- Volume 52, Issue 3, 2002
Volume 52, Issue 3, 2002
- Articles
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'Candidatus mycoplasma haemodidelphidis' sp. nov., 'Candidatus mycoplasma haemolamae' sp. nov. and Mycoplasma haemocanis comb. nov., haemotrophic parasites from a naturally infected opossum (Didelphis virginiana), alpaca (Lama pacos) and dog (Canis familiaris): phylogenetic and secondary structural relatedness of their 16S rRNA genes to other mycoplasmas.
More LessThe 16S rRNA sequence of newly characterized haemotrophic bacteria in an opossum (Didelphis virginiana) and alpaca (Lama pacos) was determined. In addition, the 16S rRNA sequence of a haemotrophic parasite in the dog (Canis familiaris) was determined. Sequence alignment and evolutionary analysis as well as secondary structural similarity and signature nucleotide sequence motifs of their 16S rRNA genes, positioned these organisms in the genus Mycoplasma. The highest scoring sequence similarities were 16S rRNA genes from haemotrophic mycoplasma species (Haemobartonella and Eperythrozoon spp.). However, the lack of several higher-order structural idiosyncrasies used to define the pneumoniae group, suggests that these organisms and related haemotrophic mycoplasmas represent a new group of mycoplasmas. It is recommended that the organisms be named 'Candidatus Mycoplasma haemodidelphidis', 'Candidatus Mycoplasma haemolamae' and Mycoplasma haemocanis comb. nov., to provide some indication of the target cell and host species of these parasites, and to reflect their phylogenetic affiliation.
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Pasteurella skyensis sp. nov., isolated from Atlantic salmon (Salmo salar L.).
More LessFrom four separate incidents of disease in farmed Atlantic salmon over a four-year period, gram-negative rod-shaped bacteria were consistently isolated by culture on sea-water blood agar. Biochemical and physiological tests indicated that the organism was related to the family Pasteurellaceae, and this was confirmed from the 16S rRNA gene sequence. Comparison of the 16S rRNA gene sequence with those of 45 members of the Pasteurellaceae showed that the closest phylogenetic relationship was with an organism termed 'Pasteurella phocoenarum', isolated from a porpoise, for which the 16S rRNA gene sequence has been recorded but for which the properties have yet to be published. It is proposed that this bacterium isolated from salmon should be classified as a new species, namely Pasteurella skyensis sp. nov. The type strain of Pasteurella skyensis sp. nov. is strain 95A1T (= NCTC 13204T = NCIMB 13593T).
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Aeromonas hydrophila subsp. dhakensis subsp. nov., isolated from children with diarrhoea in Bangladesh, and extended description of Aeromonas hydrophila subsp. hydrophila (Chester 1901) Stanier 1943 (approved lists 1980).
More LessA group of 10 Aeromonas hydrophila-like strains referred to as group BD-2, which mainly comprised haemolytic and cytotoxic isolates from diarrhoeal children in Bangladesh, was subjected to a polyphasic taxonomic study including fluorescent amplified fragment length polymorphism (FAFLP) and ERIC-PCR fingerprinting, microplate DNA-DNA hybridization and extensive phenotypic characterization. Comparison of FAFLP and ERIC-PCR genotypic profiles indicated that the group BD-2 isolates constituted a separate taxon that was most closely related to A. hydrophila DNA hybridization group (HG) 1. Determination of DNA-DNA hybridization values with type and reference strains of all known Aeromonas taxa revealed that the BD-2 group represented a homogeneous taxon (internal DNA homology, 77-94%) that exhibited 78-92% DNA relatedness with the type strain of A. hydrophila HG1. These results indicated that the BD-2 group belongs genotypically to A. hydrophila HG1, but examination of 152 phenotypic characteristics revealed that the group BD-2 isolates differed from representatives of HG1 in eight biochemical properties. The diagnostic value of at least three of these tests, namely utilization of urocanic acid and L-arabinose and acid production from L-arabinose, has been confirmed outside this study by other workers. Collectively, the genotypic and phenotypic data reported suggest that the BD-2 group represents a subspecies of A. hydrophila, for which the name Aeromonas hydrophila subsp. dhakensis subsp. nov. is proposed. Its type strain is P21T (= LMG 19562T= CCUG 45377T). An extended description of A. hydrophila subsp. hydrophila (Chester 1901) Stanier 1943 (Approved Lists 1980) is given.
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Mitsuokella jalaludinii sp. nov., from the rumens of cattle in Malaysia.
G Q Lan, Y W Ho and N AbdullahFive strains of phytase-producing, gram-negative, non-spore-forming, non-motile, small, stout, rod-shaped, strictly anaerobic, fermentative bacteria were isolated from the rumens of cattle in Malaysia. All five strains had morphological, physiological and biochemical features in common. Although these strains had many physiological and biochemical characteristics that were identical to those of the Mitsuokella multacida type strain (ATCC 27723T), they could be distinguished from this species by means of the following characteristics: a smaller cell size (1.2-2.4 microm long and 0.6-0.8 microm wide); a lower final pH value (3.8-4.0) in peptone/yeast extract/glucose broth; inhibition by 0.001% brilliant green; insensitivity to kanamycin (100 microg ml(-1)) and penicillin (10 microg ml(-1)); a higher optimum growth temperature (approx. 42 degrees C); the ability to grow at 45 and 47 degrees C; the ability to ferment glycerol, sorbitol and amidon; and the inability to ferment mannitol, rhamnose, D-tagatose and melezitose. The G+C content of the type strain (M 9T) of these five strains was 56.9 mol%. Analysis of the 16S rRNA gene sequence of type strain M 9T indicated that the strain falls within the genus Mitsuokella. The sequence similarity between type strain M 9T and Mitsuokella multacida was 98.7%. The DNA-DNA relatedness between type strain M 9T and Mitsuokella multacida type strain DSM 20544T (= ATCC 27723T) was 63.8%, indicating that, in spite of a high level of similarity for the 16S rRNA gene sequence, type strain M 9T is independent of Mitsuokella multacida at the species level. On the basis of these results, a new species, Mitsuokella jalaludinii sp. nov., is proposed for these strains. The type strain is M 9T (= DSM 13811T = ATCC BAA-307T).
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Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor.
A novel, regular to irregular, coccoid-shaped, anaerobic, Fe(III)-reducing microorganism was isolated from the Guaymas Basin hydrothermal system at a depth of 2000 m. Isolation was carried out with a new technique using Fe(III) oxide as the electron acceptor for the recovery of colonies on solid medium. The isolate, designated strain 234T, was strictly anaerobic and exhibited a tumbling motility. The cells had a single flagellum. Strain 234T grew at temperatures between 65 and 90 degrees C, with an optimum at about 88 degrees C. The optimal salt concentration for growth was around 19 g l(-1). The isolate was capable of growth with H2 as the sole electron donor coupled to the reduction of Fe(III) without the need for an organic carbon source. This is the first example of a dissimilatory Fe(III)-reducing micro-organism capable of growing autotrophically on hydrogen. In addition to molecular hydrogen, strain 234T oxidizes pyruvate, acetate, malate, succinate, peptone, formate, fumarate, yeast extract, glycerol, isoleucine, arginine, serine, glutamine, asparagine, stearate, palmitate, valerate, butyrate and propionate with the reduction of Fe(III). This isolate is the first example of a hyperthermophile capable of oxidizing long-chain fatty acids anaerobically. Isolate 234T grew exclusively with Fe(III) as the sole electron acceptor. The G+C content was 58.7 mol%. Based on detailed analysis of its 16S rDNA sequence, G+C content, distinguishing physiological features and metabolism, strain 234T is proposed to represent a novel genus within the Archaeoglobales. The name proposed for strain 234T is Geoglobus ahangari gen. nov., sp. nov..
