- Volume 50, Issue 1, 2000
Volume 50, Issue 1, 2000
- Articles
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Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana.
More LessBacteria isolates phenotypically related to Pseudomonas corrugata have frequently been isolated from the rhizosphere of Arabidopsis thaliana and Brassica napus grown on different soils. 16S rDNA (rrs) gene sequencing, DNA-DNA hybridization, biochemical characterization and siderophore typing showed that these isolates belong to two different species that are distinct from other species of the genus Pseudomonas, including P. corrugata. A description of properties of these two new species is given based on the study of 16 isolates. Proposed names are Pseudomonas brassicacearum (10 strains studied) and Pseudomonas thivervalensis (6 strains studied). The type strain of Pseudomonas brassicacearum is CFBP 11706T and that of Pseudomonas thivervalensis is CFBP 11261T.
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Description of Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from chili bo, a Malaysian food ingredient.
More LessParalactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.
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Desulfotomaculum alkaliphilum sp. nov., a new alkaliphilic, moderately thermophilic, sulfate-reducing bacterium.
More LessA new moderately thermophilic, alkaliphilic, sulfate-reducing, chemolithoheterotrophic bacterium, strain S1T, was isolated from a mixed cow/pig manure with neutral pH. The bacterium is an obligately anaerobic, non-motile, Gram-positive, spore-forming curved rod growing within a pH range of 8.0-9.15 (optimal growth at pH 8.6-8.7) and temperature range of 30-58 degrees C (optimal growth at 50-55 degrees C). The optimum NaCl concentration for growth is 0.1%. Strain S1T is an obligately carbonate-dependent alkaliphile. The G+C content of the DNA is 40.9 mol%. A limited number of compounds are utilized as electron donors, including H2+acetate, formate, ethanol, lactate and pyruvate. Sulfate, sulfite and thiosulfate, but not sulfur or nitrate, can be used as electron acceptors. Strain S1T is able to utilize acetate or yeast extract as sources of carbon. Analysis of the 16S rDNA sequence allowed strain S1T (= DSM 12257T) to be classified as a representative of a new species of the genus Desulfotomaculum, Desulfotomaculum alkaliphilum sp. nov.
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Description of Sphingomonas xenophaga sp. nov. for strains BN6T and N,N which degrade xenobiotic aromatic compounds.
More LessThe taxonomic position of two bacterial strains, BN6T and N,N, with the ability to degrade xenobiotic aromatic compounds (naphthalenesulfonates or N,N-dimethylaniline) was investigated. The 165 rRNA gene sequence, the G+C content of the DNA (62-63 mol%) and the detection of ubiquinone Q-10, 2-hydroxymyristic acid and the sphingoglycolipid present clearly placed the two strains into the genus Sphingomonas. Both strains are representatives of one species according to the level of DNA relatedness (70.7%). The strains could be separated from all validly described taxa of the genus Sphingomonas, according to the 16S rRNA gene sequence (the highest sequence similarity observed was 96 % to Sphingomonas yanoikuyae), the pattern of the polar lipids and physiological characteristics. Therefore, the new species Sphingomonas xenophaga is proposed to accommodate strains BN6T (= DSM 6383T) and N,N (= DSM 8566).
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Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb. nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov.
More LessUsing a combination of 16S rRNA analysis and antigenic fingerprinting consisting of new and published data, the phylogenetic position of 18 thermophilic isolates currently classified as Methanobacterium species was reinvestigated. The results were verified by independent methods, including, where applicable, plasmid and phage typing. Comparative analysis of 16S rRNA data for 30 strains belonging to the order Methanobacteriales strongly suggested that mesophilic and thermophilic Methanobacterium isolates are distantly related and should be assigned to separate genera. For the thermophilic strains the genus Methanothermobacter was initially proposed by Boone, Whitman and Rouvière. Furthermore, the results support a reclassification of 15 isolates in three species within the proposed genus: (i) Methanothermobacter thermautotrophicus comb. nov., containing eight isolates, six of which are able to utilize formate (type strain deltaHT); (ii) Methanothermobacter wolfeii comb. nov., containing four formate-utilizing isolates (type strain DSM 2970T); (iii) Methanothermobacter marburgensis sp. nov., containing three obligately autotrophic isolates (type strain MarburgT). Of the nine isolates formerly referred to as Methanobacterium thermoformicicum, six were reclassified as Methanothermobacter thermautotrophicus and three as Methanothermobacter wolfeii.
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A new species of oral Streptococcus isolated from Sprague-Dawley rats, Streptococcus orisratti sp. nov.
H Zhu, M D Willcox and K W KnoxTaxonomic studies were performed on an unusual oral Streptococcus strain isolated from Sprague-Dawley rats. The isolates were alpha-haemolytic, bile-tolerant, aesculin-hydrolytic and unable to grow in 6.5% NaCl. They fermented lactose, sucrose and trehalose. They were distinguished from other recognized species of oral and viridans streptococci by several biochemical characteristics and by Lancefield's group antigen, as well as by unique DNA-DNA hybridization characteristics. 16S rDNA sequence studies confirmed the genealogical distinctiveness of the species. The results of the study demonstrated that the isolates represented a new species of the oral and viridans streptococci. The name Streptococcus orisratti sp. nov. is proposed for the new species. The type strain is A63T (= ATCC 700640T).
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'Candidatus Odyssella thessalonicensis' gen. nov., sp. nov., an obligate intracellular parasite of Acanthamoeba species.
More LessAn intracellular bacterium, strain L13, was observed infecting an environmental isolate of an Acanthamoeba species. The bacterium could not be recovered on axenic medium but was recovered and cultivated in vitro using cultures of Acanthamoeba polyphaga. The 16S rRNA gene sequence of L13 was found to be new, sharing less than 84% similarity with other sequences in the GenBank/EMBL database. L13 was found to be a member of the alpha-Proteobacteria, sharing an evolutionary line of descent with a group of uniquely obligate intracellular organisms comprised of Caedibacter and Holospora species and the NHP bacterium. Viable bacteria appeared to be highly motile within amoebae. Ultrastructural analysis of the bacterium demonstrated that it is rod-shaped and possesses a typical Gram-negative cell wall, but has no other outstanding features except small vesicle-like structures often associated with the outer surface of each bacterium. The host range of L13 was found to be limited to the genus Acanthamoeba. In A. polyphaga, L13 infection was slow to manifest when cultures were incubated below 30 degrees C, but at higher temperatures bacteria multiplied prolifically and induced host cell lysis. The protein profile of the bacterium purified from the amoebae was assessed by SDS-PAGE and its G+C content was estimated to be 41 mol%. Although these results support the proposal of L13 as a new species, its obligate intracellular nature prevented isolation of a definitive type strain. L13 is therefore proposed as 'Candidatus Odyssella thessalonicensis' gen. nov., sp. nov.
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Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov.
