- Volume 50, Issue 4, 2000
Volume 50, Issue 4, 2000
- Articles
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Pelczaria aurantia ATCC 49321T (=DSM 12801T) is a strain of Kocuria rosea (Flügge 1886) Stackebrandt et al. 1995.
More LessPhylogenetic and chemotaxonomic analyses of Pelczaria aurantia ATCC 49321T (= DSM 12801T) indicate that this species is very closely related to Kocuria rosea. The DNA-DNA reassociation value of 87.1% determined for the type strains of the two species supports this finding. The results of phylogenetic analysis of the 16S rDNA of a subculture of the original strain of Pelczaria aurantia, deposited at the National Institutes of Health, Bethesda, MD, USA, as 'Neisseria aurantia', are identical to those for strain ATCC 49321T and indicate that Pelczaria aurantia ATCC 49321T is an authentic subculture of the original culture described by Poston (1993). On the basis of these findings it is concluded that P. aurantia ATCC 49321T and K. rosea DSM 20447T are members of the same taxon. The taxonomic consequences of this union are discussed.
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Streptococcus infantarius sp. nov., Streptococcus infantarius subsp. infantarius subsp. nov. and Streptococcus infantarius subsp. coli subsp. nov., isolated from humans and food.
More LessEighteen strains isolated from human specimens or from food products were characterized as atypical variants of mannitol-negative Streptococcus bovis. They were tested for extended biochemical criteria, ribotyping and DNA-DNA hybridization in order to define their taxonomic status. These strains were demonstrated to constitute a DNA relatedness group that includes strains of DNA group 4 of Farrow et al. (1984). Comparative analysis of 16S rRNA sequences demonstrated that these strains represent a new species which belongs to the Streptococcus bovis/Streptococcus equinus complex and which has been provisionally named S. infantarius by Bouvet et al. (1997). Biotyping and ribotyping allowed differentiation of these strains from the aesculin-positive strains of S. bovis belonging to the previously described biotypes I, II.1 and II.2. The results of the ribotyping and hybridization assays demonstrated the presence of two different DNA subgroups within the 18 strains. On the basis of these data, the names S. infantarius subsp. infantarius (aesculin-negative for five strains out of seven, including the type strain HDP 90056T = NCDO 599T) and S. infantarius subsp. coli (aesculin-positive, reference strain HDP 90248 = NCDO 2620) are proposed as the names for these two subspecies within the S. infantarius species.
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Actinoalloteichus cyanogriseus gen. nov., sp. nov.
More LessPhylogenetic analysis of 'Actinoalloteichus cyanogriseus' based on its 16S rDNA sequence confirmed that the organism belongs to the family Pseudonocardiaceae. It contains glutamic acid, alanine and meso-diaminopimelic acid as cell wall amino acids, and menaquinone 9 (H4). Its taxonomic characteristics differ from those of the previously described organisms of the family Pseudonocardiaceae. On the basis of these morphological, physiological, chemotaxonomic and phylogenetic analyses, a new genus, Actinoalloteichus, is proposed, along with a new species, namely Actinoalloteichus cyanogriseus sp. nov. The type strain is A. cyanogriseus IFO 14455T (= AS 4.1159T = JCM 6095T).
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Thiocapsa litoralis sp. nov., a new purple sulfur bacterium from microbial mats from the White Sea.
More LessA new phototrophic purple sulfur bacterium, isolated from benthic microbial mats from the White Sea littoral zone, is described. Individual cells were spherical, non-motile and lacked gas vesicles. In pure cultures cells appeared in regular platelet-like arrangements of four, eight or sixteen cells. Cell division occurred inside a common envelope, surrounded by a thick capsule. Internal photosynthetic membranes were of the vesicular type. The colour of cell suspensions was pink to rose-red. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series were found as photosynthetic pigments. Under anoxic conditions in the light, photolithoautotrophic growth occurred with sulfide, thiosulfate, sulfite and elemental sulfur as electron donors. Sulfur globules were stored as an intermediary oxidation product and were visible microscopically inside the cells. In the presence of sulfide and bicarbonate, photomixotrophic growth occurred with a number of organic substrates. Sulfate could serve as sole assimilatory source of sulfur. Chemolithoautotrophic growth in the dark was possible with sulfide and thiosulfate as electron donors. Optimum growth occurred in the presence of 1% NaCl, at pH 6.5 and at 30 degrees C. The DNA base composition of the type strain, BM5T, was 64.0 mol% G+C. According to 16S rDNA sequence information and DNA-DNA hybridization, the new isolate clearly belongs to the genus Thiocapsa, but is sufficiently different from other recognized Thiocapsa species to be described as a new species of this genus for which the name Thiocapsa litoralis sp. nov. is proposed. The type strain is BM5T (= ATCC 700894).
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Phylogenetic analysis of members of the genus Rickettsia using the gene encoding the outer-membrane protein rOmpB (ompB).
