens were sequenced directly after polymerase chain reaction (PCR) amplification and λ exonuclease treatment. The genomes of some Nocardioides strains included two types of 16S-23S ITS sequences. The sizes of the 16S-23S ITS sequences of Nocardioides strains ranged from 328 to 539 bp. The 16S-23S ITS sequences of Aeromicrobium erythreum NSP37T, Aeromicrobium fastidiosum NSP38Tand T. tumescens NSP39Twere 349, 355 and 386 bp long, respectively. Nucleotide similarity among 16S-23S ITS sequences of Nocardioides albus strains and of Nocardioides simplex strains was 84·1-100% and 97·7-100%, respectively. The 16S-23S ITS sequence of Nocardioides luteus was identical to that of “Nocardioides fulvus” NSP32Tand was only 1 bp different from that of “Nocardioides fulvus” strains. However, the 16S-23S ITS sequences of “N. fulvus” NSP32Tshowed only a low degree of similarity to “N. fulvus“ NSP32T(54·8%). The degree of 16S-23S ITS similarity between N. luteus NSP20Tand N. albus strains ranged from 85 to 93%. The mean nucleotide similarity values between the type strains of validly described Nocardioides species were highly divergent at 68·1±16·8%. The two Aeromicrobium species showed a level of 16S-23S ITS similarity of 71·2%. In this study, 16S-23S ITS sequences of the members of the genera Nocardioides and Aeromicrobium were useful for inferring the relationships between closely related strains and species. However, they were not found to be appropriate for elucidating the phylogenetic relationships between distantly related organisms at the genus level.
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Staphylococcus condimenti sp. nov., from soy sauce mash, and Staphylococcus carnosus (Schleifer and Fischer 1982) subsp. utilis subsp. nov.
Based on the sequence data of 23S rRNA of Staphylococcus carnosus, Staphylococcus piscifermentans, Staphylococcus aureus and Staphylococcus epidermidis, species-specific probes were constructed. Their application revealed a heterogeneity within 18 strains previously identified as S. carnosus. Strains of this group were selected, and their 23S rRNA sequence was determined. It was revealed that the strains of S. carnosus can be placed in at least three sub-groups. This grouping was supported by physiological data and DNA-DNA similarity studies. Based on these results, we propose the new species Staphylococcus condimenti sp. nov. The type strain is S. condimenti F-2T (= DSM 11674T). The phylogenetic position of the new species within the radiation of other staphylococcal strains is reflected by a 16S rRNA-based tree. Furthermore, it is proposed to designate the new subspecies of Staphylococcus carnosus Schleifer and Fischer 1982, Staphylococcus carnosus subsp. utilis subsp. nov. The type strain of S. carnosus subsp. utilis is SK 11T(= DSM 11676T).
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Population genetic analysis of Serpulina pilosicoli and its molecular epidemiology in villages in the Eastern Highlands of Papua New Guinea
More LessThe population genetics of Serpulina pilosicoli and its molecular epidemiology in villages in the Eastern Highlands province of Papua New Guinea were investigated. Multilocus enzyme electrophoresis (MLEE) was used to analyse 164 isolates from humans and animals. These were divided into 33 electrophoretic types (ETs), four of which contained 65% of the isolates. The mean genetic diversity (n = number of ETs) for 145 human isolates was 0·18, and the mean number of alleles at five polymorphic loci was 2·6. The species appeared to be recombinant, as there was a lack of linkage disequilibrium, and 25% of all the possible combinations of alleles was present in the population. PFGE analysis using the enzymes Mlul and Sall divided 157 of the isolates into 99 PFGE types, demonstrating the existence of considerable strain diversity in a geographically restricted area. The two techniques were in excellent agreement; however, PFGE was more discriminatory for strain typing than was MLEE. Nine out of 19 (47·4%) culture-positive individuals were colonized by the same PFGE type of S. pilosicoli when retested after 6 weeks. For three individuals, the PFGE profiles of the second isolate differed from the first in only one or two DNA bands, while the other seven individuals were colonized with distinct PFGE types on each occasion. In two cases, strains with the same PFGE pattern were isolated from humans and dogs, suggesting that cross-species transmission of S. pilosicoli may occur naturally and that the infection can be zoonotic.
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Serpulina alvinipulli sp. nov., a new Serpulina species that is enteropathogenic for chickens
More LessStrain C1Tis an anaerobic spirochaete that causes intestinal disease in chickens. Multilocus enzyme electrophoresis analysis and 16S rRNA sequence comparisons have indicated that this spirochaete is a Serpulina strain. In these investigations, various phenotypic and genomic properties useful for establishing a taxonomic identity for strain C1Twere studied. As determined by electron microscopy, cells of the spirochaete measured 8-11 x 0·22-0·34 µm and had a typical spirochaete ultrastructure. Each cell had 22·30 flagella. C1Tcells formed weakly β-haemolytic colonies on trypticase soy agar plates containing 5% bovine blood. The spirochaete reached maximum population densities of 109cells ml-1with a 2·4 h population doubling time in brain heart infusion broth containing 10% calf serum (BHIS broth). C1Tcultures in BHIS broth were positive in tests for hippurate hydrolysis and negative for indole production. Glucosamine, N-acetylglucosamine, glucose, fructose, maltose and mannose were growth substrates for the spirochaete in heart infusion broth containing 7% calf serum (HS broth). During growth in HS broth beneath an O2/N2 (1:99) atmosphere, cells of the spirochaete consumed O2 and glucose and produced H2, CO2, acetate, butyrate and ethanol. Strain C1TDNA had a G+C content of 24·6 mol%. Based on DNA-DNA hybridization analyses, the DNA of strain C1Texhibited 24·39% relative reassociation with DNA of Serpulina hyodysenteriae, Serpulina innocens, Serpulina pilosicoli, Serpulina murdochii and Serpulina intermedia. These results indicate that chicken spirochaete strain C1Thas many phenotypic properties common to Serpulina species and, based on DNA hybridization analysis, represents a unique Serpulina species. For this new species the name Serpulina alvinipulli is proposed, for which the type strain is C1T(= ATCC 51933T).
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Carnimonas nigrificans gen. nov., sp. nov., a bacterial causative agent for black spot formation on cured meat products
More LessNine different strains, CTCBS1Tto CTCBS9, were identified to be the causative agents of black spots on the surface of raw cured meat products. The formation of black spots under aerobic conditions is reproducible upon reinoculation of meat products with any of these strains, indicating that they are the causative agent. The strains were Gram-negative, catalase-positive and obligately aerobic rods. The G+C content of DNA of strain CTCBS1Tis 56·0±0·3 mol%. The content of non-polar main fatty acids were 16:0, 16:1, 18:1 and 19:0 cyc. Its phylogenetic position was elucidated by comparative sequence analysis of the 16S rRNA gene. Overall sequence similarity to other bacteria does not exceed 93·3%. Isolate CTCBS1Tclustered phylogenetically within the β-subclass of the Proteobacteria and is closely related to members of Halomonas (90·5-91·9%) and to Zymobacter palmae (93·3%). A genetic homogeneity of the nine strains was demonstrated by M13 random amplified polymorphic DNA-PCR, whereas differentiation from other genera, e.g. Zymobacter and Pseudomonas, could easily be achieved by their chemotaxonomic characteristics. Taxonomic data revealed the status of a separate genus for which the name Carnimonas gen. nov., sp., nov. is proposed. Despite chemotaxonomic and physiological similarities, the new genus is at present not a member of the family Halomonadaceae because of the lack of two out of 15 descriptive 16S rRNA signature sequences. The first member of the new genus is Carnimonas nigrificans. The use of a specific, 16S rRNA-targeted oligonucleotide primer allowed the identification of all nine strains of C. nigrificans in a PCR assay. Toxicological studies showed no pathogenic potential for C. nigrificans strain CTCBS1T(CECT 4437T).
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Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae
More LessThe nitrogen-fixing rhizobial symbionts of Sesbania herbacea growing in the nature reserve at the Sierra de Huautla, Mexico, were isolated and characterized. All 104 isolates together with the type strain for Rhizobium galegae, HAMBI 540T, had similar 16S rRNA genes as revealed by PCR-RFLP analysis. Similarity in the sequences of the 16S rRNA genes placed the isolates on a phylogenetic branch shared with R. galegae. Among 66 randomly selected isolates, three closely related electrophoretic alloenzyme types (ETs) were identified, which were distinct from 10 ETs distinguished among 23 strains of R. galegae. A new species Rhizobium huautlense, represented by the Sesbania isolate S02T, is proposed based upon low estimates of DNA relatedness between our chosen type strain and the type strains for the other species, the dissimilarity of the nucleotide sequence of the 16S rRNA genes, and their distinct ETs compared with R. galegae. The description of R. huautlense is significant because in the reconstruction of the phylogeny of R. huautlense there was a shift in the node of the branch of Agrobacterium vitis relative to that of R. galegae. The revised phylogenetic tree would tend to indicate common ancestry between R. galegae and Rhizobium leguminosarum.
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Desulfurobacterium thermolithotrophum gen. nov., sp. nov., a novel autotrophic, sulphur-reducing bacterium isolated from a deep-sea hydrothermal vent
A thermophilic, anaerobic, strictly autotrophic, sulphur-reducing bacterium, designated BSAT(T = type strain), was isolated from a deep-sea hydrothermal chimney sample collected at the mid-Atlantic ridge. Gram-negative cells occurred singly or in pairs as small highly motile rods. Spores were not observed. The temperature range for growth was 40 to 75°C, with an optimum at 70 °C. The pH range for growth at 70 °C was from 4·4 to 7·5, with an optimum around 6·0. The sea salt concentration range for growth was 15-70 g I-1with an optimum at 35 g I-1. Elemental sulphur, thiosulphate and sulphite were reduced to hydrogen sulphide. Sulphate and cystine were not reduced. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses of the 16S rRNA gene indicated that the strain was a member of the domain Bacteria and formed a branch that was almost equidistant from members of the orders Aquificales and Thermotogales. The new organism possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Desulfurobacterium gen. nov., of which Desulfurobacterium thermolithotrophum sp. nov. is the type species. The type strain is BSAT(= DSM 11699T).
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Phylogenetic analysis of cultivable oral treponemes from the Smibert collection
More LessDr Robert Smibert from the Virginia Polytechnic Institute, USA, isolated and collected over 200 strains of oral treponemes over a 20-year period. Dr Smibert, Dr W. E. C. Moore and Dr L. V. Moore separated these isolates and reference strains into different groups on the basis of cellular fatty acid analysis. In this study, the 16S rRNA genes were sequenced for 47 strains that were representative of these groups. Five distinct species were identified on the basis of 16S rRNA sequence comparisons; two of these species are newly named and three have not yet been characterized. The first species, designated Treponema Smibert-1, was represented by the single strain D4B-1 and was later identified as the newly described Treponema maltophilum. However, strain D4B-1 possessed a different flagellar arrangement to that of T. maltophilum. The second species, Treponema Smibert-2, was represented by nine isolates that possessed identical 16S rRNA gene sequences. The closest relatives of this species were Treponema Smibert-3 and Treponema Smibert-4 at approximately 90% sequence similarity. Within Treponema Smibert-2, there was no correlation between phylogenetic analysis and cellular fatty acid analysis since six different cellular fatty acid groups represented the nine strains. Treponema Smibert-3 (strain D36ER-1) and Treponema Smibert-4 (D62CR-12) were each represented by only a single strain and were closely related to each other at 98% sequence similarity. Strain D36ER-1 of Treponema Smibert-3 was identified as belonging to the not-yet-cultivated phylotype 20 [Choi, B. K., Paster, B. J., Dewhirst, F. E. & Göbel, U. B. (1994). Infect Immun 62,1889-1895]. Strain D62CR-12 of Treponema Smibert-4 was nearly identical in sequence to the newly described Treponema amylovorum. The fifth species, Treponema Smibert-5, was represented by a single strain, D120CR-1, and was closely related at about 98% sequence similarity to the three subspecies of Treponema socranskii. The phylogenetic analyses of strains of Treponema vincentii and of subspecies of T. socranskii are also reported. The closest oral relatives of T. vincentii were Treponema medium at 98·7% sequence similarity and Treponema denticola at 91·5% sequence similarity. T. socranskii subspp. socranskii, buccale and paredis formed three separate phylogenetic branches with sequence similarities of about 98% to each other. The closest relative of the subspecies of T. socranskii and of Smibert-5 was Smibert-2 at about 86% sequence similarity. Historic reference strains Fuji, "Treponema ambigua", Fm, lchelson-2, N-39, TD2, TRRD, MRB, IPP, Jethro and T32A, as well as an unknown strain designated only as Treponema oralis, were identified as strains of T. denticola. Reference strains Fuji, Jethro, T32A and IPP plus three isolates of the Smibert collection were also contaminated with a mycoplasma as determined by 16S rRNA comparative analysis. Consequently, spirochaetal cultures should be screened for mycoplasmas. There are presently at least ten species of cultivable oral species of Treponema with the cut-off for separate species
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Species identification of Legionella via intergenic 16S-23S ribosomal spacer PCR analysis
Species identification of Legionella in routine laboratory testing is hampered by the lack of highly discriminatory phenotypic tests. Amplification polymorphism of the intergenic 16S-23S spacer regions (ISR) has been previously developed for identification of species within the Legionellaceae [Hookey. J. V., Birtles, R. J. & Saunders, N. A. (1995). J Clin Microbiol 33, 2377-2381], but it did not provide enough resolution to distinguish all members of the bluish-white autofluorescent species and the red autofluorescent group of the Legionellaceae. By choosing new primers that target regions 4 (positions 1521-1541 of Escherichia coli 16S rRNA gene) and 6 (positions 114-132 of E. coli 23S rRNA gene) within the rDNA operon close to the 16S-23S intergenic spacer, 34 profiles were determined among the 79 type and reference strains representing 42 species that were tested. Analysis of the RFLP generated after HintI restriction digestion of the PCR products further improved the method, allowing complete discrimination among the species and subspecies of Legionella tested. Twenty-three well-identified strains from unrelated origins belonging to seven species gave amplification patterns identical to that of their type strain. The technique was also tested on 80 field isolates that could not be unequivocally assigned to groups by phenotypic methods. Seventy-two per cent (58/80) of these isolates had a profile identical to that of a type strain, while 27% (22/80) may correspond to new taxa since their ISR-PCR profiles did not match any of the known profiles.
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Phylogenetic heterogeneity within the genus Herpetosiphon: transfer of the marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus to the genus Lewinella gen. nov. in the Flexibacter-Bacteroides-Cytophaga phylum
L. I. Sly, M. Taghavit and M. FeganAnalysis of the 16S rDNA sequences of species currently assigned to the genus Herpetosiphon revealed intrageneric phylogenetic heterogeneity. The thermotolerant freshwater species Herpetosiphon geysericola is most closely related to the type species Herpetosiphon aurantiacus in the Chloroflexus subdivision of the green non-sulfur bacteria. The marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus, on the other hand, were found to form a cluster with the sheathed bacterium Haliscomenobacter hydrossis in the Saprospira group of the Flexibacter-Bacteroides-Cytophaga (FBC) phylum. A proposal is made to transfer these marine species to the genus Lewinella gen. nov. as Lewinella cohaerens comb. nov., Lewinella nigricans comb. nov. and Lewinella persica comb. nov. The marine sheathed gliding bacterium Flexithrix dorotheae was also found to be a member of the FBC phylum but on a separate phylogenetic line to the marine herpetosiphons now assigned to the genus Lewinella.
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Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium
More LessThe 16S rRNA gene sequences of 19 strains, 11 strains representing validated Aureobacterium or Microbacterium species and eight strains of non-valid species or isolates, were determined. These sequences were aligned with the sequences of other validated Aureobacterium and Microbacterium species and related actinobacteria. A comparative sequence analysis of 43 strains revealed that the species of the genera Aureobacterium and Microbacterium form a monophyletic association in which species of both genera are intermixed. The high similarity in phylogenetic properties found in the species within both genera and the close relationship in physiological and chemotaxonomic features other than the diamino acid in the cell wall, provided strong evidence that the genera Aureobacterium and Microbacterium should be unified. An emended genus Microbacterium is proposed for the two combined genera. The following validated Aureobacterium species were combined to the genus Microbacterium: Aureobacterium arabinogalactanolyticum to Microbacterium arabinogalactanolyticum, Aureobacterium barkeri to Microbacterium barkeri, Aureobacterium esteraromaticum to Microbacterium esteraromaticum, Aureobacterium flavescens to Microbacterium flavescens, Aureobacterium keratanolyticum to Microbacterium keratanolyticum, Aureobacterium liquefaciens to Microbacterium liquefaciens, Aureobacterium luteolum to Microbacterium luteolum, Aureobacterium saperdae to Microbacterium saperdae, Aureobacterium schleiferi to Microbacterium schleiferi, Aureobacterium terrae to Microbacterium terrae, Aureobacterium terregens to Microbacterium terregens, Aureobacterium testaceum to Microbacterium testaceum, and Aureobacterium trichothecenolyticum to Microbacterium trichothecenolyticum.
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Taxonomic evidence that Vibrio carchariae Grimes et al. 1985 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981
A collection of 94 Vibrio isolates closely related to Vibrio harveyi, together with named reference and type strains, were investigated for phenotypic and genotypic properties. Using amplified fragment length polymorphism (AFLP), nine clusters were recognized. The largest cluster (n = 36), considered to be the bona fide V. harveyi group, contained the type strains of V. harveyi and Vibrio carchariae and most of the strains isolated from fish. The type strains of all other species, including Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio campbellii and Vibrio natriegens, clustered outside this group. By ribotyping, V. harveyi and V. carchariae patterns were very similar, insofar as they shared most bands. The V. campbellii type strain had several bands in common with the type strains of both V. harveyi and V. carchariae, whereas the other species were clearly distinct from these three species. DNA-DNA hybridization experiments showed 88% DNA binding between the type strains of V. harveyi and V. carchariae, whereas the DNA binding between V. harveyi and V. campbellii was 40%. Although the delineation of the species V. harveyi is still uncertain, the authors propose, on the basis of a number of tests, to delineate a core of V. harveyi strains which contained the type strains of both V. harveyi and V. carchariae. It is concluded that V. carchariae is the junior synonym of V. harveyi.
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Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp.
More LessThe relatedness of Brucella spp. and Ochrobactrum anthropi was studied by protein profiling, Western blot, immunoelectrophoresis and 16S rRNA analysis. Whole-cell and soluble proteins of brucellae and O. anthropi showed serological cross-reactivities quantitatively and qualitatively more intense than those existing with similar extracts of Agrobacterium spp. Numerical analysis of Western blot profiles of whole-cell extracts showed that O. anthropi LMG 3301 was closer to Brucella spp. than to O. anthropi LMG 3331Ta result not obtained by protein profiling. These differences were not observed by Western blot with soluble fractions, and immunoelectrophoretic analyses suggested that this was due to destruction of conformational epitopes in Western blot procedures with the subsequent simplification of antigenic profile. Analysis of the 16S rRNA sequences of strains previously used in the species definition confirmed that strain LMG 3301, and also LMG 3306, were closer to the brucellae, and that LMG 3331Twas in a separate cluster. The LMG 3301 and the LMG 3331Tclusters could also be separated by their different colistin sensitivity and by PCR with 16S rRNA Brucella primers, and both methods showed strains of both clusters among clinical isolates classified as O. anthropi by conventional tests. These results and those of previous DNA-DNA hybridization studies [Holmes, B., Popoff, M., Kiredjian, M. & Kersters, K. (1988). Int J Syst Bacteriol 38, 406-416] show that the LMG 3301 cluster and related clinical isolates should be given a new species status for which the name Ochrobactrum intermedium sp. nov. is proposed (type strain is LMG 3301T= NCTC 12171T= CNS 2-75T).
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Pseudoalteromonas bacteriolytica sp. nov., a marine bacterium that is the causative agent of red spot disease of Laminaria japonica
An aerobic, polarly flagellated marine bacterium that produces a prodigiosinlike pigment was isolated from the red-spotted culture beds of Laminaria japonica. Five isolates had unique bacteriolytic activity for both Gram-positive and -negative bacteria, which had never been observed among Alteromonas or related species. The isolates were identified as the causative agent of red spot disease of L. japonica seeds. The phenotypic features of the isolates were similar to these of Pseudoalteromonas rubra ATCC 29570T, but they could be differentiated using 10 traits (growth at 37·C, requirement for organic growth factors, bacteriolytic activity, utilization of sucrose, N-acetylglucosamine, fumarate, succinate, d-galactose, l-proline and acetate). The G+C content of DNAs from the isolates was 44-46 mol%. The isolates constitute a new species, distinct from the other Alteromonas and Pseudoalteromonas species, as shown by DNA-DNA hybridization experiments and phylogenetic clustering of 16S rRNA gene sequences, for which the name Pseudoalteromonas bacteriolytica sp. nov. (type strain = IAM 14595T) is proposed. A set of phenotypic features which differentiate this new species from closely related Pseudoalteromonas and Alteromonas species is provided.
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Microvirgula aerodenitrificans gen. nov., sp. nov., a new Gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions
A denitrifier micro-organism was isolated from an upflow denitrifying filter inoculated with an activated sludge. The cells were Gram-negative, catalase-and oxidase-positive curved rods and very motile. They were aerobic as well as anoxic heterotrophs that had an atypical respiratory type of metabolism in which oxygen and nitrogen oxides were used simultaneously as terminal electron acceptors. The G+C content was 65 mol%. Our isolate was phenotypically similar to Comamonas testosteroni, according to classical systematic classification systems. However, a phylogenetic analysis based on the 16S rRNA sequence showed that the aerobic denitrif could not be assigned to any currently recognized genus. For these reasons a new genus and species, Microvirgula aerodenitrificans gen. nov., sp. nov., is proposed, for which SGLY2Tis the type strain.
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Selenomonas lipolytica sp. nov., an obligately anaerobic bacterium possessing lipolytic activity
More LessA novel, obligately anaerobic bacterium capable of hydrolysing lipids was isolated from a tropical anaerobic lagoon receiving waste water from an edible oil mill. The isolate had many characteristics similar to those of members of the genus Selenomonas. The isolate showed lipolytic activity on tributyrin, triolein and groundnut oil in qualitative plate clearance assays, which has not been reported for the type strain of the genus Selenomonas. It did not require n-valerate supplementation for growth on glucose. Acetate and propionate were the only volatile fatty acids produced from glucose fermentation with propionate as the major end product. The isolate could grow optimally at pH 6.8 and at a temperature of 40 °C. It could tolerate NaCI concentrations of up to 40 g l-1. The G+C content of the DNA was 40 mol% as determined by thermal denaturation analysis. Comparison of partial 16S rRNA gene sequences revealed that the isolate was most closely related to genus Selenomonas with 91% sequence similarity (250 bp compared) to Selenomonas ruminantium strain GA 192. On the basis of the results obtained in the present investigation, it is suggested that a new species of Selenomonas should be created for this novel isolate and the name Selenomonas lipolytica is proposed for this new species. The type strain is strain CF1BT(= MCMB 505T).
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Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the α-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum comb. nov., of Rhodospirillum salinarum to Rhodovibrio salinarum comb, nov., of Rhodospirillum sodomense to Rhodovibrio sodomensis comb. nov., of Rhodospirillum salexigens to Rhodothalassium salexigens comb. nov. and of Rhodospirillum mediosalinum to Roseospira mediosalina comb. nov.
More LessThe 16S rDNA sequence of Rhodospirillum mediosalinum was determined and compared with corresponding sequences from other spiral-shaped purple non-sulfur bacteria classified as or related to the genus Rhodospirillum in the α subclass of the Proteobacteria. Sequence similarities separate the currently recognized Rhodospirillum species into five different groups with no more than 91% sequence similarity, clearly indicating the necessity to recognize these groups as different genera. Major diagnostic properties of these bacteria are compared and new genera Phaeospirillum gen. nov., Roseospira gen. nov., Rhodothalassium gen. nov. and Rhodovibrio gen. nov. are described with the species Phaeospirillum fulvum comb, nov., Phaeospirillum molischianum comb. nov., Rhodovibrio salinarum comb. nov., Rhodovibrio sodomensis comb. nov., Rhodothalassium salexigens comb. nov. and Roseospira mediosalina comb. nov. The genus Rhodospirillum is represented by Rhodospirillum rubrum and Rhodospirillum photometricum and an emended description of this genus is also given.
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Staphylococcus hominis subsp. novobiosepticus subsp. nov., a novel trehalose- and N-acetyl-D-glucosamine-negative, novobiocin- and multiple-antibiotic-resistant subspecies isolated from human blood cultures
A new subspecies, Staphylococcus hominis subsp. novobiosepticus, isolated from human blood cultures, a wound, a breast abscess and a catheter tip, is described on the basis of a study of 26 strains isolated between 1989 and 1996. DNA-DNA reassociation reactions, conducted under stringent conditions, and macrorestriction pattern analysis demonstrated that these strains are closely related to previously characterized S. hominis strains isolated from human skin and clinical specimens, but are significantly divergent. S. hominis subsp. novobiosepticus can be distinguished from S. hominis (now named S. hominis subsp. hominis) by its combined characteristics of novobiocin resistance and failure to produce acid aerobically from D-trehalose and N-acetyl-D-glucosamine. Furthermore, all 26 strains of the new subspecies are resistant to nalidixic acid, penicillin G, oxacillin, kanamycin and streptomycin, and were either resistant or had intermediate resistance to methicillin and gentamicin. Most strains were also resistant to erythromycin, clindamycin, chloramphenicol, trimethoprim/sulfamethoxazole and ciprofloxacin. Based on a comparison of the sequences of a 1001 bp mecA amplification product from reference methicillin-resistant staphylococci, the mecA gene present in S. hominis subsp. novobiosepticus was identified as homologue A, commonly found in S. aureus and many coagulase-negative staphylococcal species. The type strain of S. hominis subsp. novobiosepticus is ATCC 700236T. Descriptions of S. hominis subsp. novobiosepticus subsp. nov. and S. hominis subsp. hominis are given and the description of S. hominis is emended.
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Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes
More LessPhylogenetic analysis of 20 Pseudomonas strains (Pseudomonas putida, Pseudomonas fluorescens and Pseudomonas chlororaphis) was conducted by using the nucleotide sequences of the genes for 16S rRNA, DNA gyrase B subunit (gyrB) and RNA polymerase σ70factor (rpoD), which have been determined by the direct sequencing of PCR-amplified fragments. On the basis of gyrB and rpoD sequences, these strains were split into two major clusters: one including the type strain of P. putida and all biovar A strains and the other including all P. putida biovar B strains, P. fluorescens strains and the P. chlororaphis strain. In the phylogenetic tree reconstructed from the 16S rRNA sequences including variable regions, P. putida biovar A and B strains were not separated into two independent clusters, whereas in the phylogenetic tree reconstructed from the 16S rRNA sequences excluding the variable region sequences, these strains were separated into P. putida biovar A and biovar B clusters. The pairwise distances estimated from the variable regions of 16S rRNA correlated poorly with the synonymous distances estimated from the gyrB and rpoD genes. On the other hand, a highly significant correlation was observed between the pairwise distances estimated from the non-variable regions of 16S rRNA and the synonymous distances from gyrB and rpoD genes. Consequently, only the 16S rRNA sequences in the non-variable regions should be used for the phylogenetic analysis. The gyrB and rpoD analyses showed the necessity for the reclassification of P. putida biovar B strains.
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Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well
Two irregular coccoid methanogens designated SEBR 4845Tand FR1T were isolated from an oilfield in Alsace, France. Strain SEBR 4845T(T = type strain) is a hydrogenotrophic halotolerant methanogen, which grows optimally at 5% NaCI (w/v) and tolerates up to 12% NaCI. It does not use methylated compounds and therefore cannot be ascribed to any of the known genera of the halophilic methylotrophic methanogens. It differs from hydrogenotrophic members of the orders Methanococcales and Methanomicrobia les in the NaCI growth range (0-12% NaCI), which is the widest reported to date for any hydrogenotrophic methanogen. 16S rRNA gene sequence analysis indicated that strain SEBR 4845Tis a novel isolate for which a new genus is proposed, Methanocalculus halotolerans gen. nov., sp. nov. (= OCM 470T) that might be indigenous to the oilfield ecosystem. Strain FR1T (= OCM 471) is a moderately halophilic methanogen which grows optimally at 10% NaCI and tolerates up to 20% NaCI. It grows on trimethylamine and methanol as carbon and energy sources. The G+C content of its DNA is 43 mol%. It is therefore phenotypically and genotypically related to members of the genus Methanohalophilus. This report provides evidence that methylotrophic and hydrogenotrophic, but not aceticlastic methanogens are present in a saline subsurface oilfield environment, as already observed in surface saline to hypersaline environments.
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DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups
More LessAs a continuation of an ongoing study of DNA relatedness among red-spored streptomycetes, the homology between the four species comprising the Streptomyces fulvissimus phenotypic cluster (S. fulvissimus, Streptomyces aureoverticillatus, Streptomyces longispororuber and Streptomyces spectabilis) and the four species comprising the Streptomyces griseoviridis phenotypic cluster (S. griseoviridis, Streptomyces chryseus, Streptomyces daghestonicus and Streptomyces murinus) was measured spectrophotometrically from C0t05 determinations. All strains were also compared to 12 strains representing previously determined DNA-relatedness clusters in the Streptomyces lavendulae phenotypic cluster, including the type strain NRRL B-1230T. The strains segregated into 15 cluster groups at DNA relatedness <80%, including 10 single-membered clusters. S. griseoviridis and S. daghestonicus were synonymous, as were S. chryseus and S. longispororuber. S. spectabilis exhibited species-level homology with strain NRRL B-2402, which had been received as S. lavendulae. S. aureoverticillatus exhibited significant DNA relatedness to Streptomyces flavotricini. None of the strains from the S. fulvissimus or S. griseoviridis clusters exhibited significant homology to the type strain of S. lavendulae.
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Paenibacillus campinasensis sp. nov., a cyclodextrin-producing bacterium isolated in Brazil
An alkaliphilic, endospore-forming bacterium isolated from Brazilian soil was taxonomically studied and is proposed as a new Paenibacillus species. This organism (strain 324T) was particularly distinguishable from other Paenibacillus species by its ability to grow optimally at pH 10 and 40 °C. The DNA G+C content was 50-9 mol%. The diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. MK-7 was the predominant menaquinone and anteiso-C15:0 was the major fatty acid. Levels of 16S rDNA similarity between strain 324Tand other Paenibacillus species were 90-6-95-9%. Phylogenetically, strain 324Tformed an evolutionary lineage distinct from other species within the evolutionary radiation encompassing the genus Paenibacillus. Based on phenotypic and chemotaxonomic properties, and phylogenetic inference, it is proposed that strain 324Tshould be placed in the genus Paenibacillus as a new species, Paenibacillus campinasensis. The type strain of the new species is strain 324T(= KCTC 0364BPT).
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Phylogenetic analysis of spotted fever group rickettsiae by study of the outer surface protein rOmpA
More LessRickettsiae are classified in the order Rickettsiales and have been included in the α subclass of the class Proteobacteria on the basis of 16S rRNA gene sequence comparison. To estimate the evolutionary forces that have shaped the members of the spotted fever group (SFG) rickettsiae, the ompA gene (apart from the tandem repeat units), encoding an antigenic high-molecularmass membrane protein specific for the group, was amplified and sequenced from 21 isolates. The phylogenetic relationships between SFG rickettsiae were inferred from the comparison of both the gene and derived protein sequences, using the parsimony, neighbour-joining and maximum-likelihood methods. Three strongly supported phylogenetic sub-groups were distinguished: first, the Rickettsia conorii complex (R. conorii Malish, R. conorii M1, R. conorii Moroccan, R. conorii Indian tick typhus, Astrakhan fever rickettsia and Israeli tick typhus rickettsia); second, a cluster including Rickettsia africae, strain S, Rickettsia parkeri, Rickettsia sibirica and ‘Rickettsia mongolotimonae’; and, third, a cluster including Rickettsia aeschlimannii, Rickettsia rhipicephali, Rickettsia massiliae, Bar 29 and Rickettsia montanensis. Rickettsia rickettsii, Rickettsia japonica, Rickettsia slovaca and Thai tick typhus rickettsia did not cluster with any other Rickettsia species. To test whether positive selection was responsible for sequences diversity, rates of synonymous and nonsynonymous nucleotide substitutions were compared for Rickettsia ompA alleles and indicated that this gene is undergoing neutral evolution.
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Leptospira fainei sp. nov., isolated from pigs in Australia
Pathogenic leptospires can be causative agents of reproductive problems in pigs. Cultures of uteri and kidneys from two pig herds in New South Wales and Victoria (Australia) yielded five strains identified as Leptospira on morphological and cultural grounds. Phenotypic characteristics (growth at 13 and 30°C, growth in the presence of 8-azaguanine) were intermediate between those of pathogenic and saprophytic leptospires. No cross-agglutination was observed with reference antisera representing the 24 pathogenic serogroups and the main saprophytic ones. Antiserum against one of the strains did not agglutinate reference strains representative of any serogroup. This provided evidence of a new serovar, designated hurstbridge. Genomic characterization of the five strains was achieved using five molecular approaches. Mapped restriction site polymorphisms in the rrs (16S rRNA) gene were not related to those of any reference strains. Arbitrarily primed PCR fingerprints suggested clonality of the five strains. The strains all showed an identical and unique PFGE profile. PCR, using primers specific for the rrs gene of pathogenic leptospires, amplified corresponding sequences from the strains. DNA-DNA hybridization (and reciprocal experiments) using the S1 nuclease/TCA method was performed between one of the strains and the reference strains of Leptospira species. The homology ranged from 0 to 36% (the latter being with Leptospira inadai) thus satisfying the criterion of a new species, Leptospira fainei (type strain BUT 67). Phylogenetic analysis of 16S rRNA sequences showed that L. fainei and L. inadai formed a clade separate from the previously recognized ‘prophyt’ and ‘pathoge’ clades.
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Delimiting the genus Staphylococcus through description of Macrococcus caseolyticus gen. nov., comb. nov. and Macrococcus equipercicus sp. nov., Macrococcus bovicus sp. nov. and Macrococcus carouselicus sp. nov.
Four species of the newly proposed genus Macrococcus, namely Macrococcus caseolyticus gen. nov., comb. nov. (formerly Staphylococcus caseolyticus Schleifer, Kilpper-Bälz, Fischer, Faller and Endl 1982, 19VP), Macrococcus equipercicus sp. nov., Macrococcus bovicus sp. nov. and Macrococcus carouselicus sp. nov., are described on the basis of a phylogenetic analysis comparing 16S rRNA sequences, DNA-DNA liquid hybridization, DNA base composition, normalized ribotype patterns, macrorestriction pattern analysis and estimation of genome size using PFGE, cell wall composition, phenotypic characteristics and plasmid profiles. Compared with their closest relatives, members of the genus Staphylococcus, these organisms demonstrated significantly lower 16S rRNA sequence similarities (93.4—95.3%), higher DNA G+C content (38—45 mol%), absence of cell wall teichoic acids (with the possible exception of M. caseolyticus), unique ribotype pattern types and macrorestriction patterns, smaller genome size (approx. 1500—1800 kb) and generally larger Gram-stained cell size (1.1—2.5 μm in diameter). Macrococci can be distinguished from most species of staphylococci (except Staphylococcus sciuri, Staphylococcus vitulus and Staphylococcus lentus) by their oxidase activity. The four Macrococcus species can be distinguished from one another on the basis of DNA-DNA hybridization, ribotype pattern types, macrorestriction patterns and their phenotypic properties, including colony morphology, cell morphology, haemolysins, Staph Latex agglutination, acid production from a variety of carbohydrates, acetoin production, nitrate reduction, aesculin hydrolysis, and DNase and urease activities. The type species is M. equipercicus. The type strains of M. equipercicus, M. caseolyticus, M. bovicus and M. carouselicus are ATCC 51831T(= DD 9350T), ATCC 13548T(= TDD 4508T) (Schleifer et al. 1982), ATCC 51825T(= DD 4516T) and ATCC 51828T(= DD 9348T), respectively.
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Thermocladium modestius gen. nov., sp. nov., a new genus of rod-shaped, extremely thermophilic crenarchaeote
More LessThree strains of novel, extremely thermophilic, rod-shaped crenarchaeotes were isolated from acidic hot spring areas in Japan. Cells of the three strains were straight or slightly curved rods and occasionally branched out singly or extensively, or had spherical bodies protruding at the ends of the cells. They were heterotrophs that grew anaerobically or microaerobically. The presence of CO2 in the gas phase, archaeal cell-extracts and a vitamin mixture stimulated growth of the strains. Growth occurred at 45-82 °C and pH 2.6-5.9 and was optimal around 75 °C and pH 4.0. The strains utilized glycogen, starch, gelatin and various proteinaceous complex compounds as carbon sources. They required sulfur, thiosulfate or L-cystine as possible electron acceptors. The lipids mainly consisted of various cyclic glycerol-bisdiphytanyl-glycerol tetraethers. The G+C contents of the genomic DNAs were 52 mol%. Comparison of the 16S rDNA sequences indicated that they belonged to a separate lineage in the family Thermoproteaceae. The three strains were included in a single species due to high levels of DNA-DNA hybridization values. Based upon these results, the new isolates were assigned to a new genus and species in the family Thermoproteaceae, Thermocladium modestius gen. nov., sp. nov. The type strain is Thermocladium modestius IC-125T(= JCM 10088T).
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Identification of denitrifier strain T1 as Thauera aromatica and proposal for emendation of the genus Thauera definition
More LessBacterial strain T1, originally isolated by P. J. Evans on the basis of its capacity for toluene degradation under denitrifying conditions, has been classified as Thauera aromatica. In a comprehensive study of strains of this species, it was found that the cells have a different type of flagellar insertion from that of cells of the type species of the genus, Thauera selenatis, suggesting the convenience of an emendation of the description of the genus Thauera. Further studies on a larger collection of strains with the above characteristics may serve in the future as the basis for the creation of a new generic designation.