More LessSixteen strains isolated from different soils and marine sediments and 'Nocardiopsis trehalosi' VKM Ac-942T were subjected to taxonomic analyses. The morphological and chemotaxonomic characteristics of the strains matched those described for members of the Nocardiopsis. Based on 16S rDNA sequence analysis, DNA-DNA hybridization values and phenotypic characteristics, including the composition of menaquinones and cell wall teichoic acids, two new species are proposed, Nocardiopsis tropica sp. nov. (type strain VKM Ac-1457T) and Nocardiopsis trehalosi sp. nov., nom. rev. (type strain VKM Ac-942T = JCM 3357T = NRRL 12026T). Nocardiopsis dassonvillei VKM Ac-1882T (formerly Nocardiopsis albirubida) differs from other strains of this species by the presence of MK-10 as the major menaquinone, cell wall teichoic acid structure, and numerical analysis based on 115 growth and physiological characteristics. The strain is reclassified as the subspecies Nocardiopsis dassonvillei subsp. albirubida, with VKM Ac-1882T (= DSM 43465T = ATCC 23612T = ISP 5465T) designated the type.
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Pseudomonas plecoglossicida sp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, Plecoglossus altivelis.
More LessA new Pseudomonas species, for which the name Pseudomonas plecoglossicida is proposed, was isolated from cultured ayu (Plecoglossus altivelis) with bacterial haemorrhagic ascites. The causative agent was similar to Pseudomonas putida biovar A in its phenotypic characteristics and on the basis of 16S rRNA gene sequence analysis, but it reduced nitrate to nitrite. Furthermore, it was distinguished phenotypically from Pseudomonas putida biovar A by utilization of D-malate, L-(+)-tartrate, m-tartrate and nicotinate. The levels of DNA-DNA hybridization between the isolate strain FPC 951T and other reference strains of Pseudomonas species, including Pseudomonas putida, were less than 50%. The G+C content of the DNA of FPC 951T was 62.8 mol%. Strain FPC 951T (= ATCC 700383T) is designated the type strain of the new species.
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DNA relatedness among strains of Streptomyces pathogenic to potato in France: description of three new species, S. europaeiscabiei sp. nov. and S. stelliscabiei sp. nov. associated with common scab, and S. reticuliscabiei sp. nov. associated with netted scab.
More LessThe genomic relatedness was evaluated by DNA-DNA hybridization for 23 strains (21 were pathogenic and two were saprophytic strains) isolated from lesions of common and netted scab in France and 19 strains from other countries, including type strains of Streptomyces species. Three genomospecies were defined within the conventional species of Streptomyces scabies, and these genomospecies were different from other pathogenic described species (Streptomyces acidiscabies, Streptomyces caviscabies) based on previously published phenotypic data. Two of these genomospecies (1 and 3) correspond to new species, for which the names Streptomyces europaeiscabiei sp. nov. (with type strain CFBP 4497T) and Streptomyces stelliscabiei sp. nov. (with type strain CFBP 4521T) are proposed. Genomospecies 2 corresponds to S. scabies (with type strain CFBP 4517T = ATCC 49173T), and includes only one French strain. The pathogenic strains associated with netted scab lesions constituted a new species that was named Streptomyces reticuliscabiei sp. nov. (with type strain CFBP 4531T). The G+C content of DNA from the three strains CFBP 4497T (S. europaeiscabiei), CFBP 4521T (S. stelliscabiei), CFBP 4531T (S. reticuliscabiei) was 71.3, 71.0 and 69.8 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the type strain CFBP 4497T was very similar to the type strain of S. scabies, whereas, the type strain of S. stelliscabiei, CFBP 4521T, was very similar to the type strain of Streptomyces bottropensis. On the basis of 16S rRNA gene sequences, the type strain of S. reticuliscabiei, CFBP 4531T, differed extensively from the other strains of Streptomyces tested.
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Reclassification of Clostridium quercicolum as Dendrosporobacter quercicolus gen. nov., comb. nov.
More LessMorphological features, genomic DNA base composition and 16S rDNA sequence similarities, as well as a distinct phospholipid pattern, whole-cell fatty acid distribution and the occurrence of the lipoquinone 'lipid F', indicate that Clostridium quercicolum belongs to the Sporomusa-Pectinatus-Selenomonas phyletic group and possesses only a remote relationship to members of the genus Clostridium sensu stricto. On the basis of these results, the new genus and combination Dendrosporobacter quercicolus gen. nov., comb. nov. are proposed.
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Clostridium gasigenes sp. nov., a psychrophile causing spoilage of vacuum-packed meat.
More LessTwo psychrophilic Clostridium strains, DB1AT and R26, were isolated from incidences of 'blown-pack' spoilage of vacuum-packed chilled lamb. Vacuum packs of meat inoculated with these strains developed gas bubbles and pack distension within 14 d storage at 2 degrees C. The two main gases responsible for pack distension were carbon dioxide and hydrogen. 1-Butanol, butyric and acetic acid and butyl esters were the major volatile compounds produced by the strains in the artificially inoculated packs. The unknown strains were Gram-positive motile rods producing elliptical subterminal spores during the late-stationary growth phase. At pH 7.0, they grew from -1.5 to 26 degrees C, and their optimum growth temperature was 20-22 degrees C. At 20 degrees C, the pH range for growth was 5.4-8.9 and the optimum pH for growth was 6.2-8.6. In peptone/yeast extract broth, the organisms grew little or not at all in the absence of fermentable carbohydrates. Both strains hydrolysed gelatin, aesculin and starch. The fermentation products formed in peptone yeast extract glucose starch broth were ethanol, acetate, butyrate, lactate, butanol, carbon dioxide and hydrogen. The G+C contents of the DNA of strains DB1AT and R26 were 29.4 and 28.3 mol%, respectively. Phylogenetic analyses indicated that the strains belong to cluster I of the genus Clostridium (sensu Collins et al. 1994). The new strains differed from the phylogenetically related clostridia in cellular fatty acid composition, soluble protein profiles and phenotypic properties. On the basis of rDNA analysis and phenotypic and phylogenetic characterization, the strains were assigned to a new species for which the name Clostridium gasigenes is proposed. Strain DB1AT (= DSM 12272T) is designated as the type strain.
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Bifidobacterium thermacidophilum sp. nov., isolated from an anaerobic digester.
More LessA new phenotypic group of Bifidobacterium strains, isolated from an anaerobic digester for the treatment of waste water from a bean-curd farm, was described previously. In this study, the DNA-DNA relatedness between strain 36 (type strain, AS 1.2282T) of this new group and the type strains of other described Bifidobacterium species was analysed. The low level of DNA homology (0-58.9%) as well as comparison of the 16S rDNA sequences confirmed the distinct phylogenetic position of strain 36. In addition, the new species differed from other Bifidobacterium species in its phenotypic characteristics, such as its growth at moderately thermophilic conditions (49.5 degrees C) and at relatively low pH (4.0), as well as its sugar-fermentation pattern. On the basis of phenotypic, genetic and phylogenetic studies, a new Bifidobacterium species, Bifidobacterium thermacidophilum sp. nov., was designated.
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Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness.
