- Volume 51, Issue 6, 2001
Volume 51, Issue 6, 2001
- Articles
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Legionella gresilensis sp. nov. and Legionella beliardensis sp. nov., isolated from water in France.
Novel Legionella-like isolates, strains Montbéliard A1T and Gréoux 11 D13T, isolated from two different French water sources, were studied taxonomically and phylogenetically. Morphological and biochemical characterization revealed that they were Gram-negative, aerobic, non-spore-forming bacilli with a cut-glass appearance that grew only on L-cysteine-supplemented buffered charcoal yeast extract agar. Phenotypic characterization using fatty acid and ubiquinone profiles and SDS-PAGE analysis confirmed that they were closely related, but distinct from, other species of the genus Legionella, since serotyping could not relate them to any existing serogroup. Genotypic profiles generated by randomly amplified polymorphic DNA and 16S-23S rDNA spacer region PCR analyses were unique for each of these isolates. DNA-DNA relatedness values of strains Montbéliard A1T and Gréoux 11 D13T to each other and to other Legionella type strains were less than 25%. Phylogenetic affiliation of these organisms obtained by 16S rDNA sequence comparisons confirmed that they were distinct from any other known Legionella species. All the above results confirm that these strains constitute two novel species for which the names Legionella gresilensis sp. nov. (type strain Gréoux 11 D13T = ATCC 700509T = CIP 106631T) and Legionella beliardensis sp. nov. (type strain Montbéliard A1T = ATCC 700512T = CIP 106632T) are proposed.
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Fusobacterium equinum sp. nov., from the oral cavity of horses.
M Dorsch, D N Lovet and G D BaileyTwo strains of gram-negative, anaerobic, non-sporulating rod that were isolated from the normal oral cavity and oral-associated disease from horses and which phenotypically resembled Fusobacterium necrophorum were characterized by sequencing of the 16S rRNA gene, phylogenetic analysis, DNA-DNA hybridization and phenotypic characterization. The results placed the novel strains as distinct members of the genus Fusobacterium. The novel species Fusobacterium equinum sp. nov. is proposed, with strain VPB 4027T (= NCTC 13176T = JCM 11174T) as the type strain.
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Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil.
K J Chin, W Liesack and P H JanssenThree strains of obligately anaerobic bacteria were isolated from rice paddy soil microcosms. Comparative analysis of the 16S rRNA genes showed that these novel isolates have identical gene sequences and are members of the division 'Verrucomicrobia'. The novel strains are phenotypically and phylogenetically distinct from species described previously. One strain, PB90-1T, was characterized in more detail. The cells are cocci and are motile by means of a flagellum. Catalase and oxidase activities are absent. Growth-supporting substrates include mono-, di- and polysaccharides, while alcohols, amino acids and organic acids do not support growth. Propionate and acetate are the major end-products of fermentation. Nitrate is reduced to nitrite, but other external electron acceptors are not utilized. The G+C content of the genomic DNA is 74 mol%. This strain represents a taxon that has not yet been formally recognized, for which the name Opitutus terrae gen. nov., sp. nov. is proposed. The type strain is PB90-1T (= DSM 11246T).
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Microbacterium gubbeenense sp. nov., from the surface of a smear-ripened cheese.
More LessPhenotypic and phylogenetic studies were performed on 11 strains of a Microbacterium-like organism isolated from the surface of a smear-ripened cheese. The isolates were Gram-positive, catalase-positive, facultatively anaerobic, oxidase-negative, non-spore-forming, non-motile, small, slender rods and grew in 12% (w/v) NaCl. Chemotaxonomic investigation revealed that all the isolates belonged unambiguously to the genus Microbacterium. They contained type B1 peptidoglycans with L-lysine as the diamino acid and glycolyl acyl types; rhamnose and galactose were the cell wall sugars. The G+C content ranged from 69 to 72 mol%. The major menaquinones were MK-11 and MK-12 and the major fatty acids were anteiso C15:0 and C17:0 and iso C16:0. Phylogenetic analysis of the 16S rRNA sequences of four isolates showed that they represented a new subline in the genus Microbacterium, with Microbacterium barkeri as their nearest phylogenetic neighbour. M. barkeri showed the highest sequence similarity to the isolates; however, DNA-DNA hybridization showed that the isolates had only 38% chromosomal similarity to M. barkeri. Based on the phylogenetic and phenotypic distinctiveness of the isolates, it is proposed that they be classified as a new Microbacterium species, for which the name Microbacterium gubbeenense sp. nov. is suggested. The type strain has been deposited as LMG S-19263T (= NCIMB 30129T). The GenBank accession number for the 16S rDNA sequence of the type strain is AF263563.
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Lachnobacterium bovis gen. nov., sp. nov., a novel bacterium isolated from the rumen and faeces of cattle.
More LessPhenotypic and phylogenetic analysis was performed on four strains of a previously undescribed Gram-positive, rod-shaped, anaerobic bacterium isolated from the rumen and faeces of cattle. This bacterium fermented glucose primarily to lactic acid along with minor amounts of acetic and butyric acids. The four strains produced a temperature-sensitive bacteriocin-like inhibitory substance. Comparative 16S rRNA gene sequence analysis indicated that the bacterium was a member of the clostridial XIVa cluster of the low-G+C content Gram-positive bacteria. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be assigned to a new genus, Lachnobacterium, as Lachnobacterium bovis gen. nov., sp. nov. The type strain is YZ 87T (= ATCC BAA-151T = DSM 14045T = LRC 5382T). Its G+C content is 33.9 mol %.
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Phylogenetic relationships of three bacterial strains isolated from the pasture legume Biserrula pelecinus L.
More LessThree bacterial strains (WSM 1283, WSM 1284, WSM 1497) isolated from root nodules of the pasture legume Biserrula pelecinus L. growing in Morocco, Italy and Greece, respectively, were studied in order to determine their phylogenetic relationship to the other members of the family Rhizobiaceae. A polyphasic approach, which included analyses of morphological and physiological characteristics, plasmid profiles, symbiotic performance and 16S rRNA gene sequencing, indicated that these strains belong to the genus Mesorhizobium.
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Arenibacter gen. nov., new genus of the family flavobacteriaceae and description of a new species, Arenibacter latericius sp. nov.
Five dark-orange-pigmented, Gram-negative, rod-shaped, non-motile, aerobic bacterial strains were isolated from sandy sediment samples collected in the South China Sea in the Indian Ocean, from a holothurian, Apostichopus japonicus, in the Sea of Japan and from a brown alga, Chorda filum, from the Sea of Okhotsk in the Pacific Ocean. Phenotypic data were collected, demonstrating that the bacteria are chemo-organotrophic and require seawater-based media for growth. Polar lipids were analysed and 27% of the total extract comprised phosphatidylethanolamine as the major component. The predominant cellular fatty acids were branched-chain saturated and unsaturated [i-C15:0, i-C15:1, a-C15:0, C15:0, C16:1(n-7)]. The DNA base composition was 37.5-38.2 mol % G+C. The level of DNA homology of the five isolates was 83-94%, indicating that these isolates belong to the same species. A 16S rDNA sequence of the type strain KMM 426T was determined and phylogenetic analysis, based on neighbour-joining and Fitch-Margoliash methods, revealed that the type strain formed a distinct phyletic line in a clade corresponding to the family Flavobacteriaceae and represented a new genus. From the results of this polyphasic taxonomic analysis, it is proposed that the bacterial strains be classified in a new genus, Arenibacter gen. nov., and species, Arenibacter latericius sp. nov. The type strain is KMM 426T (VKM B 2137DT = LMG 19694T = CIP 106861T).
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Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment.
A Bruns, M Rohde and L Berthe-CortiA gram-negative, facultatively anaerobic bacterium with appendages was isolated from continuous cultures with a seawater-sediment suspension containing hexadecane as the sole carbon source. Although this organism was isolated from a hexadecane-degrading bacterial community, it was not able to degrade hexadecane. However, this bacterium was able to use different sugars and amino acids for growth, indicating that it probably profits from the lysis or from products like surfactants of other cells in the community. 16S rDNA analysis demonstrated that the isolated strain is phylogenetically related to the family Flavobacteriaceae of the phylum 'Cytophaga-Flavobacterium-Bacteroides'. Evidence based on phenotypic characteristics and 16S rDNA analysis supports the conclusion that this bacterium is distinct from its nearest relative, Zobellia uliginosa (90.72% similarity in 16S rRNA gene sequence), and from the other genera of the Flavobacteriaceae. It is therefore proposed that the isolated marine bacterium represents a novel taxon, designated Muricauda ruestringensis gen. nov., sp. nov. The type strain is strain B1T (= DSM 13258T = LMG 19739T).
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Mycobacterium doricum sp. nov.
More LessA novel mycobacterial species is described in this study. The strain was isolated from the cerebrospinal fluid of a severely immunocompromised AIDS patient. It was scotochromogenic and slow-growing. Characteristic features for its differentiation from other mycobacteria are its lipid pattern and the unique gene sequences within the hypervariable regions of the 16S rDNA. The strain shows susceptibility to current antimycobacterial drugs. The pathogenicity of the novel mycobacterium and its clinical significance are not certain, as the neurological symptoms of the patient could also be due to concomitant infection with Cryptococcus neoformans. The name Mycobacterium doricum sp. nov. is proposed for the novel mycobacterium; the type strain is strain FI-13295T (= DSM 44339T = CIP 106867T).
