- Volume 49, Issue 1, 1999
Volume 49, Issue 1, 1999
- Validation List
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- Notification List
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- New Taxa - Archaea
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Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov.
More LessThe 16S rRNA gene sequences of Halococcus saccharolyticus and Halococcus salifodinae were closely related (94·5–94–7% similarity) to that of Halococcus morrhuae, the type species of the genus Halococcus. However, Halococcus turkmenicus was distinct from the other members of this genus, with low 16S rRNA similarities when compared to Halococcus morrhuae (88·7%). On the basis of phylogenetic tree reconstruction, detection of signature bases and DNA-DNA hybridization data, it is proposed to transfer Halococcus turkmenicus to a novel genus, Haloterrigena, as Haloterrigena turkmenica gen. nov., comb. nov., and to accommodate Halobacterium trapanicum JCM 9743 and strain GSL-11 in the same species. On the basis of morphological, cultural and 16S rRNA sequence data, it is also proposed that the culture collection strains of Halobacterium trapanicum NCIMB 767, ATCC 43102 and JCM 8979 should be renamed as Halococcus sp.
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Reclassification of Methanogenium tationis and Methanogenium liminatans as Methanofollis tationis gen. nov., comb. nov. and Methanofollis liminatans comb. nov. and description of a new strain of Methanofollis liminatans
Sequencing of 16S rRNA genes and phylogenetic analysis of Methanogenium tationis DSM 2702T (OCM 43T) (T = type strain) and Methanogenium liminatans GKZPZT ( = DSM 4140T) as well as other members of the family Methanomicrobiaceae revealed that both species belong to a separate line of descent within this family. In addition, a new strain of Methanogenium liminatans, strain BM1 ( DSM 10196), was isolated from a butyrate-degrading, fluidized bed reactor and characterized. Cells of both species are mesophilic, highly irregular cocci that use H2/CO2 and formate for growth and methanogenesis. In addition, Methanogenium liminatans strains GKZPZT and BM1 used 2-propanol/CO2, 2-butanol/CO2 and cyclopentanol/CO2. Both species contained diether and tetraether lipids. The polar lipids comprised amino-phosphopentanetetrol derivatives, which appear to be characteristic lipids within the family Methanomicrobiaceae. The pattern of glycolipids, phosphoglycolipids and amino-phosphoglycolipids was consistent with the assignment of these two species to a taxon within the family Methanomicrobiaceae, but also permitted them to be distinguished from other higher taxa within this family. The G+C contents of the DNA of Methanogenium tationis and Methanogenium liminatans were 54 and 60 mol% (T m and HPLC), respectively. On the basis of the data presented, the transfer of Methanogenium tationis and Methanogenium liminatans to the genus Methanofollis gen. nov. as Methanofollis tationis comb. nov. and Methanofollis liminatans comb, nov., respectively, is proposed, with Methanofollis tationis as the type species.
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Characterization of two novel haloalkaliphilic archaea Natronorubrum bangense gen. nov., sp. nov. and Natronorubrum tibetense gen. nov., sp. nov.
Yi Xu, Peijin Zhou and Xinyu TianTwo haloalkaliphilic archaea were isolated from a soda lake in Tibet. The two strains, designated A33T and GA33T, were Gram-negative, pleomorphic, flat, non-motile and strictly aerobic. Growth required at least 12% NaCI. Growth was between pH 8·0 and pH 11 with an optimum at pH 9·0–9·5. Cells were chemo-organotrophic. Polar lipids were C20–C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate. The nucleotide sequences of the 16S rRNA genes from the two strains were obtained by the analysis of the cloned rDNAs. On 16S rRNA phylogenetic trees, the two strains formed a monophyletic cluster. They differed from their closest neighbours, Halobacterium trapanicum and Natrialba asiatica, in polar lipid composition, as well as physiological and phenotypic characteristics. DNA-DNA hybridization indicated that the two strains belonged to different species of the same genus. The results indicated that the strains A33T and GA33T should be classified in a new genus Natronorubrum gen. nov. as Natronorubrum bangense sp. nov. (strain A33T) and Natronorubrum tibetense sp. nov. (strain GA33T).