H Kasai, T Tamura and S HarayamaThe phylogenetic structure of genus Micromonospora within actinomycetes was examined by analysing the gyrB sequences of 15 validly described species and four subspecies. All but one of the Micromonospora strains formed a tight cluster, as had previously been demonstrated by a 16S rDNA-based phylogenetic analysis. However, the intrageneric relationships deduced from the gyrB-based phylogeny were different from those based on their 16S rDNA sequences. To examine which phylogeny would be more relevant for classifying genus Micromonospora, DNA-DNA hybridization experiments were performed. The gyrB-based classification agrees with the results of the DNA-DNA hybridization studies, indicating that this classification method is useful for analysing the phylogenetic relationships of high G+C Gram-positive bacteria at the level of the genomic species. Genus Micromonospora was reclassified into the following 14 species: Micromonospora echinospora, Micromonospora pallida, Micromonospora nigra, Micromonospora purpureochromogenes, Micromonospora aurantiaca, Micromonospora carbonacea, Micromonospora chalcea, Micromonospora chersina, Micromonospora coerulea, Micromonospora gallica, Micromonospora halophytica, Micromonospora inositola, Micromonospora olivasterospora and Micromonospora rosaria.
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Phocoenobacter uteri gen. nov., sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from a harbour porpoise (Phocoena phocoena).
More LessPhenotypic and phylogenetic studies were performed on a Gram-negative, rod-shaped bacterium isolated from the uterus of a porpoise. 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 within this family of organisms. Based on the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacterium be assigned to a new genus, Phocoenobacter uteri gen. nov., sp. nov. The type strain of Phocoenobacter uteri sp. nov. is NCTC 12872T.
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Reclassification of Alteromonas distincta Romanenko et al. 1995 as Pseudoalteromonas distincta comb. nov.
More LessThe 16S rRNA gene of Alteromonas distincta KMM 638T was amplified, cloned and sequenced. The nucleotide sequence was aligned with sequences of representative strains of Alteromonas, Moritella, Pseudoalteromonas and Shewanella. Results of phylogenetic analysis, using neighbour-joining and Fitch-Margoliash methods, clearly indicated that this species should be assigned to the genus Pseudoalteromonas. On the basis of polyphasic data obtained from previous work and this study, it is proposed that the species Alteromonas distincta be reclassified as Pseudoalteromonas distincta comb. nov. with type strain KMM 638T (= ATCC 700518T).
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Bacteroides acidifaciens sp. nov., isolated from the caecum of mice.
Y Miyamoto and K ItohDuring studies of the bacterial flora in the intestines of mice, we isolated characteristic strains which lowered the pH of peptone-yeast broth containing Fildes' digest. Based on 16S rRNA sequence comparison, these isolates were considered to belong to the Bacteroides cluster in the bacteroides subgroup of the Cytophaga-Flavobacterium-Bacteroides phylum, and were divided into two groups. Their phenotypic characteristics, i.e. growth in 20% bile, aesculin hydrolysis, and glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) activity, were the same as those of the 'Bacteroides fragilis group'. The low level of DNA-DNA hybridization with type strains in the Bacteroides cluster confirmed the novel species status of these isolates. It is proposed that these isolates be named Bacteroides acidifaciens, the type strain of which is A40T (= JCM 10556T).
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Characterization of the rnpB gene and RNase P RNA in the order Chlamydiales.
More LessThe sequence of the RNase P RNA gene (rnpB) was determined for 60 strains representing all nine species in the family Chlamydiaceae and for the related Chlamydiales species, Parachlamydia acanthamoebae and Simkania negevensis. These sequences were used to infer evolutionary relationships among the Chlamydiaceae. The analysis separated Chlamydophila and Chlamydia into two lineages, with Chlamydophila forming three distinct clusters: the Chlamydophila pneumoniae strains; the Chlamydophila pecorum strains; and a third cluster comprising the species Chlamydophila psittaci, Chlamydophila abortus, Chlamydophila caviae and Chlamydophila felis. The Chlamydia line of descent contained two clusters, with the Chlamydia suis strains distinctly separated from strains of Chlamydia trachomatis and Chlamydia muridarum. This analysis indicated that the rnpB sequence and structure are distinctive markers for species in the Chlamydiaceae. It was also demonstrated that the RNase P RNA derived from Chlamydia trachomatis is able to cleave a tRNA precursor in the absence of protein. These findings are discussed in relation to the structure of Chlamydia RNase P RNA.
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Polyphasic characterization of rhizobia that nodulate Phaseolus vulgaris in West Africa (Senegal and Gambia).
More LessFifty-eight new isolates were obtained from root nodules of common bean (Phaseolus vulgaris) cultivated in soils originating from different agroecological areas in Senegal and Gambia (West Africa). A polyphasic approach including both phenotypic and genotypic techniques was used to study the diversity of the 58 Rhizobium isolates and to determine their taxonomic relationships with reference strains. All the techniques performed, analysis of multilocus enzyme electrophoretic patterns, SDS-PAGE profiles of total cell proteins, PCR-RFLP analysis of the genes encoding 16S rRNA and of the 16S-23S RNA intergenic spacer region (ITS-PCR-RFLP), auxanographic tests using API galleries and nodulation tests lead to the consensus conclusion that the new rhizobial isolates formed two main distinct groups, I and II, belonging to Rhizobium tropici type B and Rhizobium etli, respectively. By MLEE R. etli and group II strains showed several related electrophoretic types, evidencing some extent of internal heterogeneity among them. This heterogeneity was confirmed by other techniques (ITS-PCR-RFLP, SDS-PAGE and host-plant-specificity) with the same nine distinct strains of group II showing some differences from the core of group II (54 strains).
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Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment.
More LessMethanosarcina semesiae MD1T (T = type strain), a novel obligately methylotrophic methanogenic archaeon is described. Strain MD1T was isolated from an enrichment on dimethylsulfide inoculated with mangrove sediment. The cells were irregularly coccoid, non-motile, 1.4+/-0.2 microm in diameter and stained Gram-positive. The catabolic substrates used included dimethylsulfide, methanethiol, methanol and methylated amines, but not acetate, formate, H2/CO2 or a combination of these substrates. When cells grown on dimethylsulfide were transferred to trimethylamine or methanol and vice versa, a lag phase was observed. The same lag phase occurred when cells grown on trimethylamine were transferred to methanol and vice versa, indicating that for each substrate different enzymes were induced. Fastest growth occurred within a temperature range of 30-35 degrees C and a pH of 6.5-7.5. Both Na+ and Mg2+ were required for growth, with maximum growth rates at 200-600 mM Na+ and 20-100 mM Mg2+. The cells exhibited specific growth rates (h-1) of 0.07+/-0.02, 0.15+/-0.04 and 0.18-/+0.05 on dimethylsulfide, methanol and trimethylamine, respectively. Analysis of the 16S rRNA gene sequence showed that strain MD1T was phylogenetically closely related to members of the genus Methanosarcina, but clearly differed from all described species of this genus (94-97% sequence similarity).
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Luteococcus peritonei sp. nov., isolated from the human peritoneum.
More LessAn unusual catalase-positive pleomorphic Gram-positive rod isolated from a human clinical specimen was subjected to a polyphasic taxonomic analysis. Comparative 16S rRNA gene sequence analysis revealed the unknown bacterium was a member of the high G+C branch of the Gram-positive bacteria (Actinobacteria), and was phylogenetically a member of the family Propionibacteriaceae, with Luteococcus japonicus as its nearest relative. Based on both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium be classified in the genus Luteococcus, as Luteococcus peritonei sp. nov. The type strain of Luteococcus peritonei is CCUG 38120T.