More LessTo confirm the phylogenetic analysis previously inferred by comparison of the citrate synthase and rOmpA gene sequences (gitA and ompA, respectively), the rOmpB gene (ompB) of 24 strains of the genus Rickettsia was amplified and sequenced. rOmpB is an outer-membrane protein of high molecular mass, the presence of which can be demonstrated in most rickettsiae by immunological cross-reactivity in Western blots. No PCR amplification was obtained with Rickettsia bellii or Rickettsia canadensis. For the other rickettsiae, phylogenetic analysis was inferred from the comparison of both the gene and derived protein sequences by using parsimony, maximum-likelihood and neighbour-joining methods which gave the same organization. All nodes were well supported (>86% bootstrap values), except in the cluster including Rickettsia africae strain S and Rickettsia parkeri, and this analysis confirmed the previously established phylogeny obtained from combining results from gltA and ompA. Based on phylogenetic data, the current classification of the genus Rickettsia is inappropriate, specifically its division into two groups, typhus and spotted fever. Integration of phenotypic, genotypic and phylogenetic data will contribute to the definition of a polyphasic taxonomy as has been done for other bacterial genera.
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Polyphasic evidence for the reclassification of Rhodothermus obamensis Sako et al. 1996 as a member of the species Rhodothermus marinus Alfredsson et al. 1988.
More LessDNA-DNA reassociation studies, 16S rRNA gene sequence comparisons and fatty acid analysis were used to reassess the taxonomic status of the type strain of Rhodothermus obamensis and several strains of the genus Rhodothermus isolated from widely distributed shallow marine hot springs. The results show that the type strain of R. obamensis, JCM 9785T, has a DNA-DNA reassociation value of 78% with the type strain of R. marinus, DSM 4252T. The other strains examined had DNA-DNA reassociation values that varied between about 68 and 94% with R. marinus. The 165 rRNA gene sequence was determined for the type strain of R. obamensis and found to share 99.5% similarity with the type strain of R. marinus. The fatty acid composition of R. obamensis was slightly different from that of the other strains examined, but indicated that this strain is very closely related to the other strains examined in this study. On the basis of DNA-DNA reassociation values, 16S rRNA gene sequence comparison and fatty acid profiles, it was concluded that R. obamensis and R. marinus represent the same species and that the name Rhodothermus obamensis should be regarded as a junior synonym of Rhodothermus marinus.
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A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube.
More LessA simple and rapid method to determine the G+C content of bacterial chromosomal DNA was developed. It involves determination of Tm by a Light Cycler and calculation of the G+C content by an empirical formula relating Tm to G+C content. Instead of a conventional thermal denaturation method, which monitors the increase of absorbance at 260 nm, thermal denaturation was monitored by the decrease of fluorescence intensity in the presence of SYBR Green 1. In this method, the apparent Tm of DNA was influenced by the concentration of SYBR Green 1, DNA and salt. In addition, when the G+C content was calculated from a linear equation [(mol% G+Cx = mol% G+Cr+1.99(Tmx-Tmr), where x is the unknown organism and y is the reference organism], an error value was introduced among strains with extremely low or high G+C content. Based upon five standards (G+C contents in the range 33-66 mol%), a suitable equation was formulated for the capillary method: mol% G+Cx = mol% G+Cr+1.4652(Tmx-Tmr)+0.0063(Tmx2-Tmr2). To determine the Tm of organisms within this range of G+C contents, Escherichia coli ATCC 11775T was used as a DNA standard and fixed concentrations of SYBR Green 1, sodium citrate and DNA were used. The data from 37 bacterial strains indicated that this equation behaved well. Because it is rapid and simple, it may prove useful for bacterial identification.
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Genomic and phenotypic characterization of Xanthomonas cynarae sp. nov., a new species that causes bacterial bract spot of artichoke (Cynara scolymus L.).
More LessA bacterial disease of artichoke (Cynara scolymus L.) was first observed in 1954 in Brittany and the Loire Valley, France. This disease causes water-soaked spots on bracts and depreciates marketability of the harvest. Ten strains of the pathogen causing bacterial spot of artichoke, previously identified as a member of the genus Xanthomonas, were characterized and compared with type and pathotype strains of the 20 Xanthomonas species using a polyphasic study including both phenotypic and genomic methods. The ten strains presented general morphological, biochemical and physiological traits and G+C content characteristic of the genus Xanthomonas. Sequencing of the 165 rRNA gene confirmed that this bacterium belongs to the genus Xanthomonas, and more precisely to the Xanthomonas campestris core. DNA-DNA hybridization results showed that the strains that cause bacterial spot of artichoke were 92-100% related to the proposed type strain CFBP 4188T and constituted a discrete DNA homology group that was distinct from the 20 previously described Xanthomonas species. The results of numerical analysis were in accordance with DNA-DNA hybridization data. Strains causing the bacterial bract spot of artichoke exhibited consistent determinative biochemical characteristics, which distinguished them from the 20 other Xanthomonas species previously described. Furthermore, pathogenicity tests allowed specific identification of this new phytopathogenic bacterium. Thus, it is concluded that this bacterium is a new species belonging to the genus Xanthomonas, for which the name Xanthomonas cynarae is proposed. The type strain, CFBP 4188T, has been deposited in the Collection Française des Bactéries Phytopathogènes (CFBP).
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Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., isolated from fermented fish in Thailand.
More LessEleven strains of homofermentative, rod-shaped lactic acid bacteria and five strains of heterofermentative, sphere-shaped lactic acid bacteria were isolated from fermented fish (pla-ra and pla-chom) in Thailand. They were identified as new species and named Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., respectively, on the basis of phylogenetic analysis of the 16S rRNA gene sequences, DNA relatedness and phenotypic characteristics. The type strain of L. acidipiscis is FS60-1T (= PCU 207T = NRIC 0300T = HSCC 1411T = JCM 10692T = TISTR 1386T) and the type strain of Weissella thailandensis is FS61-1T (= PCU 210T = NRIC 0298T = HSCC 1412T = JCM 10695T = TISTR 1384T).
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Nocardia abscessus sp. nov.
More LessChemotaxonomic and 16S rRNA gene sequence analyses of four bacterial strains isolated from clinical material clearly demonstrated that these bacteria belong to the genus Nocardia. DNA-DNA hybridization data as well as the physiological characteristics of the isolates indicated that they are closely related and belong to a single species that differs from previously described members of the genus. The name Nocardia abscessus sp. nov. is proposed for these organisms represented by strain IMMIB D-1592T (= DSM 44432T). Strain IMMIB D-1592T exhibits 56.8 and 60.0% DNA-DNA relatedness to Nocardia asteroides ATCC 19247T and Nocardia paucivorans DSM 44386T, respectively.
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Paenibacillus koreensis sp. nov., a new species that produces an iturin-like antifungal compound.
More LessA bacterial strain, YC300T, that produces an iturin-like antifungal antibiotic was isolated from compost and identified as member of the genus Paenibacillus. Gram reaction of the strain was variable depending upon growth stages and culture media. Three different types of colonies were developed on tryptic soy agar. The organism was facultatively anaerobic and grew at 50 degrees C. The DNA G+C content was 54 mol % and anteiso-C15:0 was the major fatty acid. A 0.9 kb fragment was produced by PCR amplification of strain YC300T DNA using primers PAEN515F and 1377R. Levels of 16S rDNA similarity between strain YC300T and other Paenibacillus species were between 89.8 and 94.8%. Phylogenetically, strain YC300T formed a significant monophyletic clade with Paenibacillus validus. It is clear from polyphasic evidence that the isolate should be classified as Paenibacillus koreensis sp. nov., the type strain of which is YC300T (= KCTC 2393T, KCCM 40903T).
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Reclassification of Bacillus marismortui as Salibacillus marismortui comb. nov.
More LessRecently, the features of a group of strains isolated from Dead Sea enrichments obtained in 1936 by one of us (B. E. Volcani) were described. They were gram-positive, moderately halophilic, spore-forming rods, and were placed in a new species, Bacillus marismortui. At the same time, the new genus Salibacillus was proposed for the halophilic species Bacillus salexigens. B. marismortui and Salibacillus salexigens have similar phenotypic characteristics and the same peptidoglycan type. Phylogenetic analysis based on 16S rRNA sequence comparisons showed that they are sufficiently closely related (96.6% similarity) as to warrant placement in the same genus. However, DNA-DNA hybridization experiments showed that they constitute two separate species (41% DNA similarity). Therefore the reclassification of Bacillus marismortui as Salibacillus marismortui comb. nov. is proposed.
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Bacteria of an anaerobic 1,2-dichloropropane-dechlorinating mixed culture are phylogenetically related to those of other anaerobic dechlorinating consortia.
More LessA 16S-rDNA-based molecular study was performed to determine the bacterial diversity of an anaerobic, 1,2-dichloropropane-dechlorinating bioreactor consortium derived from sediment of the River Saale, Germany. Total community DNA was extracted and bacterial 16S rRNA genes were subsequently amplified using conserved primers. A clone library was constructed and analysed by sequencing the 16S rDNA inserts of randomly chosen clones followed by dot blot hybridization with labelled polynucleotide probes. The phylogenetic analysis revealed significant sequence similarities of several as yet uncultured bacterial species in the bioreactor to those found in other reductively dechlorinating freshwater consortia. In contrast, no close relationship was obtained with as yet uncultured bacteria found in reductively dechlorinating consortia derived from marine habitats. One rDNA clone showed >97% sequence similarity to Dehalobacter species, known for reductive dechlorination of tri- and tetrachloroethene. These results suggest that reductive dechlorination in microbial freshwater habitats depends upon a specific bacterial community structure.