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- New Taxa - Other Bacteria
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Treponema brennaborense sp. nov., a novel spirochaete isolated from a dairy cow suffering from digital dermatitis
A novel Treponema species was isolated from an ulcerative lesion of a cow suffering from digital dermatitis (DD), a disease which causes painful ulcerations along the coronary band. Among other anaerobic bacteria, high numbers of spirochaetes have been regularly found in DD lesions. Here data are presented of a spirochaete isolated from a DD ulcer. By chemotaxonomy, protein analysis and comparative 16S rDNA sequence analysis this isolate was classified as a treponeme that differed from all Treponema species described previously. The only isolate, DD5/3T, for which the name Treponema brennaborense is proposed, is designated the type strain of the novel species. The strain is a small, highly motile spirochaete that has two periplasmic flagella, one flagellum being attached at each cell pole. Strain DD5/3T exhibits α-glucosidase and N-acetyl-β-glucosaminidase activity and growth is inhibited by rabbit serum. T. brennaborense was phylogenetically most closely related (89.5 % 16S rRNA similarity) to Treponema maltophilum, an oral spirochaete isolated from a periodontitis patient.
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Riemerella columbina sp. nov., a bacterium associated with respiratory disease in pigeons
More LessThirteen Gram-negative bacterial isolates were recovered from diseased pigeons and were tentatively classified as Riemerella anatipestifer-like strains based on conventional phenotypic features and disease symptoms. Phenotypic characteristics that differentiated the pigeon isolates from R. anatipestifer included their greyish-white to beige pigment formation on Columbia blood agar and the hydrolysis of aesculin. Furthermore, R. anatipestifer strains have thus far not been reported in pigeons. The phenotypic differences together with the unique host range of the new isolates have prompted the inclusion of these strains in a polyphasic taxonomic study. Extensive phenotypic examination, PAGE of total proteins and GC analysis of fatty acid contents revealed that the pigeon isolates constitute a homogeneous cluster, distinct from the R. anatipestifer reference strains. The phylogenetic position of representative strains was examined by using DNA–rRNA hybridizations and indicated that this taxon belongs to the genus Riemerella. Finally, DNA-binding values confirmed that the strains constitute a separate species for which the name Riemerella columbina sp. nov. is proposed. Strain LMG 11607T was selected as the type strain. Clinical observations suggest that these organisms are involved in pathogenesis of respiratory diseases, similar to those associated with R. anatipestifer infections. However, the role of co-factors and the interaction with other agents are unknown.
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- New Taxa - Proteobacteria
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Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium
More LessLindane-degrading activity under aerobic conditions has been observed in two bacterial strains: UT26, phenotypically identified as Sphingomonas paucimobilis, and a new single unidentified isolate named RP55577. The rrs (16S rDNA) sequences for both strains and the phenotypic characteristics for the unidentified isolate RP5557Twere determined. RP5557Tdoes not have high identity (less than 90% in all cases) with any sequence in the GenBank or RDP databases. A phylogenetic analysis based on rrs sequences indicated that RP5557Tbelongs to the γ-Proteobacteria in a coherent phylum that includes the genera Xanthomonas and Xylella (100% bootstrap), whereas UT26 is clearly separate from the Xanthomonas cluster. Based on the phylogenetic analyses and on the phenotypic characteristics, a new genus, Rhodanobacter, containing a single species, Rhodanobacter lindaniclasticus, is proposed for strain RP5557T(= LMG 18385T), which becomes the type strain.
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Burkholderia cocovenenans ( van Damme et al. 1960 ) Gillis et al. 1995 and Burkholderia vandii Urakami et al. 1994 are junior synonyms of Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993 and Burkholderia plantarii ( Azegami et al. 1987 ) Urakami et al. 1994 , respectively
More LessReference strains of Burkholderia cocovenenans and Burkholderia vandii were compared with strains of other Burkholderia species using SDS-PAGE of whole cell proteins, DNA-DNA hybridization and extensive biochemical characterization. Burkholderia gladioli and B. cocovenenans were indistinguishable in the chemotaxonomic and biochemical analyses. Burkholderia plantarii and B. vandii had indistinguishable whole-cell protein patterns but the B. vandii type strain differed from B. plantarii strains in several biochemical tests. The DNA-DNA binding levels (higher than 70%) indicated that (i) B. gladioli and B. cocovenenans, and (ii) B. plantarii and B. vandii each represent a single species. It is concluded that B. cocovenenans and B. vandii are junior synonyms of B. gladioli and B. plantarii. respectively.