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Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah.
More LessStrain AX-2T (T = type strain) was isolated from sediment of Great Salt Lake, Utah, USA. Optimal salinity for growth was 27% (w/v) NaCl and only a few carbohydrates supported growth of the strain. Strain AX-2T did not grow on complex substrates such as yeast extract or peptone. 16S rRNA analysis revealed that strain AX-2T was a member of the phyletic group defined by the family Halobacteriaceae, but there was a low degree of similarity to other members of this family. The polar lipid composition comprising phosphatidyl glycerol, the methylated derivative of diphosphatidyl glycerol, triglycosyl diethers and sulfated triglycosyl diethers, but not phosphatidyl glycerosulfate, was not identical to that of any other aerobic, halophilic species. On the basis of the data presented, it is proposed that strain AX-2T should be placed in a new taxon, for which the name Halorhabdus utahensis is appropriate. The type strain is strain AX-2T (= DSM 12940T).
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Hongia gen. nov., a new genus of the order Actinomycetales.
More LessAn aerobic, nocardioform actinomycete, named LM 161T, was isolated from a soil sample obtained from a gold mine in Kongiu, Republic of Korea. This organism formed well-differentiated aerial and substrate mycelia and produced branched hyphae that fragmented into short or elongated rods. The cell wall contains major amounts of LL-diaminopimelic acid, alanine, glycine, glutamic acid, mannose, glucose, galactose, ribose and acetyl muramic acid. The major phospholipids of this isolate are phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and the major isoprenologue is a tetrahydrogenated menaquinone with nine isoprene units. The whole-cell hydrolysate of strain LM 161T contains 12-methyltetradecanoic and 14-methylpentadecanoic acids as the predominant fatty acids, but does not contain mycolic acids. The G+C content of the DNA is 71.3 mol%. The phylogenetic position of the test strain was investigated using an almost complete 16S rDNA sequence. The isolate formed the deepest branch in the clade encompassing the members of the suborder Propionibacterineae Rainey et al. 1997. On the basis of chemical, phenotypic and genealogical data, it is proposed that this isolate be classified within a new genus as Hongia koreensis gen. nov., sp. nov. in the order Actinomycetales. The type strain is LM 161T (= IMSNU 50530T).
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Micropruina glycogenica gen. nov., sp. nov., a new Gram-positive glycogen-accumulating bacterium isolated from activated sludge.
More LessA new Gram-positive non-spore-forming bacterium, strain Lg2T, was isolated from an activated sludge reactor showing enhanced biological phosphorus removal activity. The new isolate was a slowly growing organism and was capable of accumulating large amounts of intracellular glycogen from substrate taken up. Both oxidase and catalase were produced. The new isolate contained meso-diaminopimelic acid (DAP) in the cell wall. Complex fatty acid patterns with iso-C14:0, anteiso-C15:0, C16:0, iso-C16:0 and four other minor saturated or unsaturated straight-chain fatty acids were detected. The isolate contained a high genomic G+C content (70.5 mol%). Phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate in the high G+C Gram-positive group with Microlunatus phosphovorus and Friedmanniella antarctica as the closest relatives (sequence similarities are 93 and 92 %, respectively). These three organisms shared common features in morphology, but strain Lg2T could be differentiated from the other species by its peptidoglycan type (meso-DAP), fatty acid composition, carbon source utilization profile and G+C content. On the basis of these findings, it is proposed that a new genus and species, Micropruina glycogenica, should be created for the new isolate; the type strain is strain Lg2T (= JCM 10248T).
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Thermus igniterrae sp. nov. and Thermus antranikianii sp. nov., two new species from Iceland.
More LessSeveral yellow-pigmented isolates, with optimum growth temperatures of about 65-70 degrees C, were recovered from hot springs in Iceland. Phylogenetic analysis of the 16S rDNA and DNA-DNA reassociation values showed that these organisms represented two new species of the genus Thermus. Strains RF-4T and HN1-8 had maximum temperatures for growth below 80 degrees C, while strains HN3-7T and HN2-7, unlike all other strains of the species of the genus Thermus except those belonging to Thermus thermophilus, grew at 80 degrees C. The new isolates from Iceland could not be distinguished easily from each other or from other strains of the species of the genus Thermus by biochemical characteristics; however, strains RF-4T and HN1-8 assimilated ribitol, a characteristic which was not detected in any of the other strains examined. Moreover, the species represented by strains RF-4T and HN1-8 and the species represented by strains HN3-7T and HN2-7 could be distinguished clearly from the other species of Thermus by their fatty acid composition. Strains RF-4T and HN1-8 have the highest combined levels of iso-15:0 and iso-17:0 and the lowest levels of iso-16:0 of any of the strains of the species of Thermus, while strains HN3-7T and HN2-7 are characterized by a very low iso-15:0/iso-17:0 ratio. On the basis of the phylogenetic analysis, DNA-DNA reassociation values, physiological and biochemical characteristics and fatty acid composition, the name Thermus igniterrae sp. nov. is proposed for the species represented by strains RF-4T and HN1-8 and the name Thermus antranikianii sp. nov. is proposed for the species represented by strains HN3-7T and HN2-7.
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A proposal for the reclassification of Bdellovibrio stolpii and Bdellovibrio starrii into a new genus, Bacteriovorax gen. nov. as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively.
M L Baer, J Ravel, J Chun, R T Hill and H N WilliamsBdellovibrios are unique bacteria with the ability to prey upon a wide variety of susceptible Gram-negative bacteria. Micro-organisms exhibiting this trait have been included in the genus Bdellovibrio despite their isolation from diverse habitats and relatively unstudied taxonomic relatedness. In this study, 16S rDNA sequences were compared from known terrestrial Bdellovibrio species, Bdellovibrio bacteriovorus 100T, Bdellovibrio stolpii Uki2T and Bdellovibrio starrii A3.12T in order to study their phylogenetic relationship. The two sequences from B. stolpii Uki2T and B. starrii A3.12T were 90.0% similar to each other but exhibited only 81.7% and 81.2% similarity, respectively to B. bacteriovorus 100T. Phylogenetic analysis indicated that B. bacteriovorus 100T clustered in a separate clade from B. starrii A3.12T and B. stolpii Uki2T, demonstrating only a distant relationship between B. bacteriovorus 100T and the other two recognized type species. DNA-DNA hybridization experiments also demonstrated <4% hybridization between these three species. On the basis of the results obtained from the phylogenetic analysis and DNA-DNA hybridization studies, it is proposed that B. stolpii Uki2T and B. starrii A3.12T should be transferred to a new genus, Bacteriovorax gen. nov. as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively. It is also proposed that the type species for the new genus Bacteriovorax should be Bacteriovorax stolpii comb. nov.
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Bradyrhizobium spp. (TGx) isolates nodulating the new soybean cultivars in Africa are diverse and distinct from bradyrhizobia that nodulate North American soybeans.
More LessThe newly developed cultivars of soybean in Africa, known as Tropical Glycine cross (TGx), are nodulated by bradyrhizobia indigenous to African soils, here designated Bradyrhizobium spp. (TGx). Isolates of Bradyrhizobium spp. (TGx) obtained from nodules of TGx soybeans that were inoculated with soils from 65 locations in six African countries were characterized and grouped into 11 phylogenetic clusters on the basis of RFLP of the 16S rRNA gene. Five restriction enzymes (RsaI, HinfI, MspI, CfoI and HaeIII) established RFLP groups within these Bradyrhizobium spp. (TGx) isolates, which were used to construct a phylogenetic tree showing their genetic relationship with other Bradyrhizobium species. RFLP analysis indicated that Bradyrhizobium spp. (TGx) is a heterogeneous group with some isolates related to Bradyrhizobium japonicum and Bradyrhizobium elkanii strains and some to Bradyrhizobium spp. (misc.) reference strains isolated from a variety of tropical legumes. The heterogeneity within the large phylogenetic clusters was further examined through analysis of randomly amplified polymorphic DNA (RAPD) using GC-rich PCR primers. The RAPD analysis showed additional heterogeneity in the Bradyrhizobium spp. (TGx) phylogenetic clusters, which was not revealed by separations based on RFLP analysis. The Bradyrhizobium spp. (TGx) isolates were classified into effective and ineffective types based on their symbiotic performance on TGx soybean. The isolates were randomly distributed throughout the phylogenetic clusters regardless of their symbiotic effectiveness on TGx soybean.
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Acidovorax anthurii sp. nov., a new phytopathogenic bacterium which causes bacterial leaf-spot of anthurium.
L Gardan, C Dauga, P Prior, M Gillis and G S SaddlerThe bacterial leaf-spot of anthurium emerged during the 1980s, in the French West Indies and Trinidad. This new bacterial disease is presently wide spread and constitutes a serious limiting factor for commercial anthurium production. Twenty-nine strains isolated from leaf-spots of naturally infected anthurium were characterized and compared with reference strains belonging to the Comamonadaceae family, the genera Ralstonia and Burkholderia, and representative fluorescent pseudomonads. From artificial inoculations 25 out of 29 strains were pathogenic on anthurium. Biochemical and physiological tests, fatty acid analysis, DNA-DNA hybridization, 16S rRNA gene sequence analysis, DNA-16S RNA hybridization were performed. The 25 pathogenic strains on anthurium were clustered in one phenon closely related to phytopathogenic strains of the genus Acidovorax. Anthurium strains were 79-99% (deltaTm range 0.2-1.6) related to the strain CFBP 3232 and constituted a discrete DNA homology group indicating that they belong to the same species. DNA-rRNA hybridization, 16S rRNA sequence and fatty acid analysis confirmed that this new species belongs to the beta-subclass of Proteobacteria and to rRNA superfamily III, to the family of Comamonadaceae and to the genus Acidovorax. The name Acidovorax anthurii is proposed for this new phytopathogenic bacterium. The type strain has been deposited in the Collection Française des Bactéries Phytopathogènes as CFBP 3232T.
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DNA-DNA reassociation studies of Streptococcus constellatus with unusual 16S rRNA sequences.
More LessDNA-DNA reassociation studies were performed on previously described 'CI strains', which form an unusual 16S rRNA population within the 'anginosus' group of Streptococcus. The CI strains displayed reassociation values of >70% with the Streptococcus constellatus NCDO 2226T strain, with Tm values <1 degrees C, indicating phylogenetic species identity.
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Lactobacillus mucosae sp. nov., a new species with in vitro mucus-binding activity isolated from pig intestine.
S Roos, F Karner, L Axelsson and H JonssonA new Lactobacillus species from pig small intestine has been identified. In an attempt to isolate Lactobacillus reuteri strains carrying the putative colonization-factor gene (mub, for mucus binding) a mub-derived gene probe was used to screen pig intestinal material. A number of isolates were obtained and primary characterization showed that they were Gram-positive, catalase-negative, non-spore-forming, non-motile rods. Growth occurred at 45 degrees C but not at 15 degrees C and the DNA G+C content was 46 mol%. Cell wall analysis together with DNA-DNA hybridization and analysis of the 16S rRNA sequence revealed that the new isolates represent a previously undescribed Lactobacillus species closely related to L. reuteri, Lactobacillus fermentum and Lactobacillus pontis. The name Lactobacillus mucosae is proposed for this species and the type strain is S32T.
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Aminobacterium mobile sp. nov., a new anaerobic amino-acid-degrading bacterium.
More LessA novel, curved (0.3 x 4.0-5.0 microm), Gram-negative, non-sporulating, mesophilic bacterium, designated strain ILE-3T (T = type strain), was isolated from an anaerobic lagoon in a dairy wastewater treatment plant. Optimal growth occurred at 37 degrees C and pH 7.4 on a medium containing serine as an energy source and yeast extract. The strain was motile by means of one or two lateral flagella. It required yeast extract for growth on serine, glycine, threonine and pyruvate. Poor growth was obtained on cysteine, Casamino acids, biotrypcase, peptone and 2-oxoglutarate. In the presence of Methanobacterium formicicum, strain ILE-3T oxidized alanine, glutamate, leucine, isoleucine, valine and aspartate to a minor extent. The G+C content of the DNA was 44 mol%. Phylogenetic analysis of the 16S rRNA gene of strain ILE-3T indicated that it was related to Aminobacterium colombiense (95% similarity value). On the basis of the phenotypic and phylogenetic characteristics, strain ILE-3T is designated as a new species of the genus Aminobacterium, namely Aminobacterium mobile sp. nov. (= DSM 12262T).
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Assignment of Alteromonas elyakovii KMM 162T and five strains isolated from spot-wounded fronds of Laminaria japonica to Pseudoalteromonas elyakovii comb. nov. and the extended description of the species.
More LessA marine bacterium, Alteromonas elyakovii KMM 162T, which was described recently, and five strains isolated from spot-wounded fronds of Laminaria japonica have been subjected to phylogenetic analysis, and geno- and phenotypic characterization. The phenotypic features of Pseudoalteromonas elyakovii strains were closely related to that of Pseudoalteromonas espejiana IAM 12640T, but utilization of three carbon compounds (D-mannose, L-tyrosine and trehalose) distinguished both species. The G+C content of Pseudoalteromonas elyakovii was between 38.5 and 38.9 mol%. Pseudoalteromonas elyakovii KMM 162T and the five Laminaria isolates constitute a single species different from any other Alteromonas and Pseudoalteromonas species as revealed by DNA-DNA hybridization data, especially Pseudoalteromonas distincta KMM 638T (52.4%), Pseudoalteromonas citrea KMM 216 (49.5%), Pseudoalteromonas carrageenovora NCIMB 302T (46.9%) and Pseudoalteromonas espejiana IAM 12640T (29.9%). All the data indicated that Alteromonas elyakovii KMM 162T should be reclassified as Pseudoalteromonas elyakovii and five strains isolated from Laminaria japonica have to be included in the species. Pseudoalteromonas elyakovii comb. nov. (type strain, KMM 162T = ATCC 700519T) is proposed and a set of phenotypic features which differentiate the Pseudoalteromonas species is described.