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Emendation of Pseudomonas straminea Iizuka and Komagata 1963.
M Uchino, Y Kosako, T Uchimura and K KomagataThe description of Pseudomonas straminae lizuka and Komagata 1963 was emended with data newly obtained. The spelling of the name of this taxon is also corrected as Pseudomonas straminea. Strains that were previously named 'Pseudomonas ochracea' were identified as P. straminea.
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Staphylococcus fleurettii sp. nov., isolated from goat's milk cheeses.
More LessA new coagulase-negative and novobiocin-resistant species of the genus Staphylococcus, Staphylococcus fleurettii, isolated from raw-milk cheeses, is described. This species is differentiated from the other novobiocin-resistant staphylococci on the basis of ribotype and intergenic transcribed spacer patterns, DNA-DNA reassociation reactions, cell wall composition and phenotypic characteristics. S. fleurettii could be distinguished by its oxidase activity, by its ability to produce acid aerobically from D-trehalose, D-mannose, D-turanose and maltose and by its inability to produce acid from D-cellobiose. The type strain of S. fleurettii is CIP 106114T (= DSM 13212T).
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Proposal of Oscillochloridaceae fam. nov. on the basis of a phylogenetic analysis of the filamentous anoxygenic phototrophic bacteria, and emended description of Oscillochloris and Oscillochloris trichoides in comparison with further new isolates.
More LessThe nucleotide sequences of the genes of 16S rRNAs were determined for the type strain Oscillochloris trichoides DG-6T and three new strains of Oscillochloris-like mesophilic filamentous green bacteria. Two major clusters have been found within the family Chloroflexaceae by phylogenetic-analysis: one cluster includes thermophilic species of Chloroflexus and the second includes mesophilic strains of Oscillochloris. The degree of relatedness of these clusters was below an intergeneric level, having only 82.5-86.5% of 16S rDNA sequence similarity. These phylogenetic data correlate well with the significant physiological, biochemical and chemotaxonomical differences between members of both groups. Therefore, the Oscillochloris and Chloroflexus clusters should be considered as two separate families. The description of the new family, Oscillochloridaceae fam. nov., and emended descriptions of the genus Oscillochloris and the species Oscillochloris trichoides are presented.
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Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments.
A Hiraishi, Y Matsuzawa, T Kanbe and N WakaoFour strains of aerobic, mesophilic, acidophilic bacteria that produced bacteriochlorophyll (BChl) a were isolated from acidic hot springs and mine drainage. The characteristics of the four isolates were almost identical. The isolates were strictly aerobic and chemo-organotrophic. They were gram-negative, non-motile cocci and coccobacilli, formed salmon-pink colonies on solidified media and produced BChl a and carotenoids only under aerobic growth conditions. The cells also produced small amounts of zinc-substituted BChl a when grown in the presence of 1 mM zinc sulfate. Anaerobic growth in the light was not found, but aerobic growth was stimulated by continuous incandescent illumination. The isolates grew in a pH range of 3.5-6.0, with pH optima of 4.5-5.0. A phylogenetic analysis based on 16S rDNA sequences showed that the isolates clustered in the major acidophilic group of the class Proteobacteria, which includes species of the genera Acidiphilium and Rhodopila. The anaerobic phototrophic bacterium Rhodopila globiformis was the closest relative to the new isolates (95% level of sequence similarity). The G+C content of the genomic DNA of the isolates was 69.1-69.8 mol%. On the basis of these results, it was concluded that the four isolates should be classified into a new genus and a new species, for which the name Acidisphaera rubrifaciens is proposed. The type strain is strain HS-AP3T (= JCM 10600T).
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Actinomyces canis sp. nov., isolated from dogs.
More LessThree strains of a previously undescribed catalase-positive Actinomyces-like bacterium were isolated from dogs. Biochemical testing and PAGE analysis of whole-cell proteins indicated that the strains were phenotypically highly related to each other but different from previously described Actinomyces and Arcanobacterium species. Sequencing of 16S rRNA showed that the unknown bacterium represents a new subline within a cluster of species which includes Actinomyces hyovaginalis, Actinomyces georgiae, Actinomyces meyeri, Actinomyces odontolyticus, Actinomyces radingae and Actinomyces turicensis. On the basis of phenotypic evidence and 16S rRNA sequence divergence levels (greater than 5% with recognized Actinomyces species) it is proposed that the unknown strains from canine sources be classified as a new species with the name Actinomyces canis sp. nov. The type strain of Actinomyces canis is CCUG 41706T (= CIP 106351T).
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Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica.