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Pseudomonas sp. strain KC represents a new genomovar within Pseudomonas stutzeri.
More LessPseudomonas sp. strain KC (= ATCC 55595 = DSM 7136) is a denitrifying aquifer isolate that produces and secretes pyridine-2,6-bis(thiocarboxylate) (PDTC), a chelating agent that fortuitously transforms carbon tetrachloride without producing chloroform. Although KC has been used successfully for full-scale bioremediation of carbon tetrachloride, its taxonomy has proven difficult to resolve, as it retains properties of both Pseudomonas stutzeri and Pseudomonas putida. In the present work, a polyphasic approach was used to conclude that strain KC represents a new genomovar (genomovar 9) within the species P. stutzeri.
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Detailed phylogeny of ammonia-oxidizing bacteria determined by rDNA sequences and DNA homology values.
More LessA comparison of the phylogeny of 38 isolates of chemolithoautotrophic ammonia-oxidizing bacteria (AOB) based on 16S rRNA gene sequences, 16S-235 rDNA intergenic spacer region (ISR) sequences and species affiliations based on DNA homology values was performed. The organisms studied all belong to the beta-subclass of the Proteobacteria and included representatives of Nitrosomonas, Nitrosococcus and Nitrosospira. The similarity values of the 16S rDNA sequences were high, particularly within the Nitrosospira genus, and based on these sequences it is difficult to determine the phylogenetic position of some AOB. As an alternative and supplement to 16S rRNA gene sequencing, the ISR was sequenced and analysed phylogenetically. Due to considerably lower similarity values, the ISR-based phylogeny gives a better resolution than the phylogeny based on the functional 16S rRNA gene. Since the ISR-based phylogeny of AOB is highly consistent with the 16S rDNA based phylogeny, ISR sequencing appears as a suitable tool for resolving the detailed phylogeny of AOB. The phylogenetic position of two isolates of the former genus 'Nitrosolobus' (now included in the Nitrosospira genus) is not clear. These organisms are close relatives of the former Nitrosospira spp. and 'Nitrosovibrio' spp. (now Nitrosospira), but based on their marginal positions in the phylogenetic trees, DNA-DNA hybridization data and phenotypic characteristics, it is suggested that 'Nitrosolobus' should be a separate genus. DNA homology determination of 11 Nitrosospira isolates revealed two new species of Nitrosospira. The phylogeny of AOB reflected in the trees based on the rDNA sequences is consistent with the species affiliations of AOB by DNA homology values. This observation will probably be important for the interpretation of results from studies of natural diversity of AOB.
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Vibrio agarivorans sp. nov., a novel agarolytic marine bacterium.
More LessIt is proposed that the new Vibrio species Vibrio agarivorans accommodates two agarolytic, halophilic, fermentative bacterial strains isolated from Mediterranean sea water. The cells were gram-negative, oxidase-positive, polarly flagellated bacilli that fermented glucose without gas production and that produced no decarboxylases. They used a wide range of compounds as sole carbon and energy sources. The DNA G+C content was 44.8 mol%. Phylogenetic analysis based on complete 16S and 23S rDNA sequences revealed that the strains belong to the gamma-Proteobacteria, and are specifically related to Vibrio species. Their nearest relatives were species of the Vibrio fischeri group, sharing 16S rDNA sequence similarities below 97% with the agarolytic strains. The type strain is 289T (= CECT 5085T = DSM 13756T).
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Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia.
More LessThe current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the alpha-Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination.
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Isolation of a cinnamic acid-metabolizing Clostridium glycolicum strain from oil mill wastewaters and emendation of the species description.
M Chamkha, M Labat, B K Patel and J L GarciaA strictly anaerobic, gram-positive, motile, sporulated bacterium, designated strain CIN5, was isolated from olive mill wastewaters after enrichment on cinnamic acid. The rod-shaped cells were slightly curved (0.4-1.1 x 2.0-15 microm) and occurred singly or in pairs. Strain CIN5 utilized a limited number of carbohydrates (glucose, fructose, maltose, sorbitol), grew optimally at 37 degrees C and at pH 7.3-7.5 and had a DNA G+C content of 29.1+/-0.3 mol%. Strain CIN5 was very closely related to Clostridium glycolicum DSM 1288T. Both strain CIN5 and the type strain of C. glycolicum transformed cinnamic acid to hydrocinnamic acid and a wide range of other cinnamic acid derivatives, including o-, m- and p-coumaric, o-, m- and p-methoxycinnamic, p-methylcinnamic, caffeic, ferulic and isoferulic acids, to their corresponding 3-phenylpropionic acids by reducing the double bond of the side chain. Glucose supplementation increased the rate of conversion markedly. The emendation of the description of C. glycolicum is proposed to include these new characteristics.