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Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov.
More LessA group of yellow-pigmented isolates from ammonia-supplied biofilters showed an unusual denitrification reaction. All strains reduced nitrite but not nitrate without production of nitrogen (N2). The only product found was nitrous oxide (N2O). The strains were divided into two clusters and one separate strain by their fatty acid profiles, which were similar to the fatty acid profiles of the genera Xanthomonas and Stenotrophomonas. Analyses of the 165 rDNA sequences showed that these clusters and the separate strain form three independent lines within the Xanthomonas branch of the Proteobacteria. The evolutionary distances of the isolates to members of the related genera Xanthomonas, Stenotrophomonas and Xylella calculated by the 16S rDNA sequences led to the proposal of two new genera and three new species, Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. The type strains are Stenotrophomonas nitritireducens L2T (= DSM 12575T), Luteimonas mephitis B1953/27.1T (= DSM 12574T) and Pseudoxanthomonas broegbernensis B1616/1T (= DSM 12573T).
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Mycobacterium xenopi and related organisms isolated from stream waters in Finland and description of Mycobacterium botniense sp. nov.
More LessThree scotochromogenic Mycobacterium xenopi-like organisms were isolated from stream waters in Finland. These strains grew at 36-50 degrees C but not at 30 degrees C. One of the three strains was fully compatible with the M. xenopi type strain according to GLC-MS, biochemical tests, and 16S rDNA and 16S-23S rDNA internal transcribed spacer (ITS) sequencing. Two of the strains closely resembled M. xenopi in lipid analyses and biochemical tests, but analysis by GLC-MS verified the presence of two new marker fatty acids (2,4,6,x-tetramethyl-eicosanoic acid and 2,4,6,x,x-pentamethyl-docosanoic acid). The 16S rDNA and ITS region sequences of these two strains differed from those of M. xenopi and other previously described mycobacterial sequences. Therefore, the strains are regarded as new species of slow-growing mycobacteria, for which the name Mycobacterium botniense sp. nov. is proposed. The chemical, physical and microbiological quality of the water reservoirs of M. xenopi and M. botniense are described. As far as is known, this is the first time that M. xenopi has been isolated from natural waters. The strains of M. botniense sp. nov. (E347T and E43) have been deposited in the ATCC as strains 700701T and 700702, respectively.
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Updated phylogenetic description of the Mycoplasma hominis cluster (Weisburg et al. 1989) based on 16S rDNA sequences.
More LessThe fastidious nature of the mollicutes (mycoplasmas), their lack of a classic bacterial cell wall, and their very small genome, make phylogenetic placements of new species in this enlarging group of prokaryotes an important and valuable aid in their classification. In this report we have determined the phylogeny of the Mycoplasma hominis cluster of the hominis group. The 16S rDNA sequences from several previously described Mycoplasma species were determined and ten species were found to belong to the M. hominis cluster. With almost complete sequences available, the phylogenetic analysis revealed that the M. hominis cluster currently comprises 19 species, forming a distinct clade as judged from branch lengths, bootstrap percentage values, nucleotide signature analysis, and structural elements in the 16S rRNA molecule. The 16S rRNA gene sequences of species in the M. hominis cluster were found to be > or = 94% similar and the range within which similarities can be used in the classification of new species is discussed. Members of the M. hominis cluster all share a major biochemical property of M. hominis, in that they hydrolyse arginine and are incapable of fermenting glucose. This consistency in phenotypic pattern has not been found in any of the other phylogenetic clusters of the hominis group. Two species, the non-cultivable agent of Grey Lung disease in rodents (tentatively named 'Candidatus Mycoplasma ravipulmonis') and the avian species Mycoplasma gypis strain B1/T1T, were regarded as close relatives to the M. hominis cluster, but are clearly separated from the species of this cluster. Both species formed early branches of the M. hominis cluster and should be regarded as individual lines containing one species.
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Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., alpha-3-Proteobacteria from hypersaline, heliothermal and meromictic antarctic Ekho Lake.
More LessTwo Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). 16S rRNA gene sequence comparisons show the isolates to be phylogenetically close to the genera Sulfitobacter and Roseobacter. Cells can be motile and contain storage granules. Sulfite addition does not stimulate growth. Isolate EL-38T can produce bacteriochlorophyll a and has a weak requirement for sodium ions; polar lipids include phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid, but not diphosphatidylgycerol. The dominant fatty acid is 18:1omega7c; other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0, 18:0, 18:2 and 19:1. The DNA base composition is 55.0-56.3 mol% G+C. Isolate EL-162T has an absolute requirement for sodium ions. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid are present in the polar lipids. Dominant fatty acids of this isolate are 18:1omega7c and 18:1omega9c as well as 18:2 which is present as two isomers. Other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0 and 18:0. The G+C content is 57.9-58.1 mol%. Morphological, physiological and genotypic differences from related, thus far known genera support the description of Staleya guttiformis gen. nov. and sp. nov. with EL-38T (= DSM 11458T) as the type strain and of Sulfitobacter brevis sp. nov. with the type strain EL-162T (= DSM 11443T).
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Thermobacillus xylanilyticus gen. nov., sp. nov., a new aerobic thermophilic xylan-degrading bacterium isolated from farm soil.
More LessAn aerobic, thermophilic, xylanolytic, spore-forming bacterium, XETP (T = type strain; P = patent strain), has been isolated from farm soil situated underneath a manure heap in northern France. Strain XETP, which stained negative in the Gram test, occurs as short rods which sometimes form chains. Its spores are ellipsoidal, central to subterminal and occur in swollen sporangia. It grows at temperatures up to 63 degrees C and in the pH range 6.5-8.5. When grown on glucose in optimal conditions, its doubling time was found to be 33 min. CO2 was observed to have a growth-stimulating effect at the start of the culture. In addition to glucose, the isolate utilizes xylose, arabinose, mannose, cellobiose, galactose, maltose, sucrose, xylan and starch. Growth is inhibited by 5% NaCl. The G+C content of strain XETP is 57.5 mol%. The 16S rDNA sequence analysis indicated that strain XETP falls into the radiation of the Bacillus-Lactobacillus-Streptococcus subdivision of the Gram-positive phylum. Its three closest phylogenetic relatives are 'Bacillus viscosus', Paenibacillus curdlanolyticus and Bacillus popilliae with identity values of 91.15, 90.94 and 90.92%, respectively. The major cellular fatty acids are 14-methyl pentadecanoic acid (16:0 iso), hexadecanoic acid (16:0) and 14-methyl hexadecanoic acid (17:0 anteiso). On the basis of 16S rRNA sequence and chemotaxonomic characteristics, the isolate is different enough for it to be considered as a member of a new genus. It is therefore proposed that this isolate represents a new genus and species: Thermobacillus xylanilyticus. Strain XETP, the type strain of Thermobacillus xylanilyticus, has been deposited in the Collection Nationale de Cultures Microbiennes (CNCM I-1017) as a patent strain.
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Vibrio aerogenes sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production.