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Haloferax alexandrinus sp. nov., an extremely halophilic canthaxanthin-producing archaeon from a solar saltern in Alexandria (Egypt).
More LessAn extremely halophilic red micro-organism designated strain TM(T) was isolated from a solar saltern in Alexandria, Egypt. The micro-organism stains gram-negative, is very pleomorphic, non-motile and strictly aerobic and requires at least 10 g NaCl l(-1) for growth. The growth optimum is 250 g NaCl l(-1). Growth is also observed over a wide range of MgSO4 concentrations (10-40 g l(-1)). Aerobic reduction of nitrate without gas production was detected. Cells grew aerobically in a minimal salts medium containing ammonium chloride and glucose. Strain TM(T) produced acid from fructose, glucose, rhamnose, maltose and glycerol. The G+C content of the DNA was 59.5+/-0.3 mol %. On the basis of polar lipid analysis, the isolate belonged to the genus Haloferax. Analysis of the 16S rDNA sequence showed the highest similarity (>99%) to be to the type strain Haloferax volcanii. Although the spectrum of antibiotic susceptibility was similar to that of validly described species of the genus Haloferax, the strain could be distinguished from them by its different response to josamycin and rifampicin. Strain TM(T) is unique within the genus Haloferax in producing canthaxanthin. Comparative analysis of phenotypic properties and DNA-DNA hybridization between strain TM(T) and Haloferax species supported the conclusion that TM(T) is a novel species within this genus, for which the name Haloferax alexandrinus sp. nov. is proposed. The type strain is TM(T) (= JCM 10717T = IFO 16590T).
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Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov.
More LessThe phylogenetic relationships of Oceanospirillum strains were analysed by using the nucleotide sequences of 16S rRNA and gyrB genes. Results from sequence analysis demonstrated that the Oceanospirillum core group consisted of four species, Oceanospirillum linum, Oceanospirillum maris, Oceanospirillum beijerinckii and Oceanospirillum multiglobuliferum, with enough distance to separate them as different species. However, four other Oceanospirillum species occupied taxonomic positions separate from the Oceanospirillum core group: Oceanospirillum jannaschii, Oceanospirillum japonicum and Oceanospirillum kriegii in the gamma-Proteobacteria and Oceanospirillum pusillum in the alpha-Proteobacteria. Oceanospirillum jannaschii clustered with Marinobacterium georgiense, Pseudomonas iners and Pseudomonas stanieri on the basis of phylogenetic analysis of 16S rRNA and gyrB genes. The other three species did not cluster with known genera. Also, the sequence similarity values of the gyrB genes between the three subspecies of Oceanospirillum maris and those between the two subspecies of Oceanospirillum beijerinckii were above 99%. The close relationships between the subspecies of Oceanospirillum maris and of Oceanospirillum beijerinckii were further supported by similar physiological properties and high DNA-DNA hybridization values, suggesting that these subspecies should not be regarded as valid. From these results, Oceanospirillum sensu stricto should be defined to consist of Oceanospirillum linum, Oceanospirillum maris, Oceanospirillum beijerinckii and Oceanospirillum multiglobuliferum. We propose to create the following new genera: Pseudospirillum gen. nov. for Oceanospirillum japonicum as Pseudospirillum japonicum comb. nov.; Oceanobacter gen. nov. for Oceanospirillum kriegii as Oceanobacter kriegii comb. nov.; and Terasakiella gen. nov. for Oceanospirillum pusillum as Terasakiella pusilla comb. nov. The transfer is proposed of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Furthermore, Pseudomonas iners should be reclassified as a strain of Marinobacterium georgiense. Finally, the subspecies of Oceanospirillum maris (O. maris subsp. maris, O. maris subsp. hiroshimense and O. maris subsp. williamsae) and Oceanospirillum beijerinckii (O. beijerinckii subsp. beijerinckii and O. beijerinckii subsp. pelagicum) should be combined as Oceanospirillum maris and Oceanospirillum beijerinckii, respectively.
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Transfer of Tsukamurella wratislaviensis Goodfellow et a. 1995 to the genus Rhodococcus as Rhodococcus wratislaviensis comb. nov..
More LessA polyphasic study was undertaken to clarify the taxonomic position of the type strain (N805T) of Tsukamurella wratislaviensis. This organism showed a combination of phenotypic properties, notably chemotaxonomic markers, consistent with its classification in the genus Rhodococcus. Comparative 16S rDNA sequencing studies indicated that strain 805T falls into the Rhodococcus erythropolis subclade, where it forms a monophyletic group with the type strains of Rhodococcus opacus and Rhodococcus percolatus. The close relationship between these strains was underpinned by the results of mycolic acid analyses. However, strain N805T was distinguished from the R. opacus and R. percolatus strains in DNA-DNA pairing experiments and by using a range of phenotypic properties. In light of these studies, it is clear that strain N805T is misclassified in the genus Tsukamurella. It is, therefore, proposed that Tsukamurella wratislaviensis Goodfellow et al. 1995 be transferred to the genus Rhodococcus as Rhodococcus wratislaviensis comb. nov..
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Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs.
More LessIn spite of its shortcoming, analysis of PCR-derived rDNA libraries is being employed increasingly to investigate microbial diversity within many ecosystems. In the present investigation, the effects of the number of PCR cycles (10 vs 25 cycles) on the inferred structure of a 16S rDNA library have been examined. Seventy-five 25-cycle sequences were retrieved and analysed in comparison with 284 10-cycle sequences already described in a previous study. The 359 clones obtained were classified into 94 molecular species (at least 98% sequence similarity). At the level of large phylogenetic groups, the two cloned rDNA libraries were not different. A mathematical model was developed in order to estimate the number of molecular species expected if further sequencing was performed. Coverage-based computing, projections and statistical analysis demonstrated that the structures of the two PCR-derived rDNA libraries were different and that the 25-cycle rDNA library displayed reduced diversity. It is suggested that the number of PCR cycles used for amplification of 16S rDNA genes for phylogenetic diversity studies must therefore be kept as small as possible.
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Thermodesulfobacterium hydrogeniphilum sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent at Guaymas Basin, and emendation of the genus Thermodesulfobacterium.
A thermophilic, non-spore-forming, marine, sulfate-reducing bacterium, strain SL6T, was isolated from deep-sea hydrothermal sulfides collected at Guaymas Basin. The gram-negative-staining cells occurred singly or in pairs as small, highly motile rods. The temperature range for growth was 50-80 degrees C with an optimum at 75 degrees C. The pH range for growth at 70 degrees C was 6.3-6.8, with an optimum at 6.5. The NaCl concentration range for growth was 5-55 g l(-1), with an optimum at 30 g l(-1). H2 and CO2 were the only substrates for growth and sulfate reduction. However, growth was stimulated by several organic compounds. Sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not used as electron acceptors. Pyruvate, lactate and malate did not support fermentative growth. Desulfoviridin was not detected. The G+C content of the genomic DNA was 28 mol%. On the basis of 16S rRNA sequence analysis, strain SL6T is related to members of the genus Thermodesulfobacterium. However, the novel organism possesses phenotypic and phylogenetic traits that differ from those of its closest relatives. Therefore, it is proposed that this isolate, which constitutes the first marine representative of this genus, should be described as the type strain of a novel species, Thermodesulfobacterium hydrogeniphilum sp. nov. The type strain is SL6T (= DSM 14290T = JCM 11239T). Because of the phenotypic characteristics of the novel species, it is also proposed that the description of the genus Thermodesulfobacterium requires emendation.
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Methylobacterium suomiense sp. nov. and Methylobacterium lusitanum sp. nov., aerobic, pink-pigmented, facultatively methylotrophic bacteria.
Two aerobic, pink-pigmented, facultatively methylotrophic bacteria, strains F20T and RXM(T), are described taxonomically. On the basis of their phenotypic and genotypic properties, the isolates are proposed as novel species of the genus Methylobacterium, Methylobacterium suomiense sp. nov. (type strain F20T = VKM B-2238T = NCIMB 13778T) and Methylobacterium lusitanum sp. nov. (type strain RXMT = VKM B-2239T = NCIMB 13779T).
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Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission.
More LessIf open reading frames (ORFs) have been transmitted primarily by vertical descent, the distributional profile of orthologues of each ORF should be congruent with the organismal tree or a subtree thereof. Distributional patterns not reconciled parsimoniously with tree-like descent and loss are prima facie evidence of lateral gene transfer. Herein, a rigorous criterion for recognizing ORF distributions is described and implemented; it does not require the inference of phylogenetic trees, nor does it assume any specific tree. Because lineage-specific differences in rates of sequence change can also generate unexpected distributional patterns, rate artefacts were controlled for by requiring pairwise matches between ORFs to exceed a rigorous inclusion threshold, but absence of a match was assessed against a more-permissive exclusion threshold. Applying this dual-threshold criterion to cross-domain and cross-phylum distributional patterns for ORFs in 23 bacterial genomes, a relative abundance of ORFs was observed that find a match in exactly seven other bacterial phyla; 94-99% of these ORFs also find matches among the Archaea and/or Eukarya. In the larger (and some smaller) bacterial genomes, ORFs that find matches in exactly one other bacterial phylum are also relatively abundant, but fewer of these have non-bacterial homologues; most of their matches within the Bacteria are to the Proteobacteria and/or Firmicutes, which cannot be sister lineages to all bacteria. ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes.
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Salinicoccus alkaliphilus sp. nov., a novel alkaliphile and moderate halophile from Baer Soda Lake in Inner Mongolia Autonomous Region, China.
More LessA novel alkaliphilic and moderately halophilic gram-positive coccus, designated strain T8T, was isolated from Baer Soda Lake in Inner Mongolia Autonomous Region, China. Strain T8T grew in the presence of 0-25% (w/v) NaCl and at pH 6.5-11.5, with optimum growth at 10% (w/v) NaCl and pH 9.0. It grew at 10.0-46.0 degrees C, with an optimum growth temperature of 32.0 degrees C. The organism was strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. The DNA G+C content was 49.6 mol%. The cell wall contained Lys and Gly. The major isoprenoid quinone was menaquinone 6 (MK-6). Phylogenetic analyses based on 16S rDNA sequence comparisons indicate that strain T8T is a member of the genus Salinicoccus. DNA-DNA relatedness of less than 50% with the described species of Salinicoccus supported the view that this organism represents a novel species of the genus Salinicoccus. The name Salinicoccus alkaliphilus sp. nov. is proposed for this novel species. The type strain is T8T (= AS 1.2691T = JCM 11311T).
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Thermaerobacter subterraneus sp. nov., a novel aerobic bacterium from the Great Artesian Basin of Australia, and emendation of the genus Thermaerobacter.
More LessA strictly aerobic, thermophilic, gram-positive, spore-producing, rod-shaped bacterium (2.0-10.0 x 0.3 microm), designated isolate C21T, was isolated from a sample collected from an open drain run-off channel of a bore in the Great Artesian Basin of Australia (New Lorne Bore, registered number 17263). Isolate C21T grew optimally at 70 degrees C (temperature range for growth was 55-80 degrees C) and pH 8.5 (pH range for growth was 6.0-10.5), with a generation time of 90 min. The isolate was strictly heterotrophic and grew on yeast extract and/or tryptone as carbon and energy sources. An increase in growth was not observed with carbohydrates (sucrose, cellobiose, glucose, dextrin, amylopectin, chitin, carboxymethylcellulose, xylan, inositol, arabinose, mannose, fructose, gelatin, starch, amylose, galactose, dextrose, xylose, maltose, L-sorbose or raffinose), organic acids (lactic acid, pyruvic acid or benzoic acid) or Casamino acids as sole carbon sources or in the presence of yeast extract and/or tryptone. The G+C content of the chromosomal DNA, as measured by the thermal denaturation method, was 71 mol%. Phylogenetic analysis of the 16S rRNA gene of isolate C21T placed it as a member of the phylum Firmicutes, with Thermaerobacter marianensis as the closest relative (similarity value of 98%). However, isolate C21T and T. marianensis differed in a number of key physiological and phenotypic properties and also had a DNA-DNA hybridization value of less than 5%. Based on this evidence, it is proposed that strain C21T be designated Thermaerobacter subterraneus sp. nov. (type strain C21T = ATCC BAA-137T = DSM 13965T).
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Reclassification of Clostridium hydroxybenzoicum as Sedimentibacter hydroxybenzoicus gen. nov., comb. nov., and description of Sedimentibacter saalensis sp. nov..
More LessStrain ZF2T, isolated from freshwater sediment, is a motile, rod-shaped, gram-positive, endospore-forming, amino acid- and pyruvate-utilizing, anaerobic bacterium. It requires yeast extract for growth. Carbohydrates are not utilized. The optimal temperature and pH for growth are 37 degrees C and 6.8-7.3, respectively. The G+C content of the DNA is 34.0 mol %. A 16S rDNA sequence analysis of strain ZF2T revealed that the highest similarity (94.4%) was shared with Clostridium hydroxybenzoicum JW/Z-1T. Strain ZF2T, however, was not able to carboxylate phenol or to decarboxylate 4-hydroxybenzoate, which are characteristic properties of strain JW/Z-1T. The degree of 16S rDNA relatedness, together with the physiological and chemotaxonomic properties, suggest that strain ZF2T represents a novel species that is clearly distinct from Clostridium hydroxybenzoicum JW/Z-1T. In a phylogenetic dendrogram, both strains form a separate cluster that is peripherally associated with the Peptostreptococcus group (cluster XIII) of the clostridia and the lineage of Helcococcus kunzii. Strains ZF2T and JW/Z-1T show a somewhat deeper branching from the cluster XII clostridia Clostridium purinolyticum and Clostridium acidiurici. The latter strains possessed the closest 16S rDNA similarity (between 88.4 and 90.7%), but were clearly separated by phenotypic markers. Therefore, a new genus, Sedimentibacter gen. nov., is described, comprising Sedimentibacter hydroxybenzoicus gen. nov., comb. nov., as the type species of the genus, with JW/Z-1T (= ATCC 51151T = DSM 7310T) as the type strain, and the novel species Sedimentibacter saalensis sp. nov., with strain ZF2T (= DSM 13558T = ATCC BAA-283T) as the type strain.
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Transfer of Bifidobacterium inopinatum and Bifidobacterium denticolens to Scardovia inopinata gen. nov., comb. nov., and Parascardovia denticolens gen. nov., comb. nov., respectively.
More LessBifidobacterium inopinatum Crociani et al. 1996 and Bifidobacterium denticolens Crociani et al. 1996 have distinct phenotypic characteristics and low G+C contents compared with other bifidobacteria. In the 16S rRNA phylogenetic tree, these two species grouped in an independent subcluster. In our previous work, partial heat-shock protein 60 (HSP60) gene-sequence analysis also indicated that these two species had distinct taxonomic positions. In this work, the complete HSP60 genes of five representative bacterial strains were sequenced by using an inverse PCR method. The complete sequence similarities turned out to be at the same level as those of the partial genes, thus confirming the result based on partial sequence analysis. On the basis of all the evidence mentioned above, it is proposed that these two species should be transferred to two new genera as Scardovia inopinata gen. nov., comb. nov., and Parascardovia denticolens gen. nov., comb. nov.
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Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the alpha-proteobacteria.
Four bacterial strains were isolated from palm brown sugar and ragi collected in Bali and Yogyakarta, Indonesia, by an enrichment culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates constituted a cluster separate from the genera Acetobacter, Gluconobacter, Acidomonas, Gluconacetobacter and Asaia with a high bootstrap value in a phylogenetic tree. The isolates had high values of DNA-DNA similarity (78-100%) between one another and low values of the similarity (7-25%) to the type strains of Acetobacter aceti, Gluconobacter oxydans, Gluconacetobacter liquefaciens and Asaia bogorensis. The DNA base composition of the isolates ranged from 56.8 to 57.2 mol% G+C with a range of 0-4 mol%. The major quinone was Q-10. The isolates oxidized acetate and lactate to carbon dioxide and water, but the activity was weak, as with strains of Asaia bogorensis. The isolates differed from Asaia bogorensis strains in phenotypic characteristics. The name Kozakia baliensis gen. nov., sp. nov., is proposed for the four isolates. Strain Yo-3T (= NRIC 0488T = JCM 11301T = IFO 16664T = DSM 14400T) was isolated from palm brown sugar collected in Bali, Indonesia, and was designated as the type strain.
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Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov..
More LessFormal nomenclature is proposed for five methanogens, isolated from horse, pig, cow, goose and sheep faeces, that represent four novel species of the genus Methanobrevibacter. The four species, Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov., are distinguished from each other by a lack of genomic DNA reassociation and from previously described members of the genus on the basis of differences in the sequences of the 16S rRNA genes.
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The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus.
B Lanoot, M Vancanneyt, I Cleenwerck, L Wang, W Li, Z Liu and J SwingsA collection of 93 Streptomyces reference strains were investigated using SDS-PAGE of whole-cell proteins. Computer-assisted numerical analysis revealed 24 clusters encompassing strains with very similar protein profiles. Five of them grouped several type strains with visually identical patterns. DNA-DNA hybridizations revealed homology values higher than 70% among these type strains. According to the current species concept, it is proposed that Streptomyces albosporeus subsp. albosporeus LMG 19403T is considered as a subjective synonym of Streptomyces aurantiacus LMG 19358T, that Streptomyces aminophilus LMG 19319T is considered as a subjective synonym of Streptomyces cacaoi subsp. cacaoi LMG 19320T, that Streptomyces niveus LMG 19395T and Streptomyces spheroides LMG 19392T are considered as subjective synonyms of Streptomyces caeruleus LMG 19399T, and that Streptomyces violatus LMG 19397T is considered as a subjective synonym of Streptomyces violaceus LMG 19360T.
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Weissella soli sp. nov., a lactic acid bacterium isolated from soil.
More LessPhylogenetic analysis of the 16S rRNA gene of bacterial isolates from garden soil showed relatedness to Weissella kandleri and Weissella confusa. However, the sequences had notable differences, and DNA-DNA hybridizations confirmed that the isolates are separate from these two species. The isolates could be further distinguished from all previously described Weissella species by electrophoretic analysis of whole-cell proteins, as well as by the results from different biochemical tests. The name Weissella soli is proposed for the new species, the type strain being Mi268T (= LMG 20113T = DSM 14420T).
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Chelatobacter heintzii (Auling et al. 1993) is a later subjective synonym of Aminobacter aminovorans (Urakami et al. 1992).
More LessChelatobacter heintzii, which was described as a nitrilotriacetate-utilizing organism, was re-investigated in order to clarify its taxonomic position. On the basis of 16S rDNA sequence comparisons, it is obvious that this species clusters phylogenetically with species of the genus Aminobacter. The results of investigations of the fatty acid patterns, polar lipid profiles, polyamine patterns and quinone system supported this placement. The substrate-utilization profiles and fatty acid patterns of four strains (belonging to two different genomovars) revealed homogeneous results and showed high levels of similarity to Aminobacter aminovorans. DNA-DNA similarity studies confirmed that both genomovars of Chelatobacter heintzii belong to Aminobacter aminovorans. It could be shown that all species of this group are highly interrelated. On the basis of these data and previously published results, it is obvious that Chelatobacter heintzii is a later subjective synonym of Aminobacter aminovorans.
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Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov.
More LessThe characteristics of the fusiform species Bacteroides forsythus, isolated from human periodontal pockets, were examined. 165 rDNA sequence analysis confirmed that B. forsythus was not a species within the genus Bacteroides sensu stricto. Although B. forsythus was phylogenetically related to Bacteroides distasonis and Bacteroides merdae in the phylogenetic tree, the ratio of anteiso-15:0 to iso-15:0 in whole-cell methanolysates of B. forsythus was different from those of B. distasonis, B. merdae and other Bacteroides species. B. forsythus did not grow on medium containing 20% bile, but members of the Bacteroides fragilis group did. B. forsythus was the only species tested that was trypsin-positive in API ZYM tests. The dehydrogenase enzyme pattern was of no use for the differentiation of B. forsythus and the B. fragilis group. On the basis of these data, a new genus, Tannerella, is proposed for Bacteroides forsythus, with one species, Tannerella forsythensis corrig., gen. nov., comb. nov. The type strain of Tannerella forsythensis is JCM 10827T (= ATCC 43037T).
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Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide.
More LessA marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the alpha-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov..
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The cpcB-cpcA locus as a tool for the genetic characterization of the genus Arthrospira (Cyanobacteria): evidence for horizontal transfer.
More LessTo investigate the genetic diversity of the genus Arthrospira and to compare it with other cyanobacteria, sequences of 670 nt from the phycocyanin operon were determined for 23 natural, cultivated or commercial strains of Arthrospira and compared with sequences from 20 other non-Arthrospira cyanobacterial strains. The sequenced DNA fragment comprises the last 255 nt of cpcB, the cpcB-cpcA spacer and the first 304 nt of cpcA. The resulting phylogenetic tree confirms that the genus Arthrospira is not related to Spirulina. So far, cpcB-cpcA data suggest that the closest relative of Arthrospira is Planktothrix. Based on this locus, the genus Arthrospira consists of three genetically clustered lineages. However, the distribution of nucleotide substitutions indicates that these three lineages are not the result of a simple cladogenesis characterized by the accumulation of independent substitutions. Instead, the observed clustering is the result of horizontal transfers of blocks of sequences. Analysis of the distribution of substitutions in the sequenced fragment indicates a point of intragenic recombination close to the stop codon of cpcB. The capacity of exchange of genetic material among strains probably explains why morphology and geographical origin do not correlate with the cpcB-cpcA clusters. Nevertheless, this study shows for the first time that the genus Arthrospira, represented here by cultivated and wild specimens, is clearly monophyletic. Moreover, the cpcB-cpcA DNA fragment, comprising both highly and moderately variable regions, allows (1) a strict differentiation of the taxon Arthrospira from other cyanobacteria (using the coding regions only) and (2) the study of relationships inside Arthrospira (using both the coding and non-coding regions).
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Bacillus subterraneus sp. nov., an iron- and manganese-reducing bacterium from a deep subsurface Australian thermal aquifer.