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Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov.
More LessFifty-five Chinese isolates from nodules of Amorpha fruticosa were characterized and compared with the type strains of the species and genera of bacteria which form nitrogen-fixing symbioses with leguminous host plants. A polyphasic approach, which included RFLP of PCR-amplified 16S rRNA genes, multilocus enzyme electrophoresis (MLEE), DNA-DNA hybridization, 16S rRNA gene sequencing, electrophoretic plasmid profiles, cross-nodulation and a phenotypic study, was used in the comparative analysis. The isolates originated from several different sites in China and they varied in their phenotypic and genetic characteristics. The majority of the isolates had moderate to slow growth rates, produced acid on YMA and harboured a 930 kb symbiotic plasmid (pSym). Five different RFLP patterns were identified among the 16S rRNA genes of all the isolates. Isolates grouped by PCR-RFLP of the 16S rRNA genes were also separated into groups by variation in MLEE profiles and by DNA-DNA hybridization. A representative isolate from each of these DNA homology groups had a separate position in a phylogenetic tree as determined from sequencing analysis of the 16S rRNA genes. A new species, Mesorhizobium amorphae, is proposed for the majority of the isolates, which belonged to a moderately slow- to slow-growing, acid-producing group based upon their distinct phylogenetic position, their unique electrophoretic type, their low DNA homology with reference strains representing the species within the genus Mesorhizobium and their distinct phenotypic features. Strain ACCC 19665 was chosen as the type strain for M. amorphae sp. nov.
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Taxonomic relationships of the [Pasteurella] haemolytica complex as evaluated by DNA-DNA hybridizations and 16S rRNA sequencing with proposal of Mannheimia haemolytica gen. nov., comb. nov., Mannheimia granulomatis comb. nov., Mannheimia glucosida sp. nov., Mannheimia ruminalis sp. nov. and Mannheimia varigena sp. nov.
More LessThe present paper presents the conclusions of a polyphasic investigation of the taxonomy of the trehalose-negative [Pasteurella] haemolytica complex. Clusters previously identified by ribotyping and multilocus enzyme electrophoresis (MEE) have been evaluated by 16S rRNA sequencing and DNA–DNA hybridizations. Results obtained by the different techniques were highly related and indicated that the [P.] haemolytica complex contains distinct genetic and phenotypic groups. At least seven species were outlined, five of which were named. We refrained in formal naming of more groups until additional strains are characterized. Five 16S rRNA clusters were identified corresponding to distinct lineages previously outlined by MEE. Within 16S rRNA cluster I two distinct genotypic groups have been outlined in addition to [P.] haemolytica sensu stricto (biogroup 1). Each of the clusters II, III, IV and V represent at least one new species. The investigations underline that [P.] haemolytica sensu stricto only contains strains that do not ferment l-arabinose even though they are referred to as ‘biotype A’ of [P.] haemolytica. The five 16S rRNA clusters identified had a common root relative to the other species within the family Pasteurellaceae, and the overall sequence similarity among these five clusters was higher than what is observed within the existing genera of the family. The allocation of the trehalose-negative [P.] haemolytica complex to a new genus seems to be indicated. Based on the polyphasic investigation performed a new genus Mannheimia is proposed for the trehalose-negative [P.] haemolytica complex. At the present stage two previously named species are transferred to this new genus and three new species are described. [P.] haemolytica is reclassified as Mannheimia haemolytica comb. nov., whereas Pasteurella granulomatis, Bisgaard taxon 20 and [P.] haemolytica biovar 3J are reclassified and combined in the species Mannheimia granulomatis comb. nov. