- Volume 51, Issue 4, 2001
Volume 51, Issue 4, 2001
- Articles
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Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica.
More LessA psychrophilic, aerobic bacterium designated A2iT was isolated from marine sediment recovered from shallow waters surrounding Adelaide Island, Antarctica (67 degrees 34' S, 68 degrees 07' W). The organism exhibited xylanolytic and laminarinolytic activity and was halotolerant. Basic characterization showed that it was gram-negative, non-motile, yellow-pigmented (beta,beta-carotene-3,3'-diol) and positive for oxidase and catalase synthesis. Analysis of the 16S rDNA sequence suggests that the organism belongs to the Flexibacter-Cytophaga-Bacteroides phylum. On the basis of its 16S rDNA sequence, the bacterium is 96.8% similar to Flavobacterium columnare ATCC 43622--its closest relation. The genomic DNA G+C content was 35 mol%. Growth on xylan occurs optimally at 15 degrees C, though growth also occurs at 0 degrees C, and the doubling times are 9.6 and 34.8 h, respectively. The maximum growth temperature on xylan is at 24 degrees C. The bacterium is a neutrophile, growing across the pH range 5.6-8.4 and having an optimum at pH 7.5. Analysis of the 16S rDNA sequence, together with phenotypic characterization, suggests that the organism is a member of the genus Flavobacterium. DNA-DNA hybridization experiments have shown that it is a novel species; it is proposed, therefore, that the organism be designated as the type strain of Flavobacterium frigidarium sp. nov. (= ATCC 700810T = NCIMB 13737T).
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Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.
More LessA novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.
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Bordetella petrii sp. nov., isolated from an anaerobic bioreactor, and emended description of the genus Bordetella.
More LessA novel Bordetella species was isolated from an anaerobic, dechlorinating bioreactor culture enriched from river sediment. The only strain, Se-1111R(T) (= DSM 12804T = CCUG 43448T), for which the name Bordetella petrii is proposed, is designated the type strain of the novel species. Strain Se-1111R(T) was isolated from the dechlorinating mixed culture due to its ability to anaerobically reduce selenate to elemental selenium. Comparative 16S rDNA sequence analysis showed a close relationship between Se-1111R(T) and members of the genus Bordetella within the beta-Proteobacteria. This close phylogenetic relatedness was also reflected in several metabolic properties of Se-1111R(T), including its incapacity to utilize carbohydrates, by the high G+C content (63.8 mol%) of its DNA and by the presence of Q-8 as the major isoprenoid quinone. DNA-DNA hybridization experiments with type strains of all species of the genus Bordetella and closely related species Achromobacter xylosoxidans subsp. denitrificans provided further evidence for the assignment of strain Se-1111R(T) as a novel species of the genus Bordetella. This genus currently consists of seven aerobic species, all of which are known to occur in close pathogenic, opportunistic or possibly commensal relationships with various host organisms. B. petrii is the first member of this genus isolated from the environment and capable of anaerobic growth. The proposal of the novel species and an emended description of the genus Bordetella is presented.
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Description of Microbacterium foliorum sp. nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and the surface litter after mulching the sward, and reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens comb. nov..
U Behrendt, A Ulrich and P SchumannThe taxonomic position of a group of coryneform bacteria isolated from the phyllosphere of grasses and the surface litter after sward mulching was investigated. On the basis of restriction analyses of 16S rDNA, the isolates were divided into two genotypes. According to the 16S rDNA sequence analysis, representatives of both genotypes were related at a level of 99.2% similarity and clustered within the genus Microbacterium. Chemotaxonomic features (major menaquinones MK-12, MK-11 and MK-10; predominating iso- and anteiso-branched cellular fatty acids; G+C content 64-67 mol%; peptidoglycan-type B2beta with glycolyl residues) corresponded to this genus as well. DNA-DNA hybridization studies showed a reassociation value of less than 70% between representative strains of both subgroups, suggesting that two different species are represented. Although the extensive morphological and physiological analyses did not reveal any differentiating feature for the genotypes, differences in the presence of the cell-wall sugar mannose enabled the subgroups to be distinguished from one another. DNA-DNA hybridization with type strains of closely related Microbacterium spp. indicated that the isolates represent two individual species, which can also be differentiated from previously described species of Microbacterium on the basis of biochemical features. As a result of phenotypic and phylogenetic analyses, the species Microbacterium foliorum sp. nov., type strain P 333/02T (= DSM 12966T = LMG 19580T), and Microbacterium phyllosphaerae sp. nov., type strain P 369/06T (= DSM 13468T = LMG 19581T), are proposed. Furthermore, the reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens (Funke et al. 1998) comb. nov. is proposed.
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Streptococcus australis sp. nov., a novel oral streptococcus.
M D Willcox, H Zhu and K W KnoxStrains of streptococci were isolated from the mouths of children attending the United Dental Hospital, Sydney, Australia. These strains were analysed biochemically using the Rapid ID32 Strep microsystem, were subjected to DNA-DNA hybridization with other members of the oral streptococci and had their 165 rRNA analysed. On the basis of DNA-DNA hybridization, their nearest relative was Streptococcus parasanguinis, whereas, on the basis of 16S rRNA analysis, it was Streptococcus infantis. The name Streptococcus australis sp. nov. is proposed for the new species. The type strain is AI-1T (= ATCC 700641T = NCTC 13166T).
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Thalassomonas viridans gen. nov., sp. nov., a novel marine gamma-proteobacterium.
More LessA new genus and species are proposed for two halophilic, strictly aerobic, chemo-organotrophic, marine bacterial strains. These bacteria are gram-negative, motile rods isolated from oysters cultivated off the Mediterranean coast at Valencia (Spain). They produce green/blue-green diffusible pigment. The G+C content of the DNA of the proposed type strain (XOM25T) is 48.4 mol %. A 16S rRNA gene sequence analysis of the two strains has shown that the new isolates represent a branch within the gamma-Proteobacteria, close to the genus Colwellia. The type species of the new genus is Thalassomonas viridans gen. nov., sp. nov., with the type strain XOM25T (= CECT 5083T = DSM 13754T).
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Samsonia erythrinae gen. nov., sp. nov., isolated from bark necrotic lesions of Erythrina sp., and discrimination of plant-pathogenic Enterobacteriaceae by phenotypic features.
L Sutra, R Christen, C Bollet, P Simoneau and L GardanBacterial strains isolated from diseased erythrina (Erythrina sp.) trees in Martinique (French West Indies) were studied using phenotypic tests, 16S rDNA sequence analysis and DNA-DNA hybridization. Numerical analysis of phenotypic characteristics showed that these strains formed an homogeneous phenon among plant-pathogenic Enterobacteriaceae, and gave useful and updated information for the identification of these bacteria. Results of DNA-DNA hybridization indicated that strains from erythrina belonged to a discrete genomospecies (89-100% hybridization) and had low levels of DNA relatedness (2-33% hybridization) with reference strains of phytopathogenic Erwinia, Brenneria, Pectobacterium, Pantoea and Enterobacter species. 16S rDNA sequence analysis using three different methods revealed that the position of strain CFBP 5236T isolated from erythrina was variable in the different trees, so that strains from erythrina could not be assigned to any recognized genus. It is proposed that these strains are included in a new genus, Samsonia. The name Samsonia erythrinae is proposed for the new species. The G+C content of the DNA of the type strain, CFBP 5236T (= ICMP 13937T), is 57.0 mol%.