More LessCMS 19YT, a psychrophilic bacterium, was isolated from a cyanobacterial mat sample from a pond in Antarctica and was characterized taxonomically. The bacterium was aerobic, gram-positive, non-spore-forming, non-motile, exhibited a rod-coccus growth cycle and produced a yellow pigment that was insoluble in water but soluble in methanol. No growth factors were required and it was able to grow between 5 and 30 degrees C, between pH 6 and pH 9 and tolerated up to 11.5% NaCl. The cell wall peptidoglycan was Lys-Thr-Ala3 (the A3alpha variant) and the major menaquinone was MK-9(H2). The G+C content of the DNA was 64+/-2 mol%. The 16S rDNA analysis indicated that CMS 19YT is closely related to group I Arthrobacter species and showed highest sequence similarity (97.91%) with Arthrobacter agilis. Furthermore, DNA-DNA. hybridization studies also indicated 77% homology between CMS 19YT and A. agilis. It differed from A. agilis, however, in that it was psychrophilic, non-motile, yellow in colour, exhibited a rod-coccus growth cycle, had a higher degree of tolerance to NaCl and was oxidase- and urease-negative and lipase-positive. In addition, it had a distinct fatty acid composition compared to that of A. agilis: the predominant fatty acids were C15:0, anteiso-C15:0, C16:0, iso-C16:0, C17:0, anteiso-C17:0 and C18:0. It is proposed, therefore, that CMS 19YT should be placed in the genus Arthrobacter as a new species, i.e. Arthrobacter flavus sp. nov. The type strain of A. flavus is CMS 19YT (= MTCC 3476T).
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Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence.
Y Anzai, H Kim, J Y Park, H Wakabayashi and H OyaizuThe broad and vague phenotypic definition allowed the genus Pseudomonas to become a dumping ground for incompletely characterized polarly flagellated, gram-negative, rod-shaped, aerobic bacteria, and a large number of species have been accommodated in the genus Pseudomonas. The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. These sequences were compared with the sequences of other species of the Proteobacteria. Fifty-seven valid or invalid species including Pseudomonas aeruginosa (type species of the genus Pseudomonas Migula 1894) belonged to the genus Pseudomonas (sensu stricto). Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA-DNA hybridization study by Palleroni (1984). The other species did not belong to the genus Pseudomonas (sensu stricto) and were related to other genera, which were placed in four subclasses of the Proteobacteria (alpha, beta, gamma and gamma-beta subclasses). Twenty-six examined species, which were not included in the cluster of the Pseudomonas (sensu stricto) and have not been transferred to other genera as yet, are listed alphabetically: 'Pseudomonas abikonensis', Pseudomonas antimicrobica, Pseudomonas beijerinckii, Pseudomonas beteli, Pseudomonas boreopolis, 'Pseudomonas butanovora', Pseudomonas carboxydohydrogena, Pseudomonas cissicola, Pseudomonas doudoroffii, Pseudomonas echinoides, Pseudomonas elongata, Pseudomonas flectens, Pseudomonas geniculata, Pseudomonas halophila, Pseudomonas hibiscicola, Pseudomonas huttiensis, Pseudomonas iners, Pseudomonas lanceolata, Pseudomonas lemoignei, Pseudomonas mephitica, Pseudomonas pictorum, Pseudomonas saccharophila, Pseudomonas spinosa, Pseudomonas stanier, Pseudomonas syzygii and Pseudomonas woodsii. The phylogenetic affiliations of these 26 pseudomonads species are shown.
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Anaerovorax odorimutans gen. nov., sp. nov., a putrescine-fermenting, strictly anaerobic bacterium.
C Matthies, S Evers, W Ludwig and B SchinkThe strictly anaerobic, gram-positive, non-spore-forming bacterium strain NorPut1T ferments putrescine to acetate, butyrate, molecular hydrogen and ammonia. It also utilizes 4-aminobutyrate and 4-hydroxybutyrate as growth substrates. Comparative 16S rDNA sequence analysis confirmed a phylogenetic affiliation of this strain to the phylum of gram-positive bacteria with low DNA G+C content. Together with its closest relative, 'Clostridium aminobutyricum' (DSM 2634), and several Eubacterium species, strain NorPut1T represents a well-defined monophyletic group. Moderate overall 16S rRNA sequence similarities (< 91%) were found for the NorPut1T/'Clostridium aminobutyricum' pair and several Eubacterium species. The type species, Eubacterium limosum, is not a member of the group and, together with Eubacterium barkeri and Pseudoramibacter alactolyticus, represents a distant phylogentic cluster. Therefore, a new genus, Anaerovorax, is proposed as harbouring strain NorPut1T (= DSM 5092T), which is described as a new species, i.e. Anaerovorax odorimutans.
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Catenibacterium mitsuokai gen. nov., sp. nov., a gram-positive anaerobic bacterium isolated from human faeces.