More LessA facultatively anaerobic bacterium, designated strain COOI3B(T) (= ATCC BAA 136T = DSM 13966T), was isolated from the waters emitted by a bore well tapping the deep subterranean thermal waters of the Great Artesian Basin of Australia. The cells were straight to slightly curved rods (0.5-0.8 x 2-25 microm) that occurred singly and rarely in pairs or in chains. Strain COOI3B(T) was motile by peritrichous flagella. It stained gram-negative, but electron micrographs showed a gram-positive-type cell wall. Spores were never observed and cells were heat-sensitive. Yeast extract at 0.02% (w/v) was required for growth and could also be used as a sole carbon and energy source at concentrations higher than 0.1% (w/v). The strain utilized amorphous iron(III), manganese(IV), nitrate, nitrite and fumarate as electron acceptors in the presence of yeast extract, glucose, sucrose, fructose, maltose, xylose, starch, glycerol, ethanol or lactate. Electron acceptors were not obligately required and growth was better in the presence of nitrate than in its absence. Acid was not produced from growth on carbohydrates. Tryptophan deaminase, H2S, arginine dihydrolase, lysine decarboxylase, beta-galactosidase, arabinosidase, glucuronidase, glucosaminidase, nitroanilidase, xylosidase and ornithine decarboxylase were not produced. Starch and gelatin, but not casein, were hydrolysed. Aesculin and catalase, but not oxidase and urease, were produced. Strain COOI3B(T) grew optimally at temperatures between 37 and 40 degrees C (the temperature growth range was 25-45 degrees C) and at pH 7.0-9.0 (the pH growth range was 6.0 to 9.5) with 5% (w/v) NaCl (the NaCl concentration growth range was 0.9%, w/v). The DNA base composition was 43 +/- 1 mol % G+C. Phylogenetic analysis indicated that it was a member of the family Bacillaceae, Bacillus infernus and Bacillus firmus being the closest phylogenetic neighbours (having a mean similarity value of 96%); hence, strain COOI3B(T) is designated as a novel species, Bacillus subterraneus sp. nov.
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Georgenia muralis gen. nov., sp. nov., a novel actinobacterium isolated from a medieval wall painting.
Two bacterial strains, designated 1A-C(T) and 3A-1, were studied and, using these results and previously published data, taxonomically classified. Cells of the strains exhibited a rod-coccus cycle. The peptidoglycan determined for 1A-C(T) was of type A4alpha with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of L-Lys <-- L-Glu. The menaquinone systems of the two strains contained MK-8(H4) (82-94%) and MK-7(H4) (3-11%). The polar lipid profiles consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, two unidentified phospholipids and an unidentified glycolipid. The fatty acid profiles contained predominantly ai-C15:0 and significant amounts of i-C14:0 and i-C15:1 fatty acids. Genomic fingerprints clearly distinguished strains 1A-C(T) and 3A-1 from each other. DNA-DNA relatedness between the two strains (92%) demonstrated that they are members of a single species. Analyses of the 16S rDNA sequences of strains IA-C(T) and 3A-1, which were almost identical (99.6% sequence similarity), and comparison with corresponding sequences demonstrated that they represent a novel lineage within the suborder Micrococcineae, most closely related to species of the genera Beutenbergia, Bogoriella and Cellulomonas (94.7-95.7% sequence similarity). The results demonstrate that the two strains are members of a single new genus and a single novel species. Thus, the name Georgenia muralis gen. nov., sp. nov. is proposed. The type strain is strain 1A-C(T) (= DSM 14418T = CCM 4963T). Another strain of the species is strain 3A-1 (= DSM 14419 = CCM 4964).
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Tetrasphaera elongata sp. nov., a polyphosphate-accumulating bacterium isolated from activated sludge.
More LessA new meso-diaminopimelic acid-containing, gram-positive bacterium was isolated from an activated sludge reactor showing enhanced biological phosphorus removal activity. The isolate was an asporogenous oval to rod-shaped bacterium, but occasionally formed clumps. The Neisser staining was positive, suggesting intracellular polyphosphate granules. The isolate was an aerobic chemoheterotroph which was capable of utilizing various sugars, sugar alcohols and organic acids. It contained anteiso-C15:0, iso-C15:0, iso-C14:0 and C16:0 as the major cellular fatty acids, and menaquinone-8(H4) as the major quinone. The G+C content of the genomic DNA was 69.6 mol%. Analysis of the 16S rDNA sequence revealed that the isolate is a new member of the family Intrasporangiaceae. The closest relatives were Tetrasphaera species. On the basis of the phenotypic and phylogenetic distinctiveness of the isolate, it was concluded that the organism represents a new species in the genus Tetrasphaera, for which the name Tetrasphaera elongata sp. nov. is proposed. The type strain is strain Lp2T (= JCM 11141T = DSM 14184T).
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Amycolatopsis eurytherma sp. nov., a thermophilic actinomycete isolated from soil.
The taxonomic positions of two thermophilic actinomycetes isolated from soil were established in a polyphasic taxonomic study. The organisms were shown to have phenotypic properties typical of members of the genus Amycolatopsis and formed a distinct phyletic line in the Amycolatopsis methanolica 16S rDNA subclade. They also had many phenotypic properties in common and formed a genomic species that was closely related to, albeit distinct from, the type strain of A. methanolica. A range of phenotypic properties distinguished the isolates from representatives of all validly described species of Amycolatopsis. Genotypic and phenotypic data show that the two strains should be classified in the genus Amycolatopsis as a novel species, Amycolatopsis eurytherma sp. nov.; the type strain is strain NT202T (= DSM 44348T = NCIMB 13795T).
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Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile.
More LessA poly(3-hydroxybutyrate) (PHB)-degrading, gram-negative, aerobic bacterium, strain HS(T), was isolated from a hot spring and chemotaxonomically and phylogenetically characterized. The oxidase-positive, weakly catalase-positive, non-pigmented cells (0.6 x 2.6 microm) exhibited a single polar flagellum and accumulated PHB granules. Strain HS(T) was capable of manganese oxidation. Highest growth rate was attained at 50 degrees C. The optimum pH for growth was 7-8. The major respiratory quinone was ubiquinone-8 and major cellular fatty acids were C16:0, C16:1 and C18:1. The G+C content of the DNA was 66.2 mol%. Comparative 16S rDNA analysis indicated that strain HS(T) is related to the Rubrivivax subgroup and the family Comamonadaceae. The nearest phylogenetic relatives were Ideonella dechloratans (92.1% similarity), Leptothrix discophora (93.6%), Roseateles depolymerans (92.4%) and Rubrivivax gelatinosus (92.2%). On the basis of its phylogenetic and phenotypic properties, it is proposed that this isolate be designated Caldimonas manganoxidans gen. nov., sp. nov.; the type strain is HS(T) (= JCM 10698T = IFO 16448T = ATCC BAA-369T).
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Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.
A bacterial isolate, ME102T, was obtained from an n-hexadecane enrichment culture of seawater/sediment samples collected in the harbour of Messina (Italy). This gram-negative, aerobic, motile, rod-shaped bacterium used a narrow spectrum of organic compounds, including aliphatic hydrocarbons, alkanoates and alkanoles, as carbon and energy sources. None of the sugars, organic acids or amino acids tested was used. During cultivation on n-alkanes as the sole source of carbon and energy, the cells formed a biofilm on the surface of the alkane droplets. Large-scale (sometimes >50% of the cell mass) intracellular accumulation of alkanoates occurred in cells adsorbed on the alkane surface and under nitrogen-limiting conditions. 16S rRNA gene sequence analysis showed that this isolate represents a distinct lineage in the gamma-Proteobacteria and has about 91% sequence identity to members of Marinobacter and Alcanivorax, the closest genera. Four different types of polar lipid could be detected, phosphatidyl glycerol, phosphatidyl ethylamine, phosphatidyl dimethylethylamine and lipids belonging to an unknown type of phospholipid (m/z between 861 and 879). The principal fatty acids in the polar lipid fatty acid profile were 16:0 and 16:1. The putative gene encoding the key enzyme of alkane catabolism, alkane hydroxylase (AlkB), has been cloned. The protein sequence of the putative AlkB of the isolate ME102T was related to the AlkB of Pseudomonas oleovorans and Alcanivorax borkumensis, showing about 60% sequence identity. On the basis of physiological studies and taking into account the distant phylogenetic position of isolate ME102T relative to previously described organisms, a novel genus and species is proposed, Oleiphilus messinensis gen. nov., sp. nov., within a new family, Oleiphilaceae fam. nov. Strain ME102T (= DSM 13489T = LMG 20357T) is the type and only strain of O. messinensis.
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Thioalkalimicrobium cyclicum sp. nov. and Thioalkalivibrio jannaschii sp. nov., novel species of haloalkaliphilic, obligately chemolithoautotrophic sulfur-oxidizing bacteria from hypersaline alkaline Mono Lake (California).
Two strains of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria were isolated from the oxygen-sulfide interface water layer of stratified alkaline and saline Mono Lake, California, USA. Strain ALM 1T was a dominant species in enrichment on moderate-saline, carbonate-buffered medium (0.6 M total Na+, pH 10) with thiosulfate as an energy source and nitrate as a nitrogen source. Cells of ALM 1T are open ring-shaped and are non-motile. It has a high growth rate and activity of thiosulfate and sulfide oxidation and very low sulfur-oxidizing activity. Genetic comparison and phylogenetic analysis suggested that ALM 1T (= DSM 14477T = JCM 11371T) represents a new species of the genus Thioalkalimicrobium in the gamma-Proteobacteria, for which the name Thioalkalimicrobium cyclicum sp. nov. is proposed. Another Mono Lake isolate, strain ALM 2T, dominated in enrichment on a medium containing 2 M total Na+ (pH 10). It is a motile vibrio which tolerates up to 4 M Na+ and produces a membrane-bound yellow pigment. Phylogenetic analysis placed ALM 2T as a member of genus Thioalkalivibrio in the gamma-Proteobacteria, although its DNA hybridization with the representative strains of this genus was only about 30%. On the basis of genetic and phenotypic properties, strain ALM 2T (= DSM 14478T = JCM 11372T) is proposed as Thioalkalivibrio jannaschii sp. nov..
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Clostridium lactatifermen tans sp. nov., a lactate-fermenting anaerobe isolated from the caeca of a chicken.
More LessAn obligately anaerobic, lactate-fermenting bacterium (strain G17T) was isolated from the caeca of a 31-day-old chicken. Grown at neutral pH, cells were rod-shaped with tapered ends and showed no motility and no spore formation. Electron microscopy showed that the cell walls had a gram-positive structure. The DNA G+C content was 44.6 mol %. Based on 16S rDNA sequence analysis, strain G17T was considered to belong to the low-G+C-content gram-positive bacteria of cluster XIV subgroup b and most closely related to Clostridium propionicum (93.5%) and Clostridium neopropionicum (93.5%). The optimum temperature for growth was 41 degrees C and the optimum pH was pH 6.4-7.3. The optimum temperature of 41 degrees C suggests that strain G17T might have become adapted to the body temperature of chickens. Strain G17T was able to grow on a variety of organic compounds. Most of these compounds were converted to acetate, propionate and traces of butyrate and isovalerate. In media with mixtures of substrates, lactate was degraded by strain G17T before the other substrates. This indicates that strain G17T might be important in the fermentation of lactate in the caeca of chickens. Based on its physiological and phylogenetic characteristics, it is proposed that strain G17T should be assigned to the genus Clostridium as a novel species, Clostridium lactatifermentans sp. nov.
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Lactobacillus durianis sp. nov., isolated from an acid-fermented condiment (tempoyak) in Malaysia.
Lactic acid bacteria (LAB) are the predominant micro-organisms in tempoyak, a Malaysian acid-fermented condiment. In a study on the diversity of LAB in this product, three isolates could not be identified using SDS-PAGE of whole-cell proteins or API 50 CH. The taxonomic position of the three isolates was clarified in the present study. 16S rDNA sequencing classified a representative strain in the genus Lactobacillus, clearly separated from all known species, and most closely related to the Lactobacillus reuteri phylogenetic group. DNA-DNA hybridization experiments and an extensive phenotypic description confirm that the strains represent a single and separate novel species among the obligately heterofermentative lactobacilli. The three isolates are distinguished at the intra-species level by plasmid profiling, pulsed-field gel electrophoresis of macro-restriction fragments and biochemical features. The name Lactobacillus durianis sp. nov. is proposed for the novel taxon and the type strain is LMG 19193T (= CCUG 45405T).
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Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium.
A gram-type positive, motile, coccus-shaped organism was isolated from a radioactive work area. Strain SRS30216T is an orange-pigmented bacterium that is catalase-positive, oxidase-negative and urease-negative. The orange pigment is most likely a carotenoid with absorption peaks at approximately 444, 471 and 501 nm. Cells normally grew in clusters, but individual, motile, flagellated cells were also observed. Growth of strain SRS30216T occurred at temperatures between 11 and 41 degrees C, between pH 5 and 9 and at NaCl concentrations up to and including 5%. Fatty acid composition was limited, with >90% of the fatty acids being anteiso 15:0. Alkenes of 19-24 carbons in length were detected during examination of the neutral lipids. Strain SRS30216T demonstrated high levels of resistance to gamma-radiation and desiccation. The most closely related recognized species is Kineococcus aurantiacus RA 333T, which is 93% similar in 16S rDNA sequence. DNA-DNA hybridization revealed only 31% similarity between these two organisms. It is proposed that SRS30216T (= ATCC BAA-149T = DSM 14245T) represents the type strain of a novel species in the genus Kineococcus, Kineococcus radiotolerans sp. nov..
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Isolation from a shea cake digester of a tannin-degrading Streptococcus gallolyticus strain that decarboxylates protocatechuic and hydroxycinnamic acids, and emendation of the species.
More LessA facultatively anaerobic, mesophilic, non-motile, non-sporulating bacterium, designated strain B7, was isolated from an anaerobic digester fed with shea cake rich in tannins and aromatic compounds, after enrichment on tannic acid. The coccoid cells (less than 2 microm in diameter) occurred in pairs or short chains and stained gram-positive. Strain B7 fermented a wide range of carbohydrates (cellobiose, fructose, galactose, glucose, lactose, maltose, mannitol, melibiose, raffinose and trehalose), grew optimally at pH 7.0 and had a G+C content of 40.4+/-0.3 mol%. Strain B7 was closely related to Streptococcus gallolyticus ACM 3611T, a member of the Streptococcus bovis rRNA cluster, with a sequence similarity of 98% and a DNA hybridization value of 86 mol%. Isolate B7 hydrolysed tannic acid and decarboxylated gallic acid to pyrogallol, traits also observed in S. gallolyticus ACM 3611T. In addition, both strains decarboxylated protocatechuic acid to catechol, p-coumaric acid to 4-vinylphenol, caffeic acid to 4-vinylcatechol and ferulic acid to 4-vinylguaiacol. An unsubstituted para-hydroxyl group on the benzene ring was required for decarboxylation. Glucose addition markedly increased the conversion rate. As these traits were not described previously, emendation of the description of the species Streptococcus gallolyticus is proposed.
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Comparison between Streptococcus macedonicus and Streptococcus waius strains and reclassification of Streptococcus waius (Flint et at. 1999) as Streptococcus macedonicus (Tsakalidou et al. 1998).
More LessTwo species of dairy streptococci, Streptococcus waius and Streptococcus macedonicus, were originally characterized by 16S-23S intergenic spacer sequence analysis, random amplified polymorphic DNA fingerprinting, PFGE analysis and DNA-DNA reassociation experiments. All genetic data suggested that S. waius strains belong to the previously described species S. macedonicus. Likewise, the phenotypic characterization showed that strains of S. macedonicus and S. waius were highly related and easily differentiated from the closest phylogenetic neighbour, Streptococcus bovis, principally by their failure to produce a blackening reaction in medium containing aesculin. The utilization of maltose and cellobiose by S. macedonicus/S. waius strains allowed their differentiation from the most studied dairy species, Streptococcus thermophilus. On the basis of genetic and phenotypic data S. macedonicus and S. waius species should be considered synonyms and S. macedonicus has the priority.