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Novel nitrogen-fixing acetic acid bacteria, Gluconacetobacter johannae sp. nov. and Gluconacetobacter azotocaptans sp. nov., associated with coffee plants.
Diazotrophic bacteria were isolated, in two different years, from the rhizosphere and rhizoplane of coffee (Coffea arabica L.) plants cultivated in Mexico; they were designated as type DOR and type SAd isolates. They showed characteristics of the family Acetobacteraceae, having some features in common with Gluconacetobacter (formerly Acetobacter) diazotrophicus, the only known N2-fixing species of the acetic acid bacteria, but they differed from this species with regard to several characteristics. Type DOR isolates can be differentiated phenotypically from type SAd isolates. Type DOR isolates and type SAd isolates can both be differentiated from Gluconacetobacter diazotrophicus by their growth features on culture media, their use of amino acids as nitrogen sources and their carbon-source usage. These results, together with the electrophoretic mobility patterns of metabolic enzymes and amplified rDNA restriction analysis, suggested that the type DOR and type SAd isolates represent two novel N2-fixing species. Comparative analysis of the 16S rRNA sequences revealed that strains CFN-Cf55T (type DOR isolate) and CFN-Ca54T (type SAd isolate) were closer to Gluconacetobacter diazotrophicus (both strains had sequence similarities of 98.3%) than to Gluconacetobacter liquefaciens, Gluconacetobacter sacchari (similarities < 98%) or any other acetobacteria. Strain CFN-Cf55T exhibited low levels of DNA-DNA reassociation with type SAd isolates (mean 42%) and strain CFN-Ca54T exhibited mean DNA-DNA reassociation of 39.5% with type DOR isolates. Strains CFN-Cf55T and CFN-Ca54T exhibited very low DNA reassociation levels, 7-21%, with other closely related acetobacterial species. On the basis of these results, two novel N2-fixing species are proposed for the family Acetobacteraceae, Gluconacetobacter johannae sp. nov. (for the type DOR isolates), with strain CFN-Cf55T (= ATCC 700987T = DSM 13595T) as the type strain, and Gluconacetobacter azotocaptans sp. nov. (for the type SAd isolates), with strain CFN-Ca54T (= ATCC 70098ST = DSM 13594T) as the type strain.
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DNA-DNA hybridization study of Bradyrhizobium strains.
More LessDNA-DNA hybridizations were performed between Bradyrhizobium strains, isolated mainly from Faidherbia albida and Aeschynomene species, as well as Bradyrhizobium reference strains. Results indicated that the genus Bradyrhizobium consists of at least 11 genospecies, I to XI. The genospecies formed four subgeneric groups that were more closely related to each other (>40% DNA hybridization) than to other genospecies (<40% DNA hybridization): (i) genospecies I (Bradyrhizobium japonicum), III (Bradyrhizobium liaoningense), IV and V; (ii) genospecies VI and VIII; (iii) genospecies VII and IX; and (iv) genospecies II (Bradyrhizobium elkanii), X and XI. Photosynthetic Aeschynomene isolates were found to belong to at least two distinct genospecies in one subgeneric group. DNA-DNA hybridization data are compared with data from amplified fragment length polymorphism analysis and 165-23S rDNA spacer sequence analysis.
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Actinomyces suimastitidis sp. nov., isolated from pig mastitis.
More LessAn unusual Actinomyces-like bacterium originating from a pig with mastitis was subjected to a polyphasic taxonomic investigation. The morphological and biochemical characteristics of the organism were consistent with its preliminary assignment to the genus Actinomyces but it did not appear to correspond to any recognized species. PAGE analysis of whole-cell proteins confirmed the phenotypic distinctiveness of the bacterium and 16S rRNA gene sequence analysis demonstrated that it represents a hitherto unknown sub-line amongst a cluster of Actinomyces species which embraces Actinomyces canis, Actinomyces georgiae, Actinomyces hyovaginalis, Actinomyces meyeri, Actinomyces odontolyticus, Actinomyces radingae and Actinomyces turicensis. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium isolated from pig mastitis be classified as Actinomyces suimastitidis sp. nov. The type strain of Actinomyces suimastitidis is CCUG 39279T (= CIP 106779T).
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Thermosipho geolei sp. nov., a thermophilic bacterium isolated from a continental petroleum reservoir in Western Siberia.
Three strictly anaerobic, thermophilic bacteria (SL31T, SL30 and MLM39636) were isolated from a deep continental oil reservoir in Western Siberia (Russia). Following the mid-exponential phase of growth, the non-motile rod-shaped organisms were surrounded by a sheath-like structure. As DNA-DNA hybridizations showed that these strains were highly related genomically, only strain SL31T was studied in detail. The temperature range for growth of strain SL31T was between 45 and 75 degrees C, with optimum growth at 70 degrees C. Its optimum pH and NaCl concentration for growth were pH 7.5 and 20-30 g l(-1), respectively. The novel isolate reduced elemental sulfur and cystine, but not thiosulfate or sulfate, to hydrogen sulfide. The G+C content of the genomic DNA was 30.0 mol %. As determined by 16S rDNA sequence analysis, this organism belonged to the genus Thermosipho. DNA-DNA hybridization levels between strain SL31T and type strains of the previously described species of Thermosipho were less than 10%. On the basis of physiological and molecular properties, it is proposed that this organism should be placed in a new species, Thermosipho geolei sp. nov. The novel organism represents the first species of the genus Thermosipho that has been isolated from a petroleum reservoir. The type strain is SL31T ( = DSM 13256T = JCM 10986T).
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Thermoanaerobacter tengcongensis sp. nov., a novel anaerobic, saccharolytic, thermophilic bacterium isolated from a hot spring in Tengcong, China.
More LessA new, extremely thermophilic bacterium, designated strain MB4T, was isolated from a Chinese hot spring. The new isolate was an obligately anaerobic, rod-shaped, gram-negative, saccharolytic bacterium. Spore formation was not observed. Growth occurred at temperatures between 50 and 80 degrees C, with an optimum of around 75 degrees C; at pH values between 5.5 and 9.0, with an optimum of 7.0-7.5; and at salinities between 0 and 2.5% NaCl, with an optimum of around 0.2% NaCl. The organism utilized glucose, galactose, maltose, cellobiose, mannose, fructose, lactose, mannitol and starch. Acetate was the main end product from glucose fermentation. Thiosulfate and sulfur were reduced to hydrogen sulfide. Sulfate, sulfite and nitrate were not reduced. Growth was inhibited by hydrogen. The G+C content of the DNA was 33 mol%. Phylogenetic analyses based on the 16S rDNA sequence indicated that the isolate was a new member of the genus Thermoanaerobacter and formed a monophyletic unit within the Thermoanaerobacter cluster. Based on its phenotypic and phylogenetic characteristics, the isolate was proposed as a new species, Thermoanaerobacter tengcongensis. The type strain is MB4T (= Chinese Collection of Microorganisms AS 1.2430T = JCM 11007T).
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Comparative ribotyping of Staphylococcus intermedius isolated from members of the Canoidea gives possible evidence for host-specificity and co-evolution of bacteria and hosts.
More LessA total of 41 Staphylococcus intermedius isolates were isolated from skin of healthy members of six phylogenetic groups within the Canoidea (the dog family, skunk subfamily, weasel subfamily, racoon family, red panda and bear family) of different geographical origin and compared by EcoRI ribotyping and cluster analysis. The S. intermedius isolates from the different families and subfamilies clustered together in separate groups, almost completely following the phylogenetic relationship of the animal hosts. These ribotype data indicate host-specificity of different types of S. intermedius and suggest co-evolution between the animal hosts within the Canoidea and S. intermedius.
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Corynebacterium testudinoris sp. nov., from a tortoise, and Corynebacterium felinum sp. nov., from a Scottish wild cat.
More LessTwo unknown gram-positive, rod-shaped bacteria isolated from a tortoise and a Scottish wild cat were subjected to a polyphasic taxonomic analysis. Chemical analysis revealed the presence of straight-chain and monounsaturated fatty acids and short-chain mycolic acids in the two isolates consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing confirmed that the unknown isolates were members of the genus Corynebacterium, with the two organisms displaying greater than 3% sequence divergence from each other and from established species of the genus. The unknown Corynebacterium isolates were readily distinguished from each other and from all recognized species of the genus by biochemical tests. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown organisms from a tortoise and a cat be classified in the genus Corynebacterium as Corynebacterium testudinoris sp. nov. and Corynebacterium felinum sp. nov., respectively. The respective type strains of C. testudinoris and C. felinum are CCUG 41823T and CCUG 39943T.
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Phylogeny of Rickettsia spp. inferred by comparing sequences of 'gene D', which encodes an intracytoplasmic protein.
Z Sekeyova, V Roux and D Raoult'Gene D' is the PS120-protein-encoding gene, first described in Rickettsia conorii and Rickettsia japonica. Sequence analysis of a 3030 bp fragment of 'gene D' in 24 representatives of the genus Rickettsia was carried out to complete phylogenetic analyses previously inferred by comparison of gene sequences encoding citrate synthase, 17 kDa antigen and rOmpA and rOmpB. The phylogenetic relationships between rickettsiae were inferred from the comparison of both the gene and the derived protein sequences, using the parsimony, neighbour-joining and maximum-likelihood methods. Five distinct groups of rickettsiae were identified. These were: the Rickettsia massiliae group, including R. massiliae, Bar 29, Rickettsia rhipicephali and Rickettsia aeschlimannii; the Rickettsia rickettsii group containing Rickettsia sibirica, 'Rickettsia mongolotimonae', Rickettsia parkeri, strain S, Rickettsia africae, the R. conorii complex, Rickettsia slovaca, Rickettsia honei, R. rickettsii, R. japonica and Rickettsia montanensis; the group currently containing only Rickettsia helvetica; the Rickettsia akari group including Rickettsia australis, R. akari and the ELB agent; Rickettsia prowazekii and Rickettsia typhi clustered in the typhus group. As significant bootstrap values were obtained for most of the nodes, sequence comparison of 'gene D' should be considered as a complementary approach in phylogenetic studies of rickettsiae.
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Simplified technique for identification of the aerobic spore-forming bacteria by phenotype.
More LessThe use of modern research approaches of genetics, biochemistry and molecular biology has led to progress in bacterial taxonomy. Systematic study of the aerobic spore-forming bacteria has resulted in the realignment of the genus Bacillus into several new genera. In the meantime, the identification process has become more difficult for the non-specialist in Bacillus taxonomy. This paper presents a key for the simplified phenotypic identification of the mesophilic, aerobic, spore-forming bacteria belonging to the genera Bacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Geobacillus and Virgibacillus. A total of 81 species were included and 115 morphological and physiological tests were analysed for their discriminative efficiency. This key is practical for rough but quick identification of aerobic spore-forming bacteria isolated from nature. Such preliminary identification will be helpful for the selection of reference strains and methods for more precise identification using the newest techniques. The reliability of the proposed identification key was tested on 100 cultures from the Ukrainian Collection of Microorganisms. The developed identification key is represented in interactive mode on a website (http://www/imv.kiev.ua/key/).
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Propionibacterium microaerophilum sp. nov., a microaerophilic bacterium isolated from olive mill wastewater.
More LessA new gram-positive, facultative anaerobic, microaerophilic bacterium, designated strain M5T, was isolated from a decantation reservoir of olive mill wastewater. The cells were rod-shaped, non-motile, non-spore-forming and catalase-negative. Growth occurred at pH ranging from 4.5 to 9.5, with optimum growth at 7.0. The optimum temperature for growth was around 30 degrees C. Although growth occurred under anaerobic and aerobic conditions, the optimum O2 concentration for growth was determined as 5% in the gas phase of the culture. During anaerobic growth, glucose or lactate were mainly fermented to propionate, acetate and CO2. In the presence of O2 (more than 2%), glucose was oxidized completely to CO2. The G+C content of the DNA was 67.7+/-0.6 mol% and 16S rRNA gene analysis revealed that the new isolate belonged to the cluster of 'dairy' propionibacteria, Propionibacterium acidipropionici being its closest phylogenic relative (97.5% similarity). However, the level of DNA relatedness between strain M5T and P. acidipropionici was 56.2%. Consequently, both the phenotypic (range of substrates used) and genotypic characteristics of strain M5T allow it to be assigned as a new species of the genus Propionibacterium, Propionibacterium microaerophilum sp. nov. The type strain is strain M5T (= CNCM I-2360T = DSM 13435T).
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Vibrio shiloi sp. nov., the causative agent of bleaching of the coral Oculina patagonica.
More LessThe aetiological agent of bleaching of the coral Oculina patagonica was characterized as a new Vibrio species on the basis of 16S rDNA sequence, DNA-DNA hybridization data and phenotypic properties, including the cellular fatty acid profile. Based on its 16S rDNA and DNA-DNA hybridization, the new Vibrio species is closely related to Vibrio mediterranei. The name Vibrio shiloi sp. nov. is proposed for the new coral-bleaching species, the type strain being AK1T (= ATCC BAA-91T = DSM 13774T).
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Phylogeny of the seal mycoplasmas Mycoplasma phocae corrig., Mycoplasma phocicerebrale corrig. and Mycoplasma phocirhinis corrig. based on sequence analysis of 16S rDNA.
More LessThe nucleotide sequences of the 16S rRNA genes from the type strains of three seal mycoplasmas, Mycoplasma phocicerebrale, Mycoplasma phocae and Mycoplasma phocirhinis (formerly Mycoplasma phocacerebrale, Mycoplasma phocidae and Mycoplasma phocarhinis, respectively), were determined by direct DNA cycle sequencing. Polymorphisms were found in all three 16S rRNA gene sequences, showing the existence of two different rRNA operons. In M. phocae, a length difference was found between the operons, caused by an insertion or a deletion of an adenosine in one of the operons. The sequence information was used to construct phylogenetic trees. All three species were found to belong to the hominis group, but to different clusters. M. phocicerebrale and M. phocae were found to be members of the Mycoplasma hominis cluster, within which M. phocicerebrale grouped in the Mycoplasma alkalescens subcluster. M. phocirhinis was found to be a member of the Mycoplasma bovigenitalium subcluster of the Mycoplasma bovis cluster. The 16S rRNA gene sequences of all hitherto validly described species within the M. hominis and M. bovis clusters have now been determined.
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A physical and genetic map of the Mycoplasma flocculare ATCC 27716 chromosome reveals large genomic inversions when compared with that of Mycoplasma hyopneumoniae strain J(T).
W A Blank and G W StemkePulsed-field gel electrophoresis and DNA hybridization data were used to construct a chromosomal map of Mycoplasma flocculare ATCC 27716, a non-pathogenic inhabitant of porcine respiratory tracts. Twenty-one genetic markers were placed on the map. Comparison of the genetic map with that of the closely related Mycoplasma hyopneumoniae strain J(T), the type strain of the causative agent of enzootic pneumonia in pigs, identified three chromosomal inversions that differentiate these genomes. One of these inversions involves genes that possibly may be involved in M. hyopneumoniae pathogenicity.
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Facklamia miroungae sp. nov., from a juvenile southern elephant seal (Mirounga leonina).
More LessAn unusual gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped organism that originated from a juvenile elephant seal was characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the unknown coccus represents a new subline within the genus Facklamia. The unknown strain was readily distinguishable from all currently recognized species of the genus Facklamia (Facklamia hominis, Facklamia languida, Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis) by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Facklamia miroungae sp. nov. The type strain of F. miroungae is CCUG 42728T (= CIP 106764T). F. miroungae is the first member of the genus Facklamia to be isolated from an animal other than man.
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Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.
M Takeuchi, K Hamana and A HiraishiPhylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus Sphingomonas can be divided into four clusters. Some chemotaxonomic and phenotypic differences were noted among these clusters. Three new genera, Sphingobium, Novosphingobium and Sphingopyxis, are proposed in addition to the genus Sphingomonas sensu stricto. The genus Sphingobium is proposed to accommodate Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae. The genus Novosphingobium is proposed for Sphingomonas aromaticivorans, Sphingomonas capsulata, Sphingomonas rosa, Sphingomonas stygia, Sphingomonas subarctica and Sphingomonas subterranea. Sphingomonas macrogoltabidus and Sphingomonas terrae are reclassified in the genus Sphingopyxis. The type species of Sphingobium, Novosphingobium and Sphingopyxis are Sphingobium yanoikuyae, Novosphingobium capsulatum and Sphingopyxis macrogoltabida, respectively.
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Nocardia cyriacigeorgici sp. nov..
More LessChemotaxonomic and 16S rRNA gene sequence analyses of an isolate from the bronchial secretions of a patient with chronic bronchitis demonstrated clearly that it belongs to the genus Nocardia. The 16S rRNA gene sequence data, as well as the biochemical characteristics of the isolate, indicated that it belongs to a new species that differs from previously described members of the genus Nocardia. The name Nocardia cyriacigeorgici sp. nov. is proposed for this isolate, and is represented by strain IMMIB D-1627T (= DSM 44484T).
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Hydrogenobacter subterraneus sp. nov., an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water.
K Takai, T Komatsu and K HorikoshiA novel extreme thermophile was isolated from a water sample derived from a deep subsurface geothermal water pool at a depth of 1500 m in the Hacchoubaru geothermal plant in Oita Prefecture, Japan. The cells were found to be straight rods, each being motile by means of a polar flagellum. Growth was observed at temperatures between 60 and 85 degrees C (optimum 78 degrees C; 120 min doubling time) and between pH 5.5 and pH 9.0 (optimum 7.5). The isolate was a strictly aerobic heterotroph capable of utilizing a number of substrates such as yeast extract, peptone, tryptone, various carbohydrates, sugars, amino acids and organic acids. Elemental sulfur, thiosulfate, sulfide or cysteine-hydrochloride was required as an electron donor for growth. Hydrogen gas did not support growth. The G+C content of the genomic DNA was 44.7 mol%. Phylogenetic analysis based on 16S rDNA sequences and DNA-DNA hybridization analysis indicated that the isolate was closely related to members of the hydrogen-oxidizing, autotrophic and thermophilic genera Hydrogenobacter and Calderobacterium. However this isolate was differentiated from the previously described species of these genera on the basis of the physiological and molecular properties of the new isolate. The name Hydrogenobacter subterraneus sp. nov. is proposed; the type strain is HGP1T (= JCM 10560T = IFO 16485T).
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Nonomuraea dietzii sp. nov..
More LessThe taxon 'Sebekia benihana', an actinomycete of industrial significance, has been subjected to a polyphasic taxonomic study. 16S rDNA sequence analyses of strain DSM 44320 (= NRRL 11111) revealed 100% similarity to the 16S rDNA sequence of Nonomuraea roseola DSM 43767T and high values (>98.5%) to some other species of this genus. DNA-DNA similarity values of less than 31% observed between strain DSM 44320 and N. roseola DSM 43767T, Nonomuraea recticatena DSM 43937T and Nonomuraea africana DSM 43748T indicate that this strain represents an individual genospecies. Differences between strain DSM 44320T and the 16 validly described Nonomuraea species occur in the primary structure of the 16S rDNA, the physiological test profile, the morphology of mycelium and the spore surface and the colour of substrate mycelium. The only strain of 'S. benihana', DSM 44320T (= NRRL 11111T), is proposed as the type strain of a new species of the genus Nonomuraea, Nonomuraea dietzii sp. nov..
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Transfer of Halomonas canadensis and Halomonas israelensis to the genus Chromohalobacter as Chromohalobacter canadensis comb. nov. and Chromohalobacter israelensis comb. nov..
More Less16S rRNA gene sequence comparisons and DNA-DNA hybridization data support the conclusion that two species previously described as members of the genus Halomonas, Halomonas israelensis and Halomonas canadensis, should be placed in the genus Chromohalobacter. Both H. israelensis ATCC 43985T (= Ba1T) and H. canadensis ATCC 43984T (= NRCC 41227T) have been used extensively for physiological studies for many years; nevertheless, they were not named and classified taxonomically until quite recently. Their phenotypic resemblance (at least 65% Jaccard similarity) to some members of the genus Halomonas and the degree of DNA-DNA relatedness (lower than 60%) to other described species of this genus permitted the conclusion that they were distinct species belonging to the genus Halomonas. In this study, the 16S rDNA of both species has been sequenced completely and found to share higher similarity to the available sequences of the moderately halophilic bacterium Chromohalobacter marismortui than to sequences of members of the genus Halomonas. C. marismortui is the sole species of the genus Chromohalobacter, also included in the family Halomonadaceae, and shares many phenotypic features with H. canadensis and H. israelensis. It is proposed that the two species should be renamed as Chromohalobacter canadensis comb. nov. and Chromohalobacter israelensis comb. nov. An emended description of the genus Chromohalobacter is given in order to include the features of these two species.
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Vibrio lentus sp. nov., isolated from Mediterranean oysters.
More LessTwelve phenotypically similar marine bacteria have been studied by means of ribotyping, DNA-DNA hybridization and cultural and physiological characterization. Phylogenetic analysis has been performed of the 16S and 23S rRNA genes of two representative strains. Phylogenetically, they belong to the Vibrio/Photobacterium branch of the gamma-Proteobacteria and they share all of the properties that define the genus Vibrio. The strains represent a new Vibrio species that is phenotypically similar to Vibrio splendidus. However, resistance to the vibriostatic agent 0129 and production of acid from several carbohydrates allow differentiation between V. splendidus and the proposed new species. The DNA G+C content of the proposed type strain is 44.0 mol %. The name Vibrio lentus sp. nov. is proposed for the new species and strain 40M4T (= CECT 5110T = DSM 13757T) is the type strain.
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Chromohalobacter salexigens sp. nov., a moderately halophilic species that includes Halomonas elongata DSM 3043 and ATCC 33174.
More LessTwo strains that were originally isolated and characterized as members of the moderately halophilic species Halomonas elongata, strains DSM 3043 (= 1H11) and ATCC 33174 (= 1H15), were studied in detail. Their complete 16S rRNA sequences were determined and, when compared to sequences available from the databases, they showed a close phylogenetic relationship to Chromohalobacter marismortui. In addition, DNA-DNA hybridization experiments showed that both strains are members of the same species, but their DNA relatedness to the type strains of Halomonas elongata, ATCC 33173T, and Chromohalobacter marismortui, ATCC 17056T, is very low. Phenotypically, the two strains showed very similar features, related to those of Chromohalobacter, but clear differences were found between these two strains and Chromohalobacter marismortui. On the basis of these data, it is proposed that Halomonas elongata DSM 3043 and ATCC 33174 should be included in a new species of the genus Chromohalobacter, Chromohalobacter salexigens sp. nov. The type strain is DSM 3043T (= ATCC BAA-138T = CECT 5384T = CCM4921T = CIP106854T = NCIMB 13768T).
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Limnobacter thiooxidans gen. nov., sp. nov., a novel thiosulfate-oxidizing bacterium isolated from freshwater lake sediment.
More LessTwo novel thiosulfate-oxidizing strains were isolated from sediment of the littoral zone of a freshwater lake (Lake Chiemsee, Bavaria, Germany). The new isolates, designated CS-K1 and CS-K2T, were gram-negative, slightly curved rods with pointed ends that were motile by means of single polar flagella. Both strains were obligately aerobic and grew on a variety of organic substrates, but not autotrophically. The utilization of thiosulfate led to an increase in the growth yield, indicating that these strains were able to grow chemolithoheterotrophically by oxidation of thiosulfate to sulfate. The optimum thiosulfate concentrations for growth were determined to be 10 mM for strain CS-K1 and 20 mM for strain CS-K2T. Phylogenetically, both strains were affiliated to the beta-Proteobacteria. Their characterization by a polyphasic approach resulted in the placement of both strains into a single species that is related only distantly to any known type species. Thus, the creation of a novel taxon is proposed, with the name Limnobacter thiooxidans gen. nov., sp. nov., to include the novel strains. In addition, the phylogenetic position of the chemolithoheterotrophic strain 'Thiobacillus' Q was determined.
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Description of Tropheryma whipplei gen. nov., sp. nov., the Whipple's disease bacillus.
More LessA detailed characterization was performed of the Whipple's disease bacillus, strain Twist-MarseilleT, isolated from the cardiac valve of a patient with Whipple's disease bacillus endocarditis. This strain was isolated and maintained on human embryonic lung fibroblast monolayers, but could not be cultivated in the absence of living eukaryotic cells. Two morphological forms were observed, with differing staining properties; an intracellular form with intact and degenerating bacteria within vacuoles of infected cells and an extracellular form with masses of bacteria embedded in an extracellular matrix. Determination of the DNA G+C content confirmed that it belongs to the high-G+C gram-positive bacteria. Strain Twist-MarseilleT (= CNCM I-2202T) is proposed as the type strain of a new species within a new genus, Tropheryma whipplei gen. nov., sp. nov., that was provisionally created solely on the basis of 16S rRNA gene sequence data.
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Burkholderia ambifaria sp. nov., a novel member of the Burkholderia cepacia complex including biocontrol and cystic fibrosis-related isolates.
More LessA polyphasic taxonomic study, including amplified fragment length polymorphism (AFLP) fingerprinting, DNA-DNA hybridizations, DNA base-ratio determinations, phylogenetic analysis, whole-cell fatty acid analyses and an extensive biochemical characterization, was performed on 19 Burkholderia cepacia-like isolates from the environment and cystic fibrosis (CF) patients. Several of the environmental isolates have attracted considerable interest due to their biocontrol properties. The polyphasic taxonomic data showed that the strains represent a new member of the B. cepacia complex, for which the name Burkholderia ambifaria sp. nov. is proposed. The type strain is strain LMG 19182T. B. ambifaria can be differentiated from the other members of the B. cepacia complex by means of AFLP fingerprinting, whole-cell fatty acid analysis, biochemical tests (including ornithine and lysine decarboxylase activity, acidification of sucrose and beta-haemolysis) and a newly developed recA gene-based PCR assay. 16S rDNA-based RFLP analysis and PCR tests allowed differentiation of B. ambifaria from Burkholderia multivorans, Burkholderia vietnamiensis and B. cepacia genomovar VI, but not from B. cepacia genomovars I and III and Burkholderia stabilis. The finding that this new taxon includes both strains isolated from CF patients and potentially useful biocontrol strains supports the general consensus that the large-scale use of biocontrol strains belonging to the B. cepacia complex would be ill-advised until more is known about their potential pathogenic mechanisms.
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Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water.
More LessThe taxonomic status of four strains from several mineral water sources in Taejon, Korea, was examined. The DNA base compositions of these strains ranged from 62 to 66 mol %. All of the strains contained sphingolipids and ubiquinone 10 as the main respiratory quinone. The cellular fatty acids of these strains included octadecenoic acid, hexadecanoic acid and 2-hydroxymyristic acid, without 3-hydroxy fatty acids. On the basis of morphological, physiological and chemotaxonomic characteristics, together with 16S rDNA sequence comparison and DNA-DNA reassociation data, three new species of the genus Sphingomonas are proposed for the strains isolated from natural mineral water: Sphingomonas aquatilis sp. nov. for strain JSS7T (= KCTC 2881T = KCCM 41067T), Sphingomonas koreensis sp. nov. for strains JSS26T (= KCTC 2882T = KCCM 41069T) and JSS28 (= KCTC 2883 = KCCM 41066) and Sphingomonas taejonensis sp. nov. for strain JSS54T (= KCTC 2884T = KCCM 41068T).
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Pseudoalteromonas ulvae sp. nov., a bacterium with antifouling activities isolated from the surface of a marine alga.
More LessA dark-purple marine bacterium that inhibits the germination of marine algal spores and the settlement of invertebrate larvae has been characterized and assessed for taxonomic assignment. Two strains, designated UL12T and UL13, were isolated from the surface of the common marine alga Ulva lactuca. Based on 16S rDNA sequencing, UL12T and UL13 were found to show the highest similarity (97%) to members of the genus Pseudoalteromonas. DNA-DNA hybridization studies demonstrated less than 28% genomic DNA relatedness between these isolates and closely related Pseudoalteromonas species and greater than 65% homology between UL12T and UL13. The two isolates were found to display identical characteristics and are strict aerobes, motile by means of single polar flagella, exhibit non-fermentative metabolism and require sodium ions for growth. The isolates hydrolyse gelatin and can utilize citrate, maltose, mannose and glucose but not trehalose, sucrose, fructose, lactose or glycerol as sole carbon sources. The molecular evidence together with the phenotypic characteristics show that this bacterium constitutes a new species within the genus Pseudoalteromonas. The name Pseudoalteromonas ulvae sp. nov. is proposed for this bacterium and the type strain is UL12T (= UNSW 095600T = NCIMB 13762T).
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Pseudonocardia kongjuensis sp. nov., isolated from a gold mine cave.
More LessThe taxonomic position of an isolate that was recovered from a gold mine cave near Kongju, Republic of Korea, was determined by 16S rDNA sequence studies and chemotaxonomic characterization. Comparative studies of 16S rDNA sequences indicated that this organism was phylogenetically related to members of the genus Pseudonocardia, branching outside a cluster encompassing Pseudonocardia autotrophica and Pseudonocardia compacta. The affiliation to the genus was also supported by the cell chemistry, which was represented by a type IV cell wall, MK-8(H4) as the major menaquinone, a phospholipid type PIII pattern (phosphatidylcholine as a diagnostic phospholipid) and a DNA G+C content of 71 mol%. The fatty acid profile contained saturated, unsaturated and 10-methyl branched fatty acids, but tuberculostearic acid and hydroxy fatty acids were not present. The isolate differed from its phylogenetic neighbours in the presence of phosphatidylethanolamine, dodecanoate, 16-methylheptadecenoate and 16-methylheptadecanoate and the absence of phosphatidylinositol mannoside and phosphatidylmethylethanolamine. The unique combination of physiological properties, the cellular fatty acid profile and DNA-DNA hybridization data indicates that this organism is readily differentiated from the type strains of all of the validly published species of the genus Pseudonocardia. The name Pseudonocardia kongjuensis sp. nov. is proposed for the type strain, LM 157T (= IMSNU 50583T = KCTC 9990T = DSM 44525T).
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Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium.
More LessA bacterial strain, JG07T, isolated from the Korean traditional fermented seafood jeotgal, was subjected to a polyphasic taxonomic study. Cells of strain JG07T are cocci or short rods in the early growth phase but change to rods as the cultures age. The peptidoglycan type is A4alpha, based on L-Lys-D-Glu. The menaquinone profile is characterized by the predominance of MK-8 followed by MK-7 and MK-6. The cellular fatty acid profile contains major amounts of saturated, unsaturated and branched fatty acids. The cellular phospholipids are phosphatidylethanolamine, phosphatidylglycerol and bisphosphatidylglycerol. The G+C content of the DNA is 47 mol%. Phylogenetic analysis showed that strain JG07T forms a cluster with Planococcus okeanokoites and Planococcus mcmeekinii, and the relationship between this cluster and two other Planococcus species described previously is supported by bootstrap analysis at a confidence level of 100%. The 16S-23S internally transcribed spacer (ITS) sequence similarity and DNA-DNA relatedness values between strain JG07T and the type strains of other Planococcus species are in the range 74.6-83.2% and 10.4-20.5%, respectively. On the basis of the phenotypic and phylogenetic data and the genomic distinctiveness, strain JG07T is considered to represent a new genus and a new species, for which the name Planomicrobium koreense gen. nov., sp. nov. is proposed. It is also proposed that Planococcus okeanokoites and Planococcus mcmeekinii be transferred to the new genus Planomicrobium as Planomicrobium okeanokoites and Planomicrobium mcmeekinii, respectively.
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Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus.
More LessMembers of genus Peptostreptococcus have previously been found to be distantly related to the type species, Peptostreptococcus anaerobius, on the basis of 16S rDNA sequence similarities. They were divided into three major phylogenetic groups, and their peptidoglycan structure and biochemical traits differed between groups. The reclassification of the species of these three groups into three new genera, Peptoniphilus gen. nov., Anaerococcus gen. nov. and Gallicola gen. nov., is proposed. The genus Peptoniphilus gen. nov. includes the following butyrate-producing, non-saccharolytic species that use peptone and amino acids as major energy sources: Peptoniphilus asaccharolyticus comb. nov. (type species), Peptoniphilus lacrimaris comb. nov., Peptoniphilus harei comb. nov., Peptoniphilus indolicus comb. nov. and Peptoniphilus ivorii comb. nov. The genus Anaerococcus gen. nov. contains the saccharolytic, butyrate-producing species Anaerococcus prevotii comb. nov. (type species), Anaerococcus tetradius comb. nov., Anaerococcus lactolyticus comb. nov., Anaerococcus hydrogenalis comb. nov., Anaerococcus vaginalis comb. nov. and Anaerococcus octavius sp. nov. The genus Gallicola gen. nov. contains a single species, Gallicola barnesae comb. nov.
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Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere.
M Takeuchi and K HatanoThe taxonomic positions of four strains isolated from the mangrove rhizosphere were studied by a polyphasic approach using phenotypic, chemotaxonomic and genetic methods. The four isolates contain 2,4-diaminobutyric acid in their peptidoglycan, and rhamnose as the major cell wall sugar. The predominant menaquinones are MK-12 and MK-11. The predominant cellular fatty acids are iso-C16:0, anteiso-C15:0 and/or anteiso-C17:0. The G+C content of the DNA ranges from 70.0 to 73.3 mol%. The four strains formed a coherent cluster with Agromyces species in a phylogenetic inference based on 16S rDNA sequences. Interestingly, the four isolates grew well in the presence of 5% NaCl. The differences in some phenotypic and chemotaxonomic characteristics, 16S rDNA sequence similarity data and DNA-DNA relatedness data indicate that the four isolates represent three new species in the genus Agromyces, for which are proposed the names Agromyces luteolus for strain 8T (IFO 16235T = VKM Ac-2085T), Agromyces bracchium for strain 65T (IFO 16238T = VKM Ac-2088T) and Agromyces rhizospherae for strains 14T (IFO 16236T = VKM Ac-2086T) and 58(5) (IFO 16237 = VKM Ac-2087).
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Thermoanaerobacter yonseiensis sp. nov., a novel extremely thermophilic, xylose-utilizing bacterium that grows at up to 85 degrees C.
B C Kim, R Grote, D W Lee, G Antranikian and Y R PyunA novel strictly anaerobic, extremely thermophilic, spore-forming and xylose-utilizing bacterium, designated strain KB-1TP (type and patent strain), was isolated from a geothermal hot stream at Sileri on Java island, Indonesia. The cells were rod-shaped, motile and had terminal spores. The newly isolated strain stained gram-positive and the cells occurred singly or in pairs during the exponential growth phase. The temperature optimum for growth was 75 degrees C and growth occurred in the range 50-85 degrees C. The pH range for growth was 4.5-9.0, with an optimum at pH 6.5. Strain KB-1TP grew chemo-organotrophically by fermenting a wide range of substrates such as glucose, fructose, D-xylose, lactose, maltose, sucrose, mannose, galactose, cellobiose, pullulan and soluble starch. Arabinose, xylan, cellulose, olive oil and Tween 80 were not fermented. The predominant fermentation end products after growth on glucose were lactate, acetate, ethanol, CO2 and small amounts of isovaleric acid, butyric acid, propionic acid, 1-pentanol and 2-propanol. Thiosulfate was reduced to H2S. Strain KB-1TP was sensitive to tetracycline, chloramphenicol, penicillin G, neomycin, kanamycin, vancomycin and rifampicin at concentrations of 100 microg ml(-1). No effect was observed with chloramphenicol and neomycin at concentrations of 10 microg ml(-1). This indicates that strain KB-1TP belongs to the bacterial domain. The G+C content of the DNA was 37 mol%. The comparison of the 165 rDNA sequence to that of closely related strains revealed that strain KB-1TP belonged to clostridial cluster V, showing highest sequence identities (92.7%) to members of the genus Thermoanaerobacter. Taking into account the physiological and molecular properties of the new isolate, it is proposed that strain KB-1TP should be classified as a new species of the genus Thermoanaerobacter, designated Thermoanaerobacter yonseiensis. The type strain, KB-1TP, has been deposited in the Korean Federation of Culture Collections (KFCC 11116P) as a patent strain and in the Deutsche Sammlung von Mikroorganismen und Zellkulturen as a type strain (= DSM 13777T).
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Pseudomonas kilonensis sp. nov., a bacterium isolated from agricultural soil.
More LessA total of 131 bacterial isolates related to Pseudomonas corrugata were obtained from an agricultural soil from northern Germany. Based on 16S rRNA gene sequences, PCR-based genome fingerprinting and multilocus enzyme electrophoresis, they formed two groups, A (119 strains) and B (12 strains). As members of each group were highly similar, a single strain of each group was subsequently characterized by a polyphasic taxonomic approach. The selected member of group A was identified as a strain of Pseudomonas brassicacearum, whereas the selected member of group B was distinct from other species of the genus Pseudomonas. Although DNA-DNA hybridization suggested a close affiliation of the group B strain with P. brassicacearum and Pseudomonas thivervalensis and ribotyping suggested a close affiliation with P. brassicacearum, RAPD data, 16S rRNA gene sequencing and phenotypic characterization indicated the presence of a distinct taxonomic entity. This strain differed from the type strains of P. thivervalensis and P. brassicacearum in 10 and 12 metabolic properties, respectively, whereas the two organisms differ from one another by only two properties. Strains of group B are therefore considered to be members of a new species, for which the name Pseudomonas kilonensis sp. nov. is proposed. The type strain is strain 520-20T (= DSM 13647T = CFBP 5372T).
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Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
More LessThe genus Bartonella comprises two human-specific pathogens and a growing number of zoonotic or animal-specific species. Domesticated as well as wild mammals can serve as reservoir hosts for the zoonotic agents and transmission to humans may occur by blood sucking arthropods or by direct blood to blood contact. Humans may come into intimate contact with free-ranging mammals during hunting, especially during evisceration with bare hands, when accidental blood to blood contact frequently occurs. The objective of this work was to determine the presence and the polymorphism of Bartonella strains in wild roe deer (Capreolus capreolus) as the most widely spread game in Western Europe. We report the isolation of four Bartonella strains from the blood of five roe deer. These strains carry polar flagella similar to Bartonella bacilliformis and Bartonella clarridgeiae. Based on their phenotypic and genotypic characteristics, three of the four roe deer isolates were different and they were all distinct from previously described Bartonella species. They can be distinguished from each other and from other Bartonella species by their protein profile, ERIC-PCR pattern, 16S rRNA and citrate synthase (gitA) gene sequences, as well as by whole DNA-DNA hybridization. In spite of their considerable heterogeneity, all four strains fulfil the criteria for belonging to a single new species. The name Bartonella schoenbuchii is proposed for this new species. The type strain R1T of Bartonella schoenbuchii has been deposited in the National Collection of Type Cultures as NCTC 13165T and the Deutsche Sammlung von Mikroorganismen und Zellkulturen as DSM 13525T.
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Enterococcus haemoperoxidus sp. nov. and Enterococcus moraviensis sp. nov., isolated from water.
More LessA polyphasic taxonomic approach was used to study atypical enterococci isolated from surface waters. All strains were characterized by physiological and biochemical tests as well as by genotyping. The results of biochemical tests and tRNA intergenic length polymorphism analysis (tDNA-PCR) divided all studied strains uniformly into two groups. Because these groups were clearly separated from all enterococcal species described to date, 16S rDNA sequence analysis, DNA base composition analysis and DNA-DNA hybridization of representative strains were done to elucidate the taxonomic position of the analysed groups. On the basis of the results obtained, the names Enterococcus haemoperoxidus (type strain CCM 4851T = LMG 19487T) and Enterococcus moraviensis (type strain CCM 4856T = LMG 19486T) are proposed for the two hitherto undescribed species. The type strains and reference cultures have been deposited in the Czech Collection of Microorganisms (CCM), Masaryk University, Brno, Czech Republic, and in the BCCM/LMG Culture Collection, Ghent University, Belgium.
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Crossiella gen. nov., a new genus related to Streptoalloteichus.