A Kageyama and Y BennoSix strains of Eubacterium-like strains from human faeces were characterized by biochemical tests and analysis of cell wall peptidoglycan type and 16S rRNA. They were members of the Clostridium subphylum and have a specific phylogenetic association with Lactobacillus catenaformis and Lactobacillus vitulinus. These organisms resembled L. vitulinus in possessing the same A1gamma type of murein, but they showed different fermentation end-products. On the basis of a 16S rDNA sequence divergence of greater than 8% from L. vitulinus as well as phenotypic characteristics, a new genus, Catenibacterium, with one species (Catenibacterium mitsuokai), is proposed for six strains. The type strain of C. mitsuokai is JCM 10609T.
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Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium.
S Hattori, Y Kamagata, S Hanada and H ShounA novel anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium, strain PB(T), was isolated from a thermophilic (55 degrees C) anaerobic methanogenic reactor which had been treating kraft-pulp waste water. The bacterium oxidized acetate in co-culture with a thermophilic hydrogenotrophic methanogen. Strain PB(T), a gram-positive, spore-forming, rod-shaped bacterium grew optimally at 58 degrees C and pH 6.8. The bacterium grew acetogenically on several alcohols, methoxylated aromatics, pyruvate, glycine, cysteine, formate and hydrogen/CO2. Strain PB(T) also oxidized acetate with reduction of sulfate or thiosulfate as the electron acceptor. The bacterium contained MK-7 as the major quinone. The G+C content of the DNA was 53.5 mol%. Comparative 16S rDNA analysis indicated that strain PB(T) belongs to the Bacillus-Clostridium subphylum. However, it was distant from any known genera or micro-organism. The closest known relative was Thermoterrabacterium ferrireducens with 87.4% similarity. The name Thermacetogenium phaeum gen. nov., sp. nov. is proposed. The type strain is strain PBT (= DSM 12270T).
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Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column.
More LessA novel dissimilatory, nitrate-reducing bacterium, designated strain N2460T, was isolated from an oil reservoir model column. Strain N2460T is a mesophilic, obligately anaerobic, marine, gram-negative bacterium. The cells are vibrio-shaped and motile by a bipolar flagellum. Strain N2460T reduces nitrate to ammonia in a mineral medium supplied by acetate. The presence of a 2-oxoglutarate dehydrogenase activity indicates that acetate is oxidized via the citric acid cycle. No growth is obtained on formate, higher fatty acids, malate, fumarate, benzoate, alcohols, sugar, yeast extract, crude oil, alkanes, proline, hydrogen, sulfur or thiosulfate with nitrate as electron acceptor. Oxygen, sulfate, thiosulfate and sulfur are not utilized as alternative electron acceptors. Strain N2460T grows fermentatively on fumarate, but not on pyruvate. The G+C content of the DNA is 42.6 mol%. 16S rRNA gene analysis shows that strain N2460T belongs to the Bacteria and that the closest relative is 'Geovibrio ferrireducens' (sequence similarity 86.9%). On the basis of phylogenetic as well as phenotypic data, it is proposed that strain N2460T represents the type strain of a new genus and species, Denitrovibrio acetiphilus gen. nov., sp. nov.
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Haloanaerobium fermentans sp. nov., a strictly anaerobic, fermentative halophile isolated from fermented puffer fish ovaries.
T Kobayashi, B Kimura and T FujiiA strain of strictly anaerobic and moderately halophilic bacteria isolated from salted puffer fish ovaries was studied phenotypically, genotypically and phylogenetically. On the basis of its physiological and morphological characteristics, the new isolate is considered to be a member of the genus Haloanaerobium. It is a motile, rod-shaped, non-spore-forming, gram-negative, obligate anaerobe that grows in the presence of 25% (w/v) NaCl. The optimum salt concentration for growth is 10% (w/v). It grows well at 15 and 45 degrees C, but not at 10 or 50 degrees C. The optimum temperature for growth is 35 degrees C. It grows at pH 6.0-9.0 and the optimum pH for growth is 7.5. It ferments N-acetylglucosamine, cellobiose, fructose, galactose, D-glucose, lactose, maltose, D-mannose, raffinose, D-ribose, sucrose and D-xylose. It ferments D-glucose with the production of hydrogen, carbon dioxide, ethanol and organic acids such as acetate, formate and lactate. 16S rRNA gene sequence information confirmed the phylogenetic position of the new isolate, strain R-9T, as a member of the genus Haloanaerobium. DNA-DNA hybridization data revealed that isolate R-9T exhibited low levels of reassociation (less than 30%) with previously described Haloanaerobium species. Based on these results, the new isolate appears to represent a new Haloanaerobium species, for which the name Haloanaerobium fermentans sp. nov. is proposed. The type strain is R-9T (= JCM 10494T).
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Utility of internally transcribed 16S-23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species.