More LessA mesophilic, facultatively anaerobic, marine bacterium, designated strain FG1T, was isolated from a seagrass bed sediment sample collected from Nanwan Bay, Kenting National Park, Taiwan. Cells grown in broth cultures were motile, Gram-negative rods; motility was normally achieved by two sheathed flagella at one pole of the cell. Strain FG1T required Na+ for growth, and exhibited optimal growth at 30-35 degrees C, pH 6-7 and about 4% NaCl. It grew anaerobically by fermenting glucose and other carbohydrates with production of various organic acids, including acetate, lactate, formate, malate, oxaloacetate, propionate, pyruvate and succinate, and the gases CO2 and H2. The strain did not require either vitamins or other organic growth factors for growth. Its DNA G+C content was 45.9 mol%. It contained C12:0 as the most abundant cellular fatty acid. Characterization data, together with the results of a 16S rDNA-based phylogenetic analysis, indicate that strain FG1T represents a new species of the genus Vibrio. Thus, the name Vibrio aerogenes sp. nov. is proposed for this new bacterium. The type strain is FG1T (= ATCC 700797T = CCRC 17041T).
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Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov.
More LessPartial sequences for 16S rDNA were determined for strains of the genus Saccharothrix, including most described species, as well as strains of the described species of the related genera Kutzneria, Actinokineospora and Actinosynnema. These were aligned with published sequences for other species of these genera, as well as those of the genera 'Actinoalloteichus', 'Asiosporangium', Lentzea, Kutzneria, Streptoalloteichus and representative taxa from other actinomycete families. Phylogenetic analysis of the sequence data showed that species of the genera Actinokineospora, Actinosynnema, Lentzea and Saccharothrix are members of the same clade, and distinct from the Pseudonocardiaceae. It is proposed that a new family be created within the class Actinobacteria for these genera, to be called the Actinosynnemataceae on the basis of the oldest described genus within this family, Actinosynnema Hasegawa et al. The chemotaxonomic properties of all the genera to be placed within the new family have similar cell wall type (type III), whole-cell sugars (generally galactose although mannose and rhamnose may be present), phospholipid type (PII) and menaquinones [MK-9(H4) predominant].
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Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains).
More LessOligotrophic PYGV medium, inoculated with soils from Linnaeus Terrace (1600 m, Antarctica), yielded four aerobic actinomycetes with short rods, multiple and irregular septa and often motile buds. Cells were 1.0-2.8 x 1.0-3.0 microm and colonies were beige to pink. The isolates were nearly identical in physiological and biochemical tests. Three strains grew from 0 degrees C to 25-28 degrees C, but one was psychrophilic with a maximum growth temperature of 20 degrees C. Carbon sources utilized were D-glucose, D-galactose, lactose, sucrose or mannitol; malate, succinate, fumarate, pyruvate or glutarate were decarboxylated aerobically. Peptone and yeast extract were the preferred nitrogen sources. Nitrate was reduced aerobically or anaerobically. Cell walls contained meso-diaminopimelic acid, glutamate, alanine, glycine, galactose, glucose and ribose. Major fatty acids of strains AA-802, -824, -825 and -826T were n18:1, i16:0 and ai17:0. Major respiratory quinones were MK-9(H4) and MK-8(H4). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Phosphatidylglycerol was found in most strains. The DNA G+C contents were 68-70 mol%. In 16S rDNA analyses, similarity values obtained for 500 nucleotides from the 5' terminus were > 99.5%. Almost complete sequences from AA-826T and -825 were 99.9% similar. Strain AA-826T belonged to a novel cluster of desert soil and rock isolates within the Geodermatophilaceae and was equidistantly related to members of Geodermatophilus and to a Blastococcus lineage. The four isolates represent a new genus, Modestobacter gen. nov., with Modestobacter multiseptatus sp. nov. as the type species. The type strain, Modestobacter multiseptatus AA-826T, was deposited in the DSMZ as DSM 44406T.
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Corynebacterium simulans sp. nov., a non-lipophilic, fermentative Corynebacterium.
P Wattiau, M Janssens and G WautersThree coryneform strains isolated from clinical samples were analysed. These strains fitted the biochemical profile of Corynebacterium striatum by conventional methods. However, according to recently described identification tests for fermenting corynebacteria, the strains behaved rather like Corynebacterium minutissimum. The three isolates could be distinguished from C. minutissimum by a positive nitrate and nitrite reductase test and by not fermenting maltose; from C. striatum by their inability to acidify ethylene glycol and to grow at 20 degrees C. Genetic studies based on 16S rRNA showed that the three strains were in fact different from C. minutissimum and C. striatum (96.9 and 98% similarity, respectively) and from other corynebacteria. They represent a new species for which the name Corynebacterium simulans sp. nov. is proposed. The type strain is DSM 44415T (= UCL 553T = Co 553T).
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Frigoribacterium faeni gen. nov., sp. nov., a novel psychrophilic genus of the family Microbacteriaceae.
The taxonomic position of five actinobacterial strains isolated from dust, an animal shed, the air inside a museum and soil was investigated using a polyphasic approach. The growth characteristics were unusual for actinomycetes. Optimal growth was at temperatures ranging from 2 to 10 degrees C. After small-step adaptation (5 degrees C steps) to higher temperatures, the strains were also able to grow at 20 degrees C. Cell wall analyses revealed that the organisms showed a hitherto undescribed, new group B-type peptidoglycan [type B2beta according to Schleifer & Kandler (1972), but with lysine instead of ornithine]. All strains contained menaquinone MK-9. Mycolic acids were not detected. Diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid were detected in the polar lipid extracts. The main fatty acids were 12-methyl-tetradecanoic acid (15:0 anteiso), 12-methyl-tetradecenoic acid (15:1 anteiso), 14-methyl-pentadecanoic acid (16:0 iso) and 14-methyl-hexadecanoic acid (17:0 iso), as well as an unusual compound identified as 1,1-dimethoxy-anteiso-pentadecane (15:0 anteiso-DMA). The G+C content of DNA was approximately 71 mol%. The results of 16S rRNA gene sequence comparisons revealed that the strains represent a new lineage in the suborder Micrococcineae and the family Microbacteriaceae of the order Actinomycetales. On the basis of these results the new genus Frigoribacterium gen. nov. is proposed, harbouring the new species Frigoribacterium faeni sp. nov. (type strain = 801T = DSM 10309T).
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The genus Abiotrophia (Kawamura et al.) is not monophyletic: proposal of Granulicatella gen. nov., Granulicatella adiacens comb. nov., Granulicatella elegans comb. nov. and Granulicatella balaenopterae comb. nov.
More LessThe genus Abiotrophia currently includes four species, Abiotrophia defectiva, Abiotrophia adiacens, Abiotrophia balaenopterae and Abiotrophia elegans. Recent 16S rRNA gene sequencing studies have demonstrated that the genus is not monophyletic and is in need of taxonomic revision. Phylogenetically, the genus Abiotrophia consists of two distinct lines, A. defectiva, the type species of the genus, and a robust group consisting of A. adiacens, A. balaenopterae and A. elegans. Therefore, it is formally proposed that the genus Abiotrophia should be restricted to A. defectiva and that A. adiacens, A. balaenopterae and A. elegans should be reclassified in a new genus, Granulicatella, as Granulicatella adiacens comb. nov., Granulicatella balaenopterae comb. nov. and Granulicatella elegans comb. nov.