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Application of multiplex PCR using species-specific primers within the 16S rRNA gene for rapid identification of Nocardioides strains
More LessFor the rapid identification of Nocardioides strains, multiplex PCR, using 16S rDNA as target gene, was used and its value was evaluated. Forward primers specific for Nocardioides albus, Nocardioides jensenii, Nocardioides plantarum and Nocardioides simplex, among the five validly described Nocardioides species, were designed from the alignment of 16S rDNA sequences. Nocardioides luteus has been shown to be a member of the same species as N. albus by recent molecular systematic studies and preliminary DNA-DNA relatedness tests. Therefore, N. albus and N. luteus were considered as members of the same species in this study. Each primer was found to be species-specific by specificity testing. N. albus NSP01T, N. jensenii NSP19T, N. plantarum NSP21Tand N. simplex NSP22Tcould be clearly differentiated by PCR products characteristic for each species in the multiplex PCR assay. N. luteus gave an identical result to N. albus NSP01T. The additional 17 strains of N. albus and the additional four strains of N. simplex gave PCR products identical to those of N. albus NSP01Tand N. simplex NSP22T, respectively. Multiplex PCR was found to be rapid, species-specific and reproducible. The technique evaluated in this study proved to be effective for rapidly identifying Nocardioides strains to species level.
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Nocardia flavorosea sp. nov.
An actinomycete strain, ‘Nocardia flavorosea’ JCM 3332, was found to have properties consistent with its classification in the genus Nocardia. An almost complete gene sequence of the 16S rDNA of the strain was determined following cloning and sequencing of the amplified gene. The sequence was aligned with those available for nocardiae and phylogenetic trees were inferred using four tree-making algorithms. The organisms consistently formed a distinct clade with the type strain of Nocardia carnea. However, DNA relatedness experiments showed that the strain and N. carnea DSM 43397Tbelonged to two distinct genomic species. The organism was also distinguished from representatives of all of the validly described species of Nocardia using a combination of phenotypic properties. These genotypic and phenotypic data show that the strain merits recognition as a new species of the genus Nocardia. The name proposed for the new species is Nocardia flavorosea sp. nov. The type strain is JCM 3332T.
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Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere
More LessThe taxonomic position of bacterial strain 141T, isolated from the mangrove rhizosphere, has been clarified by phenotypic, chemotaxonomic and phylogenetic studies. The strain possesses wall chemotype IV, MK-9(H2) as the predominant menaquinone, relatively long-chain mycolic acids (56-64 carbon atoms) and straight-chain saturated and monounsaturated fatty acids with a small amount of tuberculostearic acid. The G+C content of the DNA is 66.8 mol%. Similarity values for genes encoding 16S rRNA indicated that strain 141Trepresents a new species within the genus Gordonia for which the name Gordonia rhizosphera sp. nov. is proposed. The type strain of G. rhizosphera is 141T(= IFO 16068T).
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Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent
More LessAn autotrophic, extremely thermophilic methanogen (MET) was isolated from a deep-sea hydrothermal chimney sample collected on the Mid-Atlantic Ridge at a depth of 3000 m. The heavily flagellated cells are motile and coccoid shaped. The new strain grows between 55 and 91 °C, with an optimum growth temperature at 85 °C. The optimum pH for growth is 6.5, and the optimum sea salt concentration for growth is around 25 g I-1. The organism uses H2 and CO2 as the only substrate for growth and methane production. Tungsten, selenium and yeast extract stimulate growth significantly. In the presence of CO2 and H2, the organism reduces elemental sulphur to hydrogen sulphide. The G+C content of the genomic DNA is 33 mol%. As determined by 16S gene sequence analysis, this organism is closely related to Methanococcus jannaschii strain JAL-1T. However, no significant homology was observed between them with DNA-DNA hybridization. It is proposed that this organism should be placed in a new species, Methanococcus infernus. The type strain is MET(-DSM 11812T.
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Streptococcus peroris sp. nov. and Streptococcus infantis sp. nov., new members of the Streptococcus mitis group, isolated from human clinical specimens
Taxonomic studies were performed on eight strains of α-haemolytic streptococci that showed very low DNA-DNA hybridization similarity values with all established members of the mitis group of the genus Streptococcus. These strains were isolated from the tooth surface and pharynx of humans. 16S rRNA gene sequence analysis showed that these strains belonged to the mitis group, but that they fell into two new branches. DNA-DNA hybridization demonstrated two new similarity groups. From the results of the present study, the names Streptococcus peroris sp. nov. and Streptococcus infantis sp. nov. are proposed for these new groups. The type strains are 0-66T(= GTC 848T= JCM 10158T) and 0-122T(= GTC 849T= JCM 10157T), respectively.
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Actinobacillus scotiae sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from porpoises (Phocoena phocoena)
More LessPhenotypic and phylogenetic studies were performed on a Gram-negative, rod-shaped bacterium isolated from three porpoises. Biochemical and physiological studies indicated that the bacterium was related to the family Pasteurellaceae. Comparative 16S rRNA gene sequencing studies confirmed these findings and demonstrated that the bacterium represents a hitherto unknown subline. The nearest phylogenetic relative of the unknown bacterium was Actinobacillus delphinicola, an organism also originating from sea mammals, although a sequence divergence of 3% demonstrated that the newly isolated bacterium is a distinct species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacterium should be classified as a new species, Actinobacillus scotiae sp. nov. The type strain of Actinobacillus scotiae sp. nov. is NCTC 12922T(= M2000/95/1T).
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Description of Acetobacter oboediens sp. nov. and Acetobacter pomorum sp. nov., two new species isolated from industrial vinegar fermentations
More LessTwo strains of Acetobacter sp., LTH 2460Tand LTH 2458T, have been isolated from running red wine and cider vinegar fermentations, respectively. Taxonomic characteristics of the isolates were investigated. Comparative analysis of the 16S rRNA sequences revealed < 99% similarity between strain LTH 2460Tand the type strains of the related species Acetobacter europaeus and Acetobacter xylinus and between strain LTH 2458Tand Acetobacter pasteurianus. On the other hand, low levels of DNA relatedness (> 34%) were determined in DNA-DNA similarity studies. This relatedness below the species level was consistent with specific physiological characteristics permitting clear identification of these strains within established species of acetic acid bacteria. Based on these results, the names Acetobacter oboediens sp. nov. and Acetobacter pomorum sp. nov. are proposed for strains LTH 2460Tand LTH 2458T, respectively. The phylogenetic positions of the new species are reflected by a 16S rRNA-based tree. Furthermore, a 16S rRNA-targeted oligonucleotide probe specific for A. oboediens was constructed.
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Phylogenetic positions of phytoplasmas associated with dieback, yellow crinkle and mosaic diseases of papaya, and their proposed inclusion in ‘Candidatus Phytoplasma australiense’ and a new taxon, ‘Candidatus Phytoplasma australasia’
More LessDNA extracted from three papaya (Carica papaya L.) plants, individually affected by dieback, yellow crinkle or mosaic diseases, was subjected to PCR using phytoplasma-specific primers to amplify the 16S rRNA gene plus 16S-23S rRNA intergenic spacer region. Near-complete DNA sequences obtained for the three PCR amplimers were subjected to phylogenetic analyses and direct sequence comparison with other phytoplasma 16S rDNA and 16S-23S spacer region DNA sequences. The papaya yellow crinkle (PpYC) and papaya mosaic (PpM) sequences were identical to each other, but distinctly different from the papaya dieback (PpDB) sequence, showing 90.3% identity in the 16S rDNA and 87.8% identity in the 16S-23S spacer region DNA sequences. A phylogenetic tree based on 16S rDNA sequences was calculated, in which PpYC and PpM are most closely related to the tomato big bud phytoplasma (TBB; 99.7% 16S rDNA sequence identity) from Australia, within subclade iii. This subclade consists of strains only reported occurring in the Southern Asian region and Australia, which indicates an Asian/Australasian origin. PpDB is most closely related to the Phormium yellow leaf phytoplasma from New Zealand (PYL; 99.9% identity) and the Australian grapevine yellows phytoplasma (AGY; 99.7% identity). These three phytoplasma strains form a distinct clade within subclade xii, which also includes the European strains STOL and VK as another distinct clade. The origin of the closely related but geographically separated AGY-like strains and STOL-like strains of subclade xii is unclear. It is proposed that phytoplasma strains PpDB, PYL and AGY be included in the previously described taxon ‘Candidatus Phytoplasma australiense’, and that PpYC PpM and TBB be assigned to a new taxon, ‘Candidatus Phytoplasma australasia’.