C Guasp, E R Moore, J Lalucat and A BennasarBacteria identified and classified as Pseudomonas stutzeri, on the basis of traditional criteria, are recognized to be markedly heterogeneous, such that a systematic phenotypic characterization has not been correlated with genotypic groupings (i.e. genomovars) based upon DNA-DNA similarities. The internally transcribed 16S-23S rDNA spacer (ITS1) regions of P. stutzeri were analysed with respect to the ability of these nucleic acid regions to differentiate and identify the genomic groups (i.e. genomovars) of P. stutzeri. The ITS1s of 34 strains of P. stutzeri were amplified by PCR and the PCR product was subjected to RFLP analysis, which allowed the differentiation and identification of the strains to their respective genomovars. Sequence determination and analysis of ITS1s supported further the results obtained by RFLP, i.e. nucleotide signatures were identified in strains belonging to different genomovars. The ITS1s of all strains of P. stutzeri contained the tandem tRNA(Ile)/tRNA(Ala) genes and did not exhibit distinct sequence heterogeneity between different operons of a strain. Phylogenetically informative variable sites were located, exclusively, in non-coding regions. The results of the RFLP and sequence analysis of ITS1s supported and correlated with the phylogenetic relationships estimated from 16S rRNA gene sequence comparisons and DNA-DNA hybridizations, offering an alternative tool for genomovar and species differentiation.
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Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.
More LessPseudomonas sp. strain DJ77, which was described as an aromatic-degrading bacterium, was investigated to clarify its taxonomic position. Phylogenetic analysis based on 16S rDNA sequences indicated that the strain belonged to the genus Sphingomonas and formed a monophyletic clade with the type strains of Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae with sequence similarity values of 98.1, 96.1 and 95.6%, respectively. Genomic relatedness based on DNA-DNA hybridization of strain DJ77 to these strains is 7-14%. Strain DJ77 contained ubiquinone 10 as the main respiratory quinone, and the G+C content of DNA was 63 mol%. The organism contained octadecenoic acid (67%) as major cellular fatty acid. Strain DJ77 can be readily differentiated from representative members of the genus Sphingomonas using a battery of biochemical tests. On the basis of polyphasic evidence, it is proposed that strain DJ77, previously known as Pseudomonas sp., be reclassified in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. The type strain is strain DJ77T (= KCTC 2955T = IMSNU 11152T).
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Characterization of Actinomyces isolates from samples from the human urogenital tract: description of Actinomyces urogenitalis sp. nov.
More LessThree strains of a previously undescribed Actinomyces-like bacterium were isolated from human clinical sources (urine, urethra and vaginal secretion). Biochemical testing and PAGE analysis of whole-cell proteins indicated that the strains were phenotypically homogeneous and distinct from previously described Actinomyces and Arcanobacterium species. Comparative 16S rRNA gene sequencing studies showed the bacterium to be a hitherto unknown subline within a group of Actinomyces species which includes Actinomyces bovis, the type species of the genus. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium from humans be classified as Actinomyces urogenitalis sp. nov. The type strain of Actinomyces urogenitalis is CCUG 38702T (= CIP 106421T).
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Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.
S Hansmann and W MartinThirty-nine proteins encoded in a large gene cluster that is well-conserved in gene content and gene order across 18 sequenced prokaryotic genomes were extracted, aligned and subjected to phylogenetic analysis. In individual analyses of the alignments, only two probable examples of lateral gene transfer between archaea and eubacteria were detected, involving the genes for ribosomal protein Rpl23 and adenylate kinase. Amino acid sequences for 35 of the 39 proteins were concatenated to yield a data set of 9087 amino acid positions per genome. Many of these proteins, 33 of which are ribosomal proteins, are not highly conserved across distantly related organisms and thus contain many regions that are difficult to align. Phylogenetic analyses were performed with subsets of the concatenated data from which the most highly variable sites had been iteratively removed, using the number of different amino acids that occur at a given site as a criterion of variability. Glycine, which has a strong influence on protein structure, tended to be more frequent at the most conserved (least polymorphic) sites. With most subsets of the data, the proteins from the cyanobacterium Synechocystis tended to branch with their homologues from gram-positive bacteria. The results indicate that excluding only a few percentage of poorly alignable sites from phylogenetic analysis can have a severe impact upon the phylogeny inferred and that bootstrap support for branches can fluctuate substantially, depending upon which sites are excluded.
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Use of conventional taxonomy, electrophoretic karyotyping and DNA-DNA hybridization for the classification of fermentative apiculate yeasts.
More LessA taxonomic study was conducted that considered strains of the genera Hanseniaspora/Kloeckera held in the Industrial Yeasts Collection (DBVPG) of the Dipartimento di Biologia Vegetale of the Università di Perugia, Italy. Standard phenotypic as well as molecular criteria were considered in a effort to revisit the classification of these strains, some of which have been in the collection for about 50 years. Results of salient physiological tests showed that some of the DBVPG and type strains could not be identified by current taxonomic keys. Electrophoretic karyotypes were identical for some species, with the type strains of the seven accepted species showing only five distinct chromosomal patterns. DNA-DNA hybridization analyses, using a non-radioactive dot-blot technique, allowed for the distinction of taxa. The taxonomic implications of these results are discussed.
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What is the phylogenetic position of Cryptosporidium?
G Zhu, J S Keithly and H PhilippeThe phylogenetic position of Cryptosporidium is elusive. Although previous studies based solely upon small-subunit (SSU) rRNA sequences suggested that the genus was an early emerging lineage among the Apicomplexa, bootstrap support for this placement was low. Here, the phylogenetic position of Cryptosporidium has been re-evaluated for SSU rRNA, fused SSU/large-subunit (LSU) rRNA and six protein sequences using traditional distance-based neighbour-joining, maximum-parsimony and maximum-likelihood methods of phylogenetic reconstruction as well as the new Slow-Fast analysis, which focuses upon the slowly evolving positions within sequences and is especially useful if a long-branch attraction (LBA) artefact is suspected. All the methods of reconstruction indicated a trend for the early emergence of Cryptosporidium at the base of the Apicomplexa and showed that an LBA artefact plays no role in this placement. Although the inclusion of additional numbers of neither species nor genes has significantly enhanced the bootstrap support for this phylogenetic position, recent biochemical, molecular and ultrastructural data are congruent with it. Therefore, we favour a working hypothesis that this genus constitutes an early emerging branch of the Apicomplexa.
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Pichia hawaiiensis sp. nov., occurring in decaying bark of Charpentiera trees in the Hawaiian archipelago.
More LessA description is given for Pichia hawaiiensis sp. nov., a nitrate-utilizing member of the genus Pichia E. C. Hansen emend. Kurtzman. Seven strains of the new species were isolated during the years 1972, 1973 and 1978 from rotting bark of the Hawaiian tree genera Charpentiera, Pisonia and Cheirodendron. P. hawaiiensis is heterothallic but appears to occur in nature mainly in the diploid state. Asci are deliquescent and produce up to four hat-shaped spores per ascus. Phylogenetic analysis of the 600 nucleotide D1/D2 domain of the 26S rDNA showed that P. hawaiiensis is most closely related to Pichia populi and Williopsis californica (syn. Hansenula californica). The type strain of P. hawaiiensis, isolated on the island of Hawaii from the rotting bark of Charpentiera sp. containing insect larvae, is strain UCD-FST 72-181T (= ATCC MYA-137T = CBS 8760T = NRRL Y-27270T).
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The modern Latin word rhabdus belongs to the feminine gender, inducing necessary corrections according to Rules 65(2), 12c(1) and 13b of the Bacteriological Code (1990 Revision).
More LessThe modern Latin word rhabdus does belong to the feminine gender. According to Rules 65(2), 12c(1) and 13b of the Bacteriological Code (1990 Revision), the gender of six generic names and the spelling of nine specific and subspecific epithets are proposed to be corrected.
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Arguments against the replacement of type species of the genus Salmonella from Salmonella choleraesuis to 'Salmonella enterica' and the creation of the term 'neotype species', and for conservation of Salmonella choleraesuis.
E Yabuuchi and T EzakiThe proposals of Le Minor and Popoff in 1987 and again of Euzéby in 1999 on the type species of the genus Salmonella are in violation of Rule 20a of the Bacteriological Code (1990 Revision) and should be rejected. The introduction of the term 'neotype species' should be rejected. The specific epithet choleraesuis in the binary combination Salmonella choleraesuis should be conserved. The serovar name Choleraesuis should be changed to Hogcholera.
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The status of the genus Pelczaria (Poston 1994) and the species Pelczaria aurantia (Poston 1994). Request for an Opinion.
More LessBased upon the results of another publication [P. Schumann et al. (2000). Int J Syst Evol Microbiol 50, 1421-1424) it is concluded that the culture Pelczaria aurantia ATCC 49321T (= DSM 12801T) currently being distributed does not conform to the description of the type strain of Pelczaria aurantia (Poston 1994) and the type species of the genus Pelczaria (Poston 1994). It is proposed that the Judicial Commission consider (1) that the organism currently deposited as ATCC 49321T and DSM 12801T be recognized as a member of the species Kocuria rosea; (2) that the organism deposited as ATCC 49321T and DSM 12801T as the type strain of the species does not represent a strain of the species Pelczaria aurantia; (3) to place the name Pelczaria aurantia (Poston 1994) on the list of rejected names if a suitable replacement strain, or a neotype, cannot be found within 2 years of publication of this Request (Rule 18c); (4) to place the genus name Pelczaria (Poston 1994) on the list of rejected names [c.f. Recommendation 20d (3)] if a suitable replacement type strain or a neotype for the type species of the genus Pelczaria (Poston 1994) cannot be found as outlined in (3).
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Volumes and issues
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Volume 74 (2024)
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