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Desulfomusa hansenii gen. nov., sp. nov., a novel marine propionate-degrading, sulfate-reducing bacterium isolated from Zostera marina roots.
More LessThe physiology and phylogeny of a novel sulfate-reducing bacterium, isolated from surface-sterilized roots of the marine macrophyte Zostera marina, are presented. The strain, designated P1T, was enriched and isolated in defined oxygen-free, bicarbonate-buffered, iron-reduced seawater medium with propionate as sole carbon source and electron donor and sulfate as electron acceptor. Strain P1T had a rod-shaped, slightly curved cell morphology and was motile by means of a single polar flagellum. Cells generally aggregated in clumps throughout the growth phase. High CaCl2 (10 mM) and MgCl2 (50 mM) concentrations were required for optimum growth. In addition to propionate, strain P1T utilized fumarate, succinate, pyruvate, ethanol, butanol and alanine. Oxidation of propionate was incomplete and acetate was formed in stoichiometric amounts. Strain P1T thus resembles members of the sulfate-reducing genera Desulfobulbus and Desulforhopalus, which both oxidize propionate incompletely and form acetate in addition to CO2. However, sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P1T was unrelated to the incomplete oxidizers Desulfobulbus and Desulforhopalus and that it constitutes a novel lineage affiliated with the genera Desulfococcus, Desulfosarcina, Desulfonema and 'Desulfobotulus'. Members of this branch, with the exception of 'Desulfobotulus sapovorans', oxidize a variety of substrates completely to CO2. Strain P1T (= DSM 12642T = ATCC 700811T) is therefore proposed as Desulfomusa hansenii gen. nov., sp. nov. Strain p1T thus illustrates the difficulty of extrapolating rRNA similarities to physiology and/or ecological function.
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Reclassification of Saccharococcus caldoxylosilyticus as Geobacillus caldoxylosilyticus (Ahmad et al. 2000) comb. nov.
More LessA polyphasic study was performed on five thermophilic strains belonging to the genus Bacillus, isolated from soil of different geographical areas. 16S rRNA gene sequence analysis placed these isolates in RNA group 5, with Saccharococcus caldoxylosilyticus and [Bacillus] thermoglucosidasius being the closest phylogenetic neighbours. The type species of Saccharococcus, Saccharococcus thermophilus, was only moderately related to these two species and the novel isolates. DNA-DNA hybridization studies and comparison of morphological, chemotaxonomic and phenotypic features supported the close relationship between the novel isolates and Saccharococcus caldoxylosilyticus. These data justify the reclassification of Saccharococcus caldoxylosilyticus. Following the transfer of the validly described Bacillus species of group 5 into the genus Geobacillus, the reclassification of Saccharococcus caldoxylosilyticus as Geobacillus caldoxylosilyticus comb. nov. is proposed. This species can be distinguished genomically from Geobacillus thermoglucosidasius, Geobacillus stearothermophilus, Geobacillus thermodenitrificans and Saccharococcus thermophilus by a specific PCR-RFLP assay targeting the 16S rDNA.
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Agreia bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila.
More LessAgreia bicolorata gen. nov., sp. nov. (type strain VKM Ac-1804T=UCM Ac-620T) is proposed to accommodate aerobic, oxidase- and catalase-positive, weakly motile, coryneform actinobacteria isolated from leaf galls induced by the plant-parasitic nematode Heteroanguina graminophila in narrow reed grass, Calamagrostis neglecta. Bacteria assigned to Agreia bicolorata gen. nov., sp. nov. form a distinct lineage within the phylogenetic branch of the family Microbacteriaceae and possess the following chemotaxonomic characteristics: B-type peptidoglycan containing 2,4-diaminobutyric acid, ornithine, alanine, glycine, glutamate and hydroxyglutamate; cell wall sugars rhamnose, fucose and mannose; MK-10 as major menaquinone; phosphatidylglycerol and diphosphatidylglycerol as principal phospholipids; and 12-methyltetradecanoic acid (anteiso-15:0), 14-methyl-pentadecanoic acid (iso-16:0) and 14-methyl-hexadecanoic acid (anteiso-17:0) as predominant fatty acids. The DNA G+C content of Agreia bicolorata is about 67.0 mol %.
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Lactobacillus coleohominis sp. nov., isolated from human sources.
More LessFour strains of a hitherto unrecognized gram-positive, catalase-negative, facultatively anaerobic, rod-shaped bacterium isolated from human sources were characterized using phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing demonstrated that the bacterium represents a new subline within the Lactobacillus casei/Pediococcus rRNA group of the genus Lactobacillus. The unknown bacterium was readily distinguished from all other described Lactobacillus species and related taxa by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Lactobacillus coleohominis sp. nov. The type strain of Lactobacillus coleohominis is CCUG 44007T (= CIP 106820T).