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Polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of Brevibacillus invocatus sp. nov..
Thirty-three clinical, dairy and industrial isolates of aerobic endospore-forming bacteria which were unreactive in routine identification tests were characterized genotypically by using amplified rDNA restriction analysis (ARDRA), 16S rDNA sequencing and DNA-DNA reassociation, and phenotypically by using fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins, API Biotype 100 assimilation tests and 16 other routine phenotypic tests. Three isolates were identified as strains of Bacillus badius, 12 as Brevibacillus agri, including 3 strains associated with an outbreak of waterborne illness, 4 as Brevibacillus centrosporus and 2 as Brevibacillus parabrevis; 12 strains contaminating an antibiotic production plant were recognized as members of a new species, for which the name Brevibacillus invocatus is proposed, with the type strain LMG 18962T (= B2156T = CIP 106911T = NCIMB 13772T).
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Proposal to transfer Catellatospora ferruginea and 'Catellatospora ishikariense' to Asanoa gen. nov. as Asanoa ferruginea comb. nov. and Asanoa ishikariensis sp. nov., with emended description of the genus Catellatospora.
More LessThe taxonomic position of Catellatospora ferruginea and 'Catellatospora ishikariense' was investigated by phylogenetic, chemotaxonomic and physiological characterization. The 16S rDNA sequences of the organisms were compared with those of members of the genus Catellatospora and other genera of the Micromonosporaceae and phylogenetic trees were inferred by using distance-matrix and parsimony methods. The organisms formed a distinct cluster within the radiation of this family that was supported by a high bootstrap value, of 100%. The nearest neighbours were members of the genera Catenuloplanes and Verrucosispora. The organisms were readily differentiated from all of the validly described genera of the family Micromonosporaceae by using a battery of chemical and morphological characters, and the name Asanoa gen. nov. is proposed. On the basis of phenotypic and DNA-DNA hybridization data, Asanoa ferruginea comb. nov. (type strain IMSNU 22009T = IFO 14496T DSM 44099T) and Asanoa ishikariensis sp. nov. (type strain IMSNU 22004T = IFO 14551T) are described.
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Vibrio trachuri Iwamoto et al. 1995 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981.
The taxonomic position of Vibrio trachuri was examined through a polyphasic approach using 16S rDNA sequencing, fluorescent amplified fragment length polymorphisms (FAFLP), DNA-DNA hybridization experiments, G+C content of DNA and phenotypical tests. Phylogenetic analysis showed that Vibrio harveyi is the closest neighbour of V. trachuri, sharing about 98.8% similarity in the 16S rDNA gene. Moreover, numerical analysis of the FAFLP patterns revealed that both species have highly related genomes, sharing 55% pattern similarity. DNA-DNA hybridization experiments and G+C content measurements reinforced these results, since V. trachuri and V. harveyi had at least 74% DNA similarity and 44.5-45.2 mol % G+C. Phenotypical features of both species were also very similar, except that V. trachuri utilized itaconic acid, whereas V. harveyi did not. Therefore, it is proposed that the species V. trachuri should be reclassified as V. harveyi.
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Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov..
The 16S rDNA sequences of four strains, i.e. three type strains of Actinobispora and strain 6330T, were determined and compared with those of representatives of the family Pseudonocardiaceae by using two tree-making algorithms. All the validly described species of the genera Actinobispora and Pseudonocardia were consistently recovered as a mixed group in phylogenetic trees, and were distinct from the other genera of the family Pseudonocardiaceae. Strain 6330T formed a distinct phyletic line in the 16S rDNA tree and was most closely associated with the type strain of Actinobispora aurantiaca. The use of specific PCR primers designed for differentiating the genus Pseudonocardia from other genera of the family Pseudonocardiaceae showed that all the Actinobispora species and strain 6330T have the same amplified 640 bp 16S rDNA fragment as members of the genus Pseudonocardia. The DNA-DNA relatedness, chemotaxonomic and phenotypic data also supported classification of these taxa in the genus Pseudonocardia, and distinguished each from the others. On the basis of these observations, it is proposed that the genera Actinobispora and Pseudonocardia be combined in an emended genus Pseudonocardia, and that strain 6330T be classified in the same genus as Pseudonocardia zijingensis sp. nov. The type strain is 6330T (= AS 4.1545T = JCM 11117T).
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Anaeroglobus geminatus gen. nov., sp. nov., a novel member of the family Veillonellaceae.
A hitherto unknown anaerobic coccus isolated from a post-operative fluid collection was characterized by phenotypic and phylogenetic methods. 16S rDNA sequence analysis revealed an affiliation of this isolate to the family Veillonellaceae. Also, a high level of sequence similarity was observed to some oral clone sequences of Megasphaera spp. contained in the GenBank database under designations BB166, CS025 and BS073. These clones and the unknown bacterium form a well-separated phylogenetic branch that may represent a novel lineage within the family Veillonellaceae. Based on phenotypic and phylogenetic evidence, a new genus, Anaeroglobus gen. nov., is proposed for the unknown bacterium, with one species, Anaeroglobus geminatus gen. nov., sp. nov. The type strain of Anaeroglobus geminatus is strain AIP 313.00T (= CIP 106856T = CCUG 44773T). It is also suggested that the oral clones BB166, CS025 and BS073 belong to the genus Anaeroglobus.
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Okibacterium fritillariae gen. nov., sp. nov., a novel genus of the family Microbacteriaceae.
Okibacterium fritillariae gen. nov., sp. nov. (type strain VKM Ac-2059T = IFO 16404T) is proposed for aerobic, oxidase- and catalase-positive, coryneform bacteria isolated from seeds of Fritillaria ruthenica Wikstr. and Clematis recta L. Strains of the new genus form a distinct branch within the phylogenetic cluster composed of members of the family Microbacteriaceae and are characterized by B-type peptidoglycan containing amino acids glycine, glutamate, homoserine, alanine and lysine, the glycolyl type of muramic acid, the major menaquinones MK-10 and MK-11, the principal phospholipids phosphatidylglycerol and diphosphatidylglycerol, and a DNA G+C content of approximately 67 mol %.
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Bifidobacterium scardovii sp. nov., from human sources.
Five strains of an unusual catalase-negative Gram-positive asporogenous rod-shaped bacterium from human sources were subjected to a polyphasic taxonomic study. The presence of fructose-6-phosphate phosphoketolase, a key enzyme of bifidobacterial hexose metabolism, indicated the strains were members of the genus Bifidobacterium but they did not correspond to any of the recognized species of this genus on the basis of biochemical profiles and whole-cell protein analyses. Comparative 16S rRNA gene sequencing confirmed the placement of the isolates in the genus Bifidobacterium, and demonstrated they represent a hitherto unknown subline within the genus displaying > 5% sequence divergence with recognized species. Based on both phenotypic and phylogenetic criteria, it is proposed that the isolates recovered from human sources be classified as a new species, Bifidobacterium scardovii sp. nov.; the type strain is CCUG 13008T (= DSM 13734T).
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Corynebacterium aurimucosum sp. nov. and emended description of Corynebacterium minutissimum Collins and Jones (1983).
A F Yassin, U Steiner and W LudwigTwo coryneform bacteria isolated from human clinical specimens were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short-chain mycolic acids consistent with the genus Corynebacterium sensu stricto. Comparative 16S rRNA gene sequence analysis showed that the two strains are genealogically highly related (99.8% sequence similarity) and constitute a new subline within the genus Corynebacterium, with Corynebacterium minutissimum as their nearest phylogenetic neighbours (98.8% sequence similarity). However, DNA-DNA hybridization experiments demonstrated unambiguously that the isolates are genealogically distinct from Corynebacterium minutissimum (42% homology). Biochemical testing indicated that the two isolates were hardly differentiated from Corynebacterium minutissimum. Based on both phenotypic and phylogenetic evidence it is proposed that these isolates be classified as a new species, Corynebacterium aurimucosum sp. nov. The type strain of Corynebacterium aurimucosum is represented by strain IMMIB D-1488T (= DSM 44532T = NRRL B-24143T).