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Azoarcus anaerobius sp. nov., a resorcinol-degrading, strictly anaerobic, denitrifying bacterium
More LessA strictly anaerobic, nitrate-reducing bacterium, strain LuFRes1, was isolated using resorcinol as sole source of carbon and energy. The strain reduced nitrate to dinitrogen gas and was not able to use oxygen as an alternative electron acceptor. Cells were catalase-negative but superoxide-dismutase-positive. Resorcinol was completely oxidized to CO2.16S rRNA sequence analysis revealed a high similarity with sequences of Azoarcus evansii and Azoarcus tolulyticus. Strain LuFRes1T(= DSM 12081T) is described as a new species of the genus Azoarcus, Azoarcus anaerobius.
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Taxonomic rearrangements of the genera Thiocapsa and Amoebobacter on the basis of 16S rDNA sequence analyses, and description of Thiolamprovum gen. nov.
Complete nucleotide sequences of the 16S rDNAs were determined from Thiocapsa and Amoebobacter species, including all available type strains and some additional isolates. The distance-matrix analysis and the dendrogram for estimating the genetic relationships revealed that the investigated strains were found in two major clusters within the Chromatiaceae. One cluster comprises all Amoebobacter species, Thiocapsa roseopersicina and several isolates related to Thiocapsa roseopersicina. Representatives of the species Amoebobacter roseus, Amoebobacter pendens and Thiocapsa roseopersicina, the so called ‘Thiocapsa roseopersicina group’, are very closely related, justifying their inclusion into one genus, Thiocapsa, for which an emended description is presented. Amoebobacter purpureus and Amoebobacter pedioformis formed two separate lines of descent with less than 93% (89.6-92.9%) similarity to strains of the ‘Thiocapsa roseopersicina group’. Therefore, they will be considered as two separate genera. As a consequence, an emended description is presented for the genus Amoebobacter, with Amoebobacter purpureus as the new type species and A. pedioformis is transferred to Thiolamprovum pedioforme gen. nov., comb. nov. Two species, Thiocapsa pfennigii and Thiocapsa halophila, which have been classified with the genus Thiocapsa because of their morphological properties, were found within another major cluster of the Chromatiaceae and are only distantly phylogenetically related to the first cluster with 88.4-90.6% and 90.4-92.2% sequence similarity, respectively.
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Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds
More LessA new bacterial species belonging to the genus Shewanella is described on the basis of phenotypic characterization and sequence analysis of its 16S rRNA-encoding and gyrase B (gyrB) genes. This organism, isolated from shallowwater marine sediments derived from the Amazon River delta, is a Gramnegative, motile, polarly flagellated, facultatively anaerobic rod-shaped eubacterium and has a G+C content of 51.7 mol%. Strain SB2BTis exceptionally active in the anaerobic reduction of iron, manganese and sulfur compounds. SB2BTgrows optimally at 35 °C, with 1-3% NaCl and over a pH range of 7-8. Analysis of the 16S rDNA sequence revealed a clear affiliation between strain SB2BTand members of the gamma subclass of the class Proteobacteria. High similarity values were found with certain members of the genus Shewanella, especially with Shewanella putrefaciens, and this was supported by cellular fatty acid profiles and phenotypic characterization. DNA-DNA hybridization between strain SB2BTand its phylogenetically closest relatives revealed low similarity values (24.6-42.7%) which indicated species status for strain SB2BT. That SB2BTrepresents a distinct bacterial species within the genus Shewanella is also supported by gyrB sequence analysis. Considering the source of the isolate, the name Shewanella amazonensis sp. nov. is proposed and strain SB2BT(= ATCC 700329T) is designated as the type strain.
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Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. nov.
More LessReference strains, including two mis-named organisms, ‘Chromobacterium chocolatum’ and Flavobacterium marinotypicum. isolates from soil and clinical specimens, all previously recognized as Aureobacterium or Microbacterium, were characterized taxonomically. On the basis of morphological, physiological and chemotaxonomic characteristics, as well as DNA-DNA hybridization data, six new species and one new combination are proposed in the genus Microbacterium: Microbacterium ketosireducens sp. nov. (type strain IFO 14548T), Microbacterium chocolatum sp. nov. (type strain IFO 3758T), Microbacterium aurantiacum sp. nov. (type strain IFO 15234T), Microbacterium hominis sp. nov. (type strain IFO 15708T), Microbacterium thalassium sp. nov. (type strain IFO 16060T), Microbacterium halophilum sp. nov. (type strain IFO 16062T) and Microbacterium maritypicum comb. nov. (type strain IFO 15779T).
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Tissierella creatinophila sp. nov., a Gram-positive, anaerobic, non-spore-forming, creatinine-fermenting organism
More LessA strictly anaerobic, Gram-positive, non-spore-forming bacterium was isolated from sewage sludge which grew on creatinine as sole source of carbon and energy. This new isolate, designated strain KRE 4T, totally degraded creatinine via creatine, sarcosine and glycine to the products acetate, monomethylamine, ammonia and carbon dioxide. Growth on creatinine or creatine was selenium-dependent and stimulated by formate, indicating the involvement of a creatine reductase, sarcosine reductase and/or glycine reductase. This was substantiated by the fact that creatine, sarcosine and glycine were reduced by cell-free extracts. Growth on creatinine or creatine was also possible in the absence of formate, but with an increase in doubling time. The new bacterium occurred as rod-shaped cells, which exhibited an angular form (2-6 μm long and 0.7-1.1 μm wide) and showed motility by means of peritrichous flagella. The G+C content of the DNA was 30 mol%. Comparative 16S rRNA sequence analysis demonstrated that strain KRE 4Trepresents a new subline within the genus Tissierella. Due to its very restricted substrate spectrum and the inability of whole cells to utilize sarcosine and glycine as intermediates of creatine breakdown, this organism can be readily separated from currently described species of Tissierella. Therefore, based on the phenotypic and phylogenetic distinctiveness of the new isolate, it is proposed that the bacterium be classified as a new species of the genus Tissierella, Tissierella creatinophila sp. nov. The type strain is KRE 4 (= DSM 6911T).
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A new genus of the order Actinomycetales, Cryptosporangium gen. nov., with descriptions of Cryptosporangium arvum sp. nov. and Cryptosporangium japonicum sp. nov.
More LessFour strains that form sporangia with motile sporangiospores and mycelia were isolated from soil samples. Their many sporangia were covered by mycelia. They had glutamic acid, glycine, alanine and meso-diaminopimelic acid as cell wall amino acids (wall chemotype II), acofriose (3-O-methylrhamnose) as a characteristic whole-cell sugar, and menaquinone 9(H6). The taxonomic characteristics of these strains differ from those of the previously described motile actinomycetes. On the basis of the morphological, physiological, chemotaxonomic and phylogenetic analyses, a new genus is proposed, Cryptosporangium, and two new species, Cryptosporangium arvum sp. nov. (type strain IFO 15965T) for strain YU 629-21Tand Cryptosporangium japonicum sp. nov. (type strain IFO 15966T) for strains YU 636-3T, YU 655-31 and YU 656-31.
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Petrotoga mobilis sp. nov., from a North Sea oil-production well
More LessRod-shaped, thermophilic bacteria with a sheath-like outer structure (‘toga’) were isolated from hot oilfield water of a North Sea oil reservoir. One of the isolates, designated SJ95T, is an obligately anaerobic, sheathed, Gram-negative, fermentative bacterium capable of reducing elemental sulfur to hydrogen sulfide and tolerating high salt concentrations. The optimum growth conditions for this isolate are 58-60°C and pH 6.5-7.0 with 3-4% NaCl and 0.7% MgSO4.7H2O in the medium. Vitamins are required for growth. Growth is stimulated by yeast extract. Cells of strain SJ95Tvary in size from 1-2 to 40-50 μm in length and are motile with a subpolar flagellation. Cells grown on xylan have xylanase activity, presumably associated with the toga, and glucose isomerase activity was detected in xylose-grown cells. The DNA G+C content is 31 and 34 mol%, determined by the thermal denaturation and HPLC methods, respectively. Phylogenetically, strain SJ95Tis most closely related to Petrotoga miotherma with a 97.7% similarity level between their 16S rDNA sequences. The DNA-DNA reassociation value between the two DNAs was 35.6%. On the basis of differences in genotypic, phenotypic and immunological characteristics, strain SJ95T(= DSM 10674T) is proposed as the type strain of a new species, Petrotoga mobilis. It can be readily distinguished from P. miotherma by its motility.
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Bacillus pseudomycoides sp. nov.
More LessPrevious DNA relatedness studies showed that strains idnentified as Bacillus mycoides segregated into two genetically distinct yet phenotypically similar groups, one being B. mycoides sensu stricto and the other, an unclassified taxon. In the present study, the taxonomic position of this second group was assessed by measuring DNA relatedness and determining phenotypic characteristics of an increased number of B. mycoides strains. Also determined was the second group’s 16S RNA gene sequence. The 36 B. mycoides strains studied segregated into two genetically distinct groups sho wing DNA relatedness of about 30%; 18 strains represented the species proper and 18 the second group with intragroup DNA relatedness for both groups ranging from 70 to 100%. DNA relatedness to the type strains of presently recognized species with G+C contents of approximately 35 mol% (Bacillus alcalophilus, Bacillus cereus, Bacillus circulans, Bacillus lentus, Bacillus megaterium and Bacillus sphaericus) ranged from 22 to 37%. Although shown to be genetically distinct taxa, the two B. mycoides groups exhibited highly similar (98%) 16S RNA sequences. Phylogenetic analyses showed that both B. mycoides and the second group clustered closely with B. cereus. Although not distinguishable by physiological and morphological characteristics, the two B. mycoides groups and B. cereus were clearly separable based on fatty acid composition. The data established that the second B. mycoides group merits recognition as a new species for which the name Bacillus pseudomycoides is proposed. The type strain is NRRL B-617T.
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Pseudoalteromonas prydzensis sp. nov., a psychrotrophic, halotolerant bacterium from Antarctic sea ice
More LessSpecies of the genus Pseudoalteromonas are frequently isolated from marine ecosystems and appear to be particularly abundant in Antarctic coastal waters. Most Pseudoalteromon as strains isolated from sea ice and underlying seawater samples are phenotypically similar to the species Pseudoalteromonas antarctica and Pseudoalteromonas nigrifaciens. However, a minority of isolates were recognized by phenotypic, DNA-DNA hybridization and 16S rRNA-based phylogenetic studies to represent a distinct genospecies clustering at the periphery of the non-pigmented Pseudoalteromon as species clade. These strains are non-pigmented, halotolerant psychrotrophs that are capable of hydrolysing starch and chitin, and possess a DNA G+C content of 38-39 mol%. It is proposed that this group represents a novel species, Pseudoalteromon as prydzensis sp. nov., for which the type strain is ACAM 620T.
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Proposal of Craurococcus roseus gen. nov., sp. nov. and Paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil
More LessSequences of the 16S rRNA gene were determined for three strains of aerobic bacteriochlorophyll a-containing bacteria isolated from soil. The sequences of two strains (NS89Tand NS102) were identical for approximately 1500 nucleotides. Phylogenetic analysis revealed that the three strains belonged to the α-1 subclass of the Proteobacteria, constituting one line of descent. The three strains are comparatively related to Roseococcus thiosulfatophilus, which is an aerobic bacteriochlorophyll a-containing bacterium. The 16S rRNA gene sequence similarity and the DNA-DNA relatedness allow the proposal of two new genera, Craurococcus gen. nov. and Paracraurococcus gen. nov. The type species are Craurococcus roseus sp. nov. and Paracraurococcus ruber sp. nov., and their type strains are NS130T(=JCM 99331T) and NS89T(=JCM 9931T), respectively.
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Identification of Staphylococcus species by 16S-23S rDNA intergenic spacer PCR analysis
More LessTo investigate whether 16S-23S rDNA (rDNA) spacer region length polymorphisms are suitable for the identification of Staphylococcus strains, the 16S-23S rDNA intergenic spacer region lengths of 221 strains belonging to 31 species were studied by using a PCR-based method. Each species presented a specific 16S-23S pattern made of 1-8 fragments ranging from 104 to 771 bp, with the exception of the species Staphylococcus warneri, Staphylococcus caprae and Staphylococcus piscifermentans, which presented larger or smaller fragments. Very few species showed more than one pattern, Staphylococcus saprophytics subsp. saprophytics and Staphylococcus aureus being the most heterogeneous species (five different patterns for eight strains). Five clinical strains that could not be identified at the species level by phenotypical tests were finally identified using this method. Discrimination between some species that showed close patterns (Staphylococcus cohnii/Staphylococcus chromogenes/Staphylococcus equorum, Staphylococcus aureus/Staphylococcus intermedius, Staphylococcus sciuri/Staphylococcus pasteuri/Staphylococcus gallinarum, Staphylococcus delphini/Staphylococcus felis, Staphylococcus vitulus/Staphylococcus auricularis) was further achieved after Dral digestion of the PCR products. Although it does not allow discrimination of subspecies, the use of 16S-23S spacer region length data determined by PCR-mediated amplification is suitable for the identification of the 31 Staphylococcus species tested in this study. The method is rapid, easy and may be a useful tool for the identification of Staphylococcus species in the clinical microbiology laboratory.
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Characterization and reclassification of an aromatic- and chloroaromatic-degrading Pseudomonas sp., strain HV3, as Sphingomonas sp. HV3
More LessPhylogenetic analyses of 165 rRNA gene sequences showed that the Gramnegative aromatic- and chloroaromatic-degrading Pseudomonas sp. strain HV3 carrying the mega-plasmid pSKY4 belongs to the genus Sphingomonas. The 165rRNA sequence is most related to Sphingomonas chlorophenolica strains ATCC 33790T(98-5%) and SR3 (98.4%) and Sphingomonas sp. SS86 (98.4%). The G+C content was 64 mol%, and the DNA-DNA-hybridization-based relative homology of strain HV3 to the S. chlorophenolica ATCC 33790Tand S. chlorophenolica RA2 was 59.6% and 35.9%, respectively. The results showed that although strain HV3 is related to S. chlorophenolica it differs in certain characteristics. It is therefore proposed to reclassify Pseudomonas sp. strain HV3 as Sphingomonas sp. HV3.
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16S rDNA sequence variations of some Streptococcus suis serotypes
More LessStreptococcus suis 16S rDNA from selected serotypes has been sequenced and compared with the 16S rDNA sequences from serotypes 1 and 2 present in GenBank. After alignment the sequenced serotypes show clusters of variation. Based on these clusters, a limited phylogenetic tree showing the relationships of all of the serotypes was constructed.
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DNA sequencing reveals limited heterogeneity in the 16S rRNA gene from the rrnB operon among five Mycoplasma hominis isolates
More LessTo investigate the intraspecies heterogeneity within the 16S rRNA gene of Mycoplasma hominis, five isolates with diverse antigenic profiles, variable/identical P120 hypervariable domains, and different 16S rRNA gene RFLP patterns were analysed. The 16S rRNA gene from the rrnB operon was amplified by PCR and the PCR products were sequenced. Three isolates had identical 16S rRNA sequences and two isolates had sequences that differed from the others by only one nucleotide.
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Volumes and issues
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Volume 74 (2024)
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