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Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 . as mMrinibacillus marinus gen nov., comb. nov.
More LessA moderately halophilic, round-endospore-forming bacterium (strain YKJ-13T) was isolated from jeotgal, a traditional Korean fermented seafood, and studied by a polyphasic taxonomic approach. This organism was related to the phylogenetic clade comprising members of Bacillus rRNA group 2 and formed a cluster with Bacillus marinus with a bootstrap fidelity value of 93.6%. The peptidoglycan type was A1alpha linked directly through L-Lys. Based on cell morphology, peptidoglycan type and phylogeny, strain YKJ-13T, together with B. marinus, is considered to be a member of Bacillus rRNA group 2. Strain YKJ-13T was also characterized by having MK-7 and MK-8 as the predominant menaquinones and iso-C15:0 as the major fatty acid. The DNA G+C content was 44 mol%. Strain YKJ-13T exhibited a 16S rDNA similarity value of 95.7% with B. marinus DSM 1297T, its closest phylogenetic relative. Levels of 16S rDNA similarity between strain YKJ-13T and other Bacillus spp. were less than 94.2%. Therefore, on the basis of the data presented, the name Jeotgalibacillus alimentarius gen. nov., sp. nov. is proposed for strain YKJ-13T (= KCCM 80002T = JCM 10872T). It is also proposed that B. marinus be reclassified in Marinibacillus gen. nov. as Marinibacillus marinus comb. nov.
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Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov.
More LessOn the basis of 16S rRNA gene sequencing and DNA-DNA reassociation, industrial solvent-producing clostridia have been assigned to four species. In this study, the phenotypic characteristics of Clostridium acetobutylicum, Clostridium beijerinckii, 'Clostridium saccharoperbutylacetonicum', and an unnamed Clostridium sp. represented by the strains NCP 262T and NRRL B643 are compared. In addition, a further 40 strains of solvent-producing clostridia have been classified by biotyping, DNA fingerprinting and 16S rRNA gene sequencing. These included 14 C. beijerinckii strains, two strains currently designated as 'Clostridium kaneboi' and 'Clostridium butanologenum', and 24 production strains used in the commercial acetone-butanol fermentation. All of the C. beijerinckii strains were confirmed to have been classified correctly. The 'C. kaneboi' and 'C. butanologenum' strains require reclassification as C. acetobutylicum and C. beijerinckii, respectively. The commercial production strains were found to belong either to C. beijerinckii or to the unnamed Clostridium sp. For the comparative phenotypic studies of the four species, representative strains were selected from each of the DNA-fingerprint subgroups within each species. These strains were analysed for their ability to utilize different carbohydrates, hydrolyse gelatin or aesculin, and produce indole, and were tested for the presence of catalase and urease. On the basis of these results, several phenotypic traits were found to be useful for differentiating between the four species. The descriptions of C. acetobutylicum and C. beijerinckii have been emended. The names Clostridium saccharoperbutylacetonicum sp. nov. [type strain = N1-4 (HMT) = ATCC 27021T] and Clostridium saccharobutylicum sp. nov. (type strain = DSM 13864T = ATCC BAA-117T) are proposed for the two new species.
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Metabolism of cinnamic acids by some Clostridiales and emendation of the descriptions of Clostridium aerotolerans, Clostridium celerecrescens and Clostridium xylanolyticum.
M Chamkha, J L Garcia and M LabatThe ability of Clostridium aerotolerans DSM 5434T, Clostridium celerecrescens DSM 5628T, Clostridium methoxybenzovorans DSM 12182T, Clostridium stercorarium ATCC 35414T, Clostridium subterminale DSM 2636, Clostridium termitidis DSM 5398T, Clostridium thermolacticum DSM 2910T, Clostridium thermopalmarium DSM 5974T and Clostridium xylanolyticum DSM 6555T to metabolize cinnamic acid and various derivatives, with or without glucose supplementation, was examined. Only C aerotolerans DSM 5434T and C. xylanolyticum DSM 6555T, closely related species, transformed cinnamic acid to 3-phenylpropionic acid. Both species also reduced a wide range of cinnamic acid derivatives, including o-, m- and p-coumaric, o-, m- and p-methoxycinnamic, p-methylcinnamic, caffeic, ferulic, isoferulic and 3,4,5-trimethoxycinnamic acids to their corresponding 3-phenylpropionic acid derivatives. C. aerotolerans DSM 5434T, however, also decarboxylated p-coumaric acid into 4-vinylphenol, which was then reduced to 4-ethylphenol. C. celerecrescens was grouped with C. aerotolerans and C. xylanolyticum in subcluster XIVa of the Clostridiales. C. celerecrescens DSM 5628T only metabolized m- and p-methoxycinnamic and p-methylcinnamic acids to their corresponding 3-phenylpropionic acid derivatives, reducing the double bond in the C3 aliphatic side chain. Addition of glucose markedly increased the yield of the biotransformations by these three species. An emendation of the descriptions of C. aerotolerans, C. celerecrescens and C. xylanolyticum is proposed, based on these observations.