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Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.
More LessThe new genus Leifsonia gen. nov. with two new species, Leifsonia poae sp. nov. (type strain VKM Ac-1401T) and Leifsonia aquatica (ex Leifson 1962) nom. rev., comb. nov. (the type species, with VKM Ac-1400T = DSM 20146T = JCM 1368T as type strain), is proposed to accommodate bacteria found in Poa annua root gall, induced by the nematode Subanguina radicicola, and 'Corynebacterium aquaticum' Leifson 1962. Further, it is proposed to reclassify Clavibacter xyli Davis et al. 1984 with two subspecies in the new genus as Leifsonia xyli (Davis et al. 1984) comb. nov., Leifsonia xyli subsp. xyli (Davis et al. 1984) comb. nov. and Leifsonia xyli subsp. cynodontis (Davis et al. 1984) comb. nov. Members of the proposed genus are characterized by coryneform morphology, peptidoglycans based upon 2,4-diaminobutyric acid, the major menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol as principal phospholipids, the high content of anteiso- and iso-branched saturated fatty acids, and a DNA G+C base composition of 66-73 mol%. They form a distinct phylogenetic branch attached to the line of descent of Agromyces spp. The new and reclassified species of the new genus clearly differ from each other phylogenetically and phenetically and can be recognized by their morphologies, the cell wall sugar composition, the requirement of complex media for growth, and numerous physiological characteristics, including the oxidase reaction.
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Trichosporon veenhuisii sp. nov., an alkane-assimilating anamorphic basidiomycetous yeast.
More LessA morphological and physiological description of an alkane-assimilating anamorphic basidiomycetous yeast species, named Trichosporon veenhuisii, is presented. The ability to assimilate several aliphatic and aromatic compounds as sole source of carbon and energy is reported. The phylogenetic position within the genus, based on nuclear base sequencing of the D1/D2 region of the large subunit of rDNA, is discussed. The type strain is CBS 7136T.
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Candida tartarivorans sp. nov., an anamorphic ascomycetous yeast with the capacity to degrade L(+)- and meso-tartaric acid.
More LessAn undescribed anamorphic yeast species of ascomycetous affinity, for which the name Candida tartarivorans is proposed, was isolated from dried wine lees in Portugal using a selective medium with L(+)-tartaric acid as the sole source of carbon and energy. The single isolate (IGC 4854T) showed the following characteristics: sympodial holoblastic conidiogenesis, absence of asci with ascospores, a negative colour reaction with Diazonium Blue B, production of elaborate pseudomycelium and ability to grow with inositol as sole source of carbon. Analysis of the physiological data pointed to a close relationship with other inositol-assimilating taxa, namely the genera Arxula, Stephanoascus, Sympodiomyces, Zygoascus and selected Candida species. Comparative analysis of the D1/D2 variable domain of the 26S rRNA gene of all available sequences for ascomycetous yeasts showed that strain IGC 4854T did not match with any other species in the database. The closest relative was Candida auringiensis Santa Maria, but the two species differed in 24 nucleotide positions. A description of the new species is given.
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Four new yeasts in the Pichia anomala clade.
More LessFour new yeasts are described that were recognized as novel from nucleotide substitutions in domain D1/D2 of 26S rDNA, a region that is sufficiently divergent to allow resolution of most ascomycetous yeast species. The new species and their type strains are as follows: Pichia maclurae NRRL Y-5377T (= CBS 8671T); Pichia misumaiensis NRRL Y-17389T (= CBS 8062T); Candida mycetangii NRRL Y-6843T (= CBS 8675T); and Candida ulmi NRRL YB-2694T (= CBS 8670T). The two Pichia species form spherical ascospores and are heterothallic. Phylogenetic analysis of domain D1/D2 sequences placed the four new species in the Pichia anomala clade.
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Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene.
C Belloch, A Querol, M D García and E BarrioA phylogenetic analysis of 17 species belonging to the genus Kluyveromyces and 12 reference and outgroup species was performed using mitochondrial cytochrome-c oxidase II gene sequences. The genus Kluyveromyces appears as a polyphyletic taxon formed by species included within the following four main groups. The Kluyveromyces phaffii group encompasses the species Kluyveromyces blattae, K. phaffii and Kluyveromyces yarrowii. The Kluyveromyces marxianus group is a monophyletic group consisting of the species Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, K. marxianus and Kluyveromyces wickerhamii. The monophyletic Kluyveromyces thermotolerans group is formed by K. thermotolerans, Kluyveromyces waltii and Saccharomyces kluyveri (which appears in the mitochondrial tree as the sister clade of the K. marxianus group). Finally, the Saccharomyces cerevisiae group contains the remaining Kluyveromyces species, as well as the reference Saccharomyces species (sensu lato and sensu stricto) and Candida glabrata (the phylogenetic relationships within this group are unclear according to the bootstrap test). The phylogenetic relationships obtained for this mitochondrial gene are, for the most part, congruent with previous trees based on nuclear rRNA sequences, except for the position of K. yarrowii and the close relationship between the K. marxianus and K. thermotolerans groups. These differences, as well as the existence of these groups, are discussed in the context of previous studies based on phenotypic, genetic and molecular data. Although additional studies are required to decipher the phylogenetic relationships between the genus Kluyveromyces and the closely related genera Saccharomyces, Torulaspora and Zygosaccharomyces, future changes to their taxonomic status should take account of the existence of these four groups of Kluyveromyces species.
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Taxonomic relationships among the taxa in the Candida guilliermondii complex, as revealed by comparative electrophoretic karyotyping.
More LessElectrophoretic karyotypes of 15 type strains of the taxa in the Candida guilliermondii complex including Candida fukuyamaensis Nakase et al. and Candida xestobii Yarrow et S. A. Meyer were comparatively analysed by using the CHEF (contour-clamped homogeneous electric field) method of PFGE. Eighteen strains (isolated from various natural sources in China) which were originally identified as C. guilliermondii by conventional methods were also included. Six electrophoretic karyotype groups were recognized among the strains compared. The following type strains were grouped together with the type strains of C. guilliermondii (Castellani) Langeron et Guerra and Pichia guilliermondii Wickerham: Blastodendrion arztii Ota, Blastodendrion krausi Ota, Candida amidovorans Balloni et al., C. guilliermondii var. japonica Sugiyama et Goto, Candida mamillae S. Goto, Candida parapsilosis (Ashford) Langeron et Talice var. tokyoensis Suzuki et al., C. parapsilosis var. tuxtlensis Herrera et al. and six Chinese strains. The type strain of Torulopsis kestonii Scarr et Rose was classified into the group together with the type strain of Candida fermentati (Saito) Bai and seven Chinese strains. The group represented by the type strain of C. fukuyamaensis included five other strains isolated in China. The type strains of Candida xestobii, C. guilliermondii var. carpophila Phaff et M. W. Miller and Trichosporon appendiculare Batista et al. were separated into three different groups, respectively. Taxonomic relationships among the taxa studied are discussed.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)