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Cellular fatty acids as chemotaxonomic markers of the genera Anabaena, Aphanizomenon, Microcystis, Nostoc and Planktothrix (cyanobacteria).
The cellular fatty acid content of 22 cyanobacterial strains belonging to the genera Anabaena, Aphanizomenon, Calothrix, Cylindrospermum, Nostoc, Microcystis and Planktothrix were analysed. The identities of the major peaks were confirmed by MS. Correspondence analysis of the data revealed three distinct groups formed by the Microcystis strains, the Nostoc/Planktothrix strains and the Anabaena/Aphanizomenon/Cylindrospermum strains. The Calothrix strain did not cluster with the other heterocystous cyanobacteria, supporting its morphological classification separate from the Nostocaceae family. The presence of large amounts of the fatty acids 18:30omega6,9,12c and 18:0 iso distinguished the Microcystis strains from the other cyanobacteria studied. The high content of 16:1omega7c grouped the Nostoc strains with the Planktothrix strains. A free-living strain of Nostoc contained 16:1omegao5c and 16: 1omega7c (about 1: 1), separating it from the symbiotic Nostoc strain and the Planktothrix strains. the strains of Anabaena, Aphanizomenon and Cylindrospermum grouped tightly and were characterized by the presence of 16:1omega9c and 16:0 anteiso fatty acids. Correspondence analysis of Anabaena, Aphanizomenon and Cylindrospermum showed that all hepatotoxic Anabaena strains grouped together, whereas the non-toxic and neurotoxic Anabaena strains grouped with the non-toxic Aphanizomenon strains.
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Arthrobacter roseus sp. nov., a psychrophilic bacterium isolated from an antarctic cyanobacterial mat sample.
More LessStrain CMS 90rT, a red-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo, Antarctica. Based on its chemotaxonomic and phylogenetic properties, strain CMS 90r(T) was identified as a member of group I of Arthrobacter. It shared 16S rDNA similarity of 98% with Arthrobacter oxydans ATCC 14358T and Arthrobacter polychromogenes ATCC 15216T, while DNA-DNA similarities determined for these three organisms were less than 70%. It also differed from all 17 reported Arthrobacter species with A3alpha-variant peptidoglycan in that it possessed a unique peptidoglycan (Lys-Gly-Ala3) and contained galactose, glucose, ribose and rhamnose as cell-wall sugars. These data and the presence of diagnostic phenotypic traits support the description of CMS 90r(T) as a novel species of Arthrobacter, for which the name Arthrobacter roseus sp. nov. is proposed. The type strain is strain CMS 90r(T) (= MTCC 3712T = DSM 14508T).
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Bannoa hahajimensis gen. nov., sp. nov., and three related anamorphs, Sporobolomyces bischofiae sp. nov., Sporobolomyces ogasawarensis sp. nov. and sporobolomyces syzygii sp. nov., yeasts isolated from plants in Japan.
More LessFourteen ballistoconidium-forming yeast strains were isolated from leaves of plants collected in the Ogasawara Islands, which are isolated islands in the Pacific Ocean, about 1,000 km south of the Japanese mainland, in the subtropical zone. The 14 isolates were characterized by the absence of xylose in whole-cell hydrolysates, the presence of Q-10(H2) as the major ubiquinone isoprenologue, G+C contents of 47.6-52.0 mol%, the inability to ferment sugars or to assimilate nitrate and positive Diazonium blue B and urease reactions. They formed a phylogenetically coherent cluster within the Erythrobasidium lineage in the Urediniomycetes of the Basidiomycota based on 18S rDNA sequences. Analyses of the nucleotide sequences of internal transcribed spacer regions and DNA complementarity showed that four genospecies were recognized among the 14 isolates. A mating reaction was observed in one of the four genospecies, which produced one-celled basidia on dikaryotic hyphae with clamp connections. On the basis of the morphological, physiological, chemotaxonomic and phylogenetic analyses, a new teleomorphic genus, Bannoa, is proposed, in which one novel species is described, Bannoa hahajimensis gen. nov., sp. nov. (type strain OK-248(T) = JCM 10336T = CBS 9039(T)). The other three anamorphic genospecies are described as Sporobolomyces bischofiae sp. nov. (type strain OK-257T = JCM 10338T =CBS 9041T), Sporobolomyces ogasawarensis sp. nov. (type strain OK-14T = JCM 10326T = CBS 9038T) and Sporobolomyces syzygii sp. nov. (type strain OK-227T = JCM 10337T = CBS 9040T.
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Cryptococcus nyarrowii sp. nov., a basidiomycetous yeast from Antarctica.
More LessIn December 1997, 196 soil and snow samples were collected from Vestvold Hills, Davis Base, Antarctica. Two isolates, CBS 8804T (pink colonies) and CBS 8805 (yellow colonies), were shown by proteome analysis and DNA sequencing to represent the same species. Results from the sequencing of the D1/D2 region of the large rDNA subunit placed this species in the hymenomycetous tree in a unique sister clade to the Trichosporonales and the Tremellales. The clade consists of Holtermannia corniformis CBS 6979 and CBS strains 8804T, 8805, 8016, 7712, 7713 and 7743. Morphological and physiological characteristics placed this species in the genus Cryptococcus, with characteristics including the assimilation of D-glucuronate and myo-inositol, no fermentation, positive Diazonium blue B and urease reactions, absence of sexual reproduction and production of starch-like compounds. Fatty acid analysis identified large proportions of polyunsaturated lipids, mainly linoleic (C18:2) and, to a lesser extent, linolenic (C18:3) acids. On the basis of the physiological and phylogenetic data, isolates CBS 8804T and CBS 8805 are described as Cryptococcus nyarrowii sp. nov.
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Correction of the connecting vowel and gender of the specific epithet in the name Sphingomonas macrogoltabidus Takeuchi et al. 1993 to Sphingomonas macrogolitabida.
More LessIn accordance with the Bacteriological Code (1990 Revision), the connecting vowel and gender of the specific epithet macrogoltabidus in combination with the generic name Sphingomonas must be -i- and the ending must be changed to -a to agree with the gender of the generic name, respectively. Thus Sphingomonas macroboltabidus Takeuchi et al. 1993 should be Sphingomonas macrogolitabida corrig. Takeuchi et al. 1993.
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Bacillus dysentericus (sic) 1897 was the first taxonomic rather than Bacillus dysenteriae 1898.
More LessThe basonym of Shigella dysenteriae (Shiga 1898) Castellani and Chalmers 1919 was first and officially proposed in 1897 as Bacillus dysentericus (sic) in Saikingaku Zasshi, published in Japan. In accordance with Section 6 (Citation of Authors and Names) of the Bacteriological Code (1990 Revision), the year of the first proposal of Shigella dysenteriae has to be corrected from Bacillus dysenteriae 1898 to Bacillus dysentericus (sic) 1897.
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Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.
An ad hoc committee for the re-evaluation of the species definition in bacteriology met in Gent, Belgium, in February 2002. The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists.
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Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family.
In this paper minimal standards for the description of new genera and cultivable species in the family Flavobacteriaceae are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision). In addition to specified phenotypic characteristics, the description of new species should be based on DNA-DNA hybridization data, and the placement of new taxa should be consistent with phylogenetic data derived from 16S rRNA sequencing. An emended description of the family is also proposed as several new taxa have been described since 1996. These proposals have been endorsed by the members of the Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes.
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Volumes and issues
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