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Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group.
More LessThe taxonomic positions of species of the Lactobacillus casei group have been evaluated by sequencing and phylogenetic analysis of a 277 bp recA gene fragment. High sequence similarity between strain ATCC 393T, currently designated as the type strain of L. casei, and the type strain of Lactobacillus zeae, LMG 17315T, has been established, while L. casei ATCC 334 and Lactobacillus paracasei NCDO 151T form a single phylogenetic group. The taxonomic status of species and strains at issue is discussed.
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Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and 'Actinoplanes aurantiacus' to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.
More LessThe phylogenetic structure of the genus Actinoplanes was determined by comparative 16S rDNA sequence analysis of the type strains of all validly described Actinoplanes species and other strains of Actinoplanes. Actinoplanes minutisporangius IFO 15962T and 'Actinoplanes aurantiacus' IFO 13967 were placed outside the family Micromonosporaceae and appeared to be closely related to the genus Cryptosporangium. On the basis of their morphological and chemotaxonomic characteristics and phylogenetic analysis, these strains were reclassified into the genus Cryptosporangium. DNA-DNA hybridization revealed that these strains differed from the species previously described in this genus. Therefore, the transfer is proposed of Actinoplanes minutisporangius Ruan et al. 1986 and 'Actinoplanes aurantiacus' IFO 13967 to the genus Cryptosporangium as Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.
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Nocardia ignorata sp. nov.
More LessAn isolate that was received during a mycobacterial quality control test and which was thought to be a Mycobacterium species was subjected to a polyphasic taxonomic study after mycolic acid analysis showed that it possessed mycolates characteristic of the nocardiae. Further chemotaxonomic and 16S rRNA gene sequence analyses of this isolate demonstrated that it belongs to the genus Nocardia. 16S rRNA gene sequence data, DNA-DNA hybridization studies and the biochemical characteristics of the isolate indicate that it belongs to a novel species that differs from previously described members of the genus Nocardia. The name Nocardia ignorata sp. nov. is proposed for this isolate with the type strain IMMIB R-1434T (= DSM 44496T = NRRL B-24141T).
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Alcalilimnicola halodurans gen. nov., sp. nov., an alkaliphilic, moderately halophilic and extremely halotolerant bacterium, isolated from sediments of soda-depositing Lake Natron, East Africa Rift Valley.
An alkaliphilic, halotolerant, Gram-negative, heterotrophic, aerobic and rod-shaped organism was isolated from drying soda and at a water-covered site of Lake Natron, Tanzania, by means of the most-probable-number technique developed for anoxygenic, phototrophic sulfur bacteria. It had an absolute requirement for alkalinity, but not for salinity; growth occurred at salt concentrations of 0-28% (w/v), with optimal growth at 3-8% (w/v) NaCl. The bacterium preferentially metabolized volatile fatty acids and required vitamins for growth. The name Alcalilimnicola halodurans gen. nov., sp. nov. is proposed for the novel isolate, placed in the gamma-Proteobacteria within the family Ectothiorhodospiraceae on the basis of analysis of the 16S rDNA sequence, polar lipids, fatty acids and DNA base composition. Although Alcalilimnicola halodurans is closely related to the extreme anoxygenic, phototrophic sulfur bacteria of the genus Halorhodospira, it is not phototrophic.
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Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and 'HGE agent' as subjective synonyms of Ehrlichia phagocytophila.