More LessPhylogenetic analysis of the genera within the suborder Pseudonocardineae based on almost complete sequences of 16S rDNA showed that Saccharothrix cryophilis NRRL B-16238T was misplaced within the genus Saccharothrix. Saccharothrix cryophilis NRRL B-16238T appeared to be phylogenetically closest to Streptoalloteichus, but is morphologically distinct from this genus because sporangia with motile spores are not observed. The aerial mycelium fragments into rod-shaped elements and sclerotium-like bodies are observed occasionally in the substrate mycelium. The cell wall contains meso-diaminopimelic acid, whole-cell hydrolysates contain galactose, rhamnose and ribose, the phospholipid pattern is type PIV and the principal menaquinone is MK-9(H4). A new genus to accommodate Saccharothrix cryophilis is proposed, Crossiella gen. nov., in recognition of the contributions of Thomas Cross, a distinguished actinomycete biologist at the University of Bradford, UK. The type species is Crossiella cryophila gen. nov., comb. nov.
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Phylogeny of six naviculoid diatoms based on 18S rDNA sequences.
B Beszteri, E Acs, J Makk, G Kovács, K Márialigeti and K T Kiss18S rDNA sequences of six Naviculaceae species [Amphora montana, Gomphonema parvulum, Eolimna minima (syn. Navicula minima), Eolimna subminuscula (syn. Navicula subminuscula), Navicula veneta and Phaeodactylum tricornutum] were determined in order to assess the monophyly of this important group of diatoms, to date not included in 18S rDNA databases, and also that of the recently described genus Eolimna. Phylogenetic trees were constructed using other known diatom 18S rDNA sequences, and best tree topologies obtained were tested against alternative trees for their reliability. The analyses do not reject the monophyly of Naviculaceae and strongly support the separation of the genus Eolimna from Navicula sensu lato. The two species of Eolimna, however, do not appear to be each other's closest relatives among the species investigated: rather, E. subminuscula shows affinities to A. montana, and E. minima to P. tricornutum. A. montana, a species which it has been proposed should be transferred into a separate taxon from the other five species, was found to have grouped well within them in all analyses.
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Evolution of nuclear dualism in ciliates: a reanalysis in light of recent molecular data.
More LessCiliates are defined by the presence of dimorphic nuclei. Following conjugation, both the functional macronucleus (MAC) and the transcriptionally inactive germline micronucleus (MIC) develop from a zygotic nucleus. As the MAC develops, germline chromosomes are processed by excision of internal sequences, fragmentation and amplification of the remaining chromosomes. The extent of processing varies among lineages and, in all but one class of ciliates, the resulting MACs divide by an unusual process termed 'amitosis'. Research on these chromosomal rearrangements, largely from studies of only a handful of taxa from two of the nine classes of ciliates, has failed to find evidence of homologous processing among ciliate lineages. This observation, coupled with the structural diversity of MAC genomes among ciliates, led to the hypothesis of multiple origins of at least two MAC properties: (1) the ability to divide and (2) the mechanisms underlying chromosomal processing. Applying this logic to a more inclusive analysis of ciliate lineages, where an even greater diversity of MAC structure is observed, increases the potential number of origins of these MAC characteristics. Here, it is proposed that a single origin of a relatively plastic mechanism underlying MAC development better explains the observed diversity in MAC structure and processing among ciliates. Such a mechanism is suggested by the demonstration of epigenetic effects during MAC development in Paramecium and Tetrahymena.
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Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs.
H M Daniel, T C Sorrell and W MeyerThe actin gene has been studied as a potential phylogenetic marker for selected members of the anamorphic genus Candida and seven related teleomorphic genera (Debaryomyces, Issatchenkia, Kluyveromyces, Saccharomyces and Pichia from the Saccharomycetaceae; Clavispora and Metschnikowia from the Metschnikowiaceae). The nucleotide sequences of 36 fungal taxa were analysed with respect to their molecular evolution and phylogenetic relationships. A total of 460 bp (47%) of the coding 979 bp were variable and 396 bp (40%) of these were found to be phylogenetically informative. Further analysis of the sequences showed that the genic G+C contents were higher than the nuclear G+C contents for most of the taxa. A strong positive correlation was found between G+C content over all codon positions and third positions. First and second codon positions were considered to be independent of the genic G+C content. The expected transition/transversion bias was detected only for third positions. Pairwise comparisons of transitional and transversional changes (substitutions) with total percentage sequence divergences revealed that the third position transitions showed no saturation for ingroup comparisons. A specific weighting scheme was set up, combining codon-position weights with change-frequency weights to enable the inclusion of distant outgroup taxa. Parsimony analyses of the investigated taxa showed four groups, three of which corresponded to major clusters that had been established previously in Candida by rDNA analysis. Interrelationships among the species groups in this heterogeneous anamorphic genus were determined. The polyphyletic origin of the selected Candida species and their close associations with several ascomycete genera were verified and known anamorph/teleomorph pairs confirmed. The actin gene was established as a valuable phylogenetic marker with the particular advantage of an unambiguous alignment.
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Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization.
More LessThe lager brewing yeasts, Saccharomyces pastorianus (synonym Saccharomyces carlsbergensis), are allopolyploid, containing parts of two divergent genomes. Saccharomyces cerevisiae contributed to the formation of these hybrids, although the identity of the other species is still unclear. The presence of alleles specific to S. cerevisiae and S. pastorianus was tested for by PCR/RFLP in brewing yeasts of various origins and in members of the Saccharomyces sensu stricto complex. S. cerevisiae-type alleles of two genes, HIS4 and YCL008c, were identified in another brewing yeast, S. pastorianus CBS 1503 (Saccharomyces monacensis), thought to be the source of the other contributor to the lager hybrid. This is consistent with the hybridization of S. cerevisiae subtelomeric sequences X and Y' to the electrophoretic karyotype of this strain. S. pastorianus CBS 1503 (S. monacensis) is therefore probably not an ancestor of S. pastorianus, but a related hybrid. Saccharomyces bayanus, also thought to be one of the contributors to the lager yeast hybrid, is a heterogeneous taxon containing at least two subgroups, one close to the type strain, CBS 380T, the other close to CBS 395 (Saccharomyces uvarum). The partial sequences of several genes (HIS4, MET10, URA3) were shown to be identical or very similar (over 99%) in S. pastorianus CBS 1513 (S. carlsbergensis), S. bayanus CBS 380T and its close derivatives, showing that S. pastorianus and S. bayanus have a common ancestor. A distinction between two subgroups within S. bayanus was made on the basis of sequence analysis: the subgroup represented by S. bayanus CBS 395 (S. uvarum) has 6-8% sequence divergence within the genes HIS4, MET10 and MET2 from S. bayanus CBS 380T, indicating that the two S. bayanus subgroups diverged recently. The detection of specific alleles by PCR/RFLP and hybridization with S. cerevisiae subtelomeric sequences X and Y' to electrophoretic karyotypes of brewing yeasts and related species confirmed our findings and revealed substantial heterogeneity in the genome constitution of Czech brewing yeasts used in production.
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Volumes and issues
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Volume 74 (2024)
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