More LessThe genera Anaplasma, Ehrlichia, Cowdria, Neorickettsia and Wolbachia encompass a group of obligate intracellular bacteria that reside in vacuoles of eukaryotic cells and were previously placed in taxa based upon morphological, ecological, epidemiological and clinical characteristics. Recent genetic analyses of 16S rRNA genes, groESL and surface protein genes have indicated that the existing taxa designations are flawed. All 16S rRNA gene and groESL sequences deposited in GenBank prior to 2000 and selected sequences deposited thereafter were aligned and phylogenetic trees and bootstrap values were calculated using the neighbour-joining method and compared with trees generated with maximum-probability, maximum-likelihood, majority-rule consensus and parsimony methods. Supported by bootstrap probabilities of at least 54%, 16S rRNA gene comparisons consistently clustered to yield four distinct clades characterized roughly as Anaplasma (including the Ehrlichia phagocytophila group, Ehrlichia platys and Ehrlichia bovis) with a minimum of 96.1% similarity, Ehrlichia (including Cowdria ruminantium) with a minimum of 97.7% similarity, Wolbachia with a minimum of 95.6% similarity and Neorickettsia (including Ehrlichia sennetsu and Ehrlichia risticii) with a minimum of 94.9% similarity. Maximum similarity between clades ranged from 87.1 to 94.9%. Insufficient differences existed among E. phagocytophila, Ehrlichia equi and the human granulocytic ehrlichiosis (HGE) agent to support separate species designations, and this group was at least 98.2% similar to any Anaplasma species. These 16S rRNA gene analyses are strongly supported by similar groESL clades, as well as biological and antigenic characteristics. It is proposed that all members of the tribes Ehrlichieae and Wolbachieae be transferred to the family Anaplasmataceae and that the tribe structure of the family Rickettsiaceae be eliminated. The genus Anaplasma should be emended to include Anaplasma (Ehrlichia) phagocytophila comb. nov. (which also encompasses the former E. equi and the HGE agent), Anaplasma (Ehrlichia) bovis comb. nov. and Anaplasma (Ehrlichia) platys comb. nov., the genus Ehrlichia should be emended to include Ehrlichia (Cowdria) ruminantium comb. nov. and the genus Neorickettsia should be emended to include Neorickettsia (Ehrlichia) risticii comb. nov. and Neorickettsia (Ehrlichia) sennetsu comb. nov.
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Candida thermophila sp. nov., a novel thermophilic yeast isolated from soil.
More LessYeast strain Y94T, which is capable of growth at high temperature, was isolated from soil in Korea. Characteristics of the strain include asexual reproduction by multilateral budding, the absence of extracellular starch-like compounds, a negative Diazonium blue B colour reaction, and the absence of arthrospores, ballistoconidia and ascospores; the strain can therefore be placed in the genus Candida. A maximum growth temperature of 50-51 degrees C, along with certain other physiological characteristics, and a unique 26S rDNA partial sequence separate this strain from other ascomycetous yeasts. Taken together, these results suggest that the strain is a novel species and the name Candida thermophila sp. nov. (type strain is Y94T = JCM 10994T = KCCM 50661T) is proposed.
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Candida bituminiphila, a novel anamorphic species of yeast.
More LessA novel anamorphic species of yeast belonging to the genus Candida was isolated from tar in Canada. Morphological and physiological observations, as well as phylogenetic analyses, were performed. Conidiophores were produced, were usually short and had sympodial growth, numerous bud scars and a rachis-like structure. They bore one or more conidia. Pseudomycelium was scarcely produced and true mycelium was sparse. No sexual reproduction was observed on corn meal, malt, Gorodkowa, Dextrose Yeast Peptone or V8 agars. Zygoascus hellenicus was physiologically the most closely related species, but it differed from the novel species by its ability to assimilate D-galacturonate and L-rhamnose, ferment sucrose and grow at 37 degrees C. From sequence analysis of the 26S rDNA D1/D2 region, Z. hellenicus and Candida bertae var. bertae were the closest species with 54 and 56 bp substitutions, respectively. Similar results have been obtained from analysis of the 18S rDNA. All these data support the hypothesis that the yeast, named Candida bituminiphila, is a novel species closely related to Z. hellenicus. The holotype and only isolate of C. bituminiphila is strain CBS 8813T (= MUCL 41424T).
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Phylogenetic analysis of strains originally assigned to Bullera variabilis: descriptions of Bullera pseudohuiaensis sp. nov., Bullera komagatae sp. nov. and Bullera pseudoschimicola sp. nov.
F Y Bai, M Takashima and T NakaseTwenty strains previously assigned to the species Bullera variabilis Nakase & Suzuki were reclassified using a molecular taxonomic approach. The strains were regrouped first by nucleotide sequence comparison of the rDNA internal transcribed spacer (ITS) regions, including the 5.8S gene. Phylogenetic positions of B. variabilis strains with different ITS region sequences were then analysed based on their 18S rDNA sequences. The taxonomic status of the original Bullera variabilis strains was clarified further by DNA-DNA hybridization experiments. Of the 20 strains studied, five remained in the species B. variabilis, six strains were reassigned to the species Bullera mrakii and three novel species were proposed for eight of the nine remaining strains, namely Bullera pseudohuiaensis sp. nov. (one strain; type strain JCM 5984T = AS 2.2203T), Bullera komagatae sp. nov. (one strain; type strain JCM 5983T = AS 2.2202T) and Bullera pseudoschimicola sp. nov. (six strains; type strain JCM 391ST = AS 2.2201T). The remaining strain, JCM 6140, was closely related to B. pseudoschimicola. However, differences in ITS region sequences between strain JCM 6140 and strains of B. pseudoschimicola, and the intermediate DNA-DNA relatedness to representative strains of B. pseudoschimicola did not allow a definite taxonomic decision to be made for strain JCM 6140.
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Three new species of Saccharomyces sensu lato van der Walt from Yaku Island in Japan: Saccharomyces naganishii sp. nov., Saccharomyces humaticus sp. nov. and Saccharomyces yakushimaensis sp. nov.
More LessThree new yeast species were isolated from soil and partially decayed leaves in Yaku Island and Iriomote Island in the Nansei Islands of Japan. Based on DNA hybridization and physiological characters, these represent novel taxa. These are designated Saccharomyces naganishii sp. nov. (type strain IFO 10181T = CBS 8797T), Saccharomyces humaticus sp. nov. (type strain IFO 10673T = CBS 8893T) and Saccharomyces yakushimaensis sp. nov. (type strain IFO 1889T = CBS 8894T). The phylogenetic relationships of the three new species with members of other ascomycetous genera (e.g. Kluyveromyces, Saccharomyces, Torulaspora and Zygosaccharomyces) were estimated by 18S rDNA gene sequence analysis.
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Reclassification of the Cryptococcus humicola complex.
M Takashima, T Sugita, T Shinoda and T NakaseTen strains of the Cryptococcus humicola complex were reclassified on the basis of sequence analyses of 18S rDNA and internal transcribed spacer regions and DNA-DNA reassociation experiments. They were differentiated into seven species including C humicola. Five novel species are proposed: Cryptococcus daszewskae sp. nov. (type strain CBS 5123T = JCM 11166T = MUCL 30649T), Cryptococcus fragicola sp. nov. (type strain JCM 1530TT = CBS 88981), Cryptococcus longus sp. nov. (type strain CBS 5920T = JCM 11167T = MUCL 30690T), Cryptococcus musci sp. nov. (type strain JCM 1531T = CBS 8899T) and Cryptococcus pseudolongus sp. nov. (type strain JCM 9712T = CBS 8297T). A syntype of Sporobolomyces albidus JCM 1460T is also revealed to be a distinct species; the name Cryptococcus ramirezgomezianus nom. nov. is therefore proposed for Sporobolomyces albidus Ramírez Gómez (type strain IJFM 502T = CBS 2839T = JCM 1460T = NRRL Y-2478T), since the name Cryptococcus albidus (Saito) C. E. Skinner has already been recognized for a distinct species within the genus Cryptococcus. Strains possessing either Q-9 or Q-10 have been reported to occur in C. humicola; however, after reclassification, the ubiquinone type of the species in each phylogenetic group was shown to be uniform, indicating that it is a useful criterion for the taxonomy of the Trichosporonales.
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New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence.
More LessThe phylum Euglenozoa consists of three distinct groups: the euglenoids, diplonemids and kinetoplastids. The phylogenetic position of the diplonemids within this phylum remains unsettled, since both morphological and molecular data produce weak and contradictory results. It is shown here that taxonomic sampling, G+C content bias, mutational saturation and differences of evolutionary rate among lineages are major factors affecting the topology of the small-subunit rRNA euglenozoan tree. When these problems are minimized by using a larger diplonemid sampling (including a sequence of environmental origin) and correcting for G+C bias (by using both paralinear distances or an unbiased dataset), a diplonemids+euglenoids sisterhood is retrieved. Bootstrap support for this relationship is still moderate, but it is retrieved by all analysis methods, overcoming previously reported disagreements. In addition, the inclusion of a large number of euglenoid sequences in the analysis improves some phylogenetic relationships within this group. Some problematic taxa, such as the species Khawkinea quartana, are now placed with high bootstrap support and monophyly is found for two interesting groups (the photosynthetic genera Eutreptia+Eutreptiella and the loricate genera Strombomonas+Trachelomonas), although with weak statistical support.
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Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision).
More LessFrom 1990 to 2000, the number of published named taxa based upon new isolates at species and genus levels in International Journal of Systematic and Evolutionary Microbiology, formerly International Journal of Systematic Bacteriology, have increased by approximately four- and sevenfold, respectively. New taxa based upon characterization of only a single isolate remained at around 40% for both categories. The Bacteriological Code (1990 Revision) has no recommendations on the number of strains required for definition of new taxa. For a few groups, a minimum number of 5-10 strains has been suggested in minimal standards. Since an exponential increase in new taxa can be expected in the future, the authors discuss problems related to naming new species and genera based upon descriptions of a single isolate and suggest that this practice is re-evaluated. It is proposed that the following should be added to Recommendation 30b of the Bacteriological Code: 'Descriptions should be based on as many strains as possible (minimum five), representing different sources with respect to geography and ecology in order to be well characterized both phenotypically and genotypically, to establish the centre (from which the type strain could be chosen) and the extent of the cluster to be named. In addition, comparative studies should be performed, including reference strains that represent neighbouring species and/or genera, in order to give descriptions that are sufficiently detailed to allow differentiation from these neighbours.'
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 1 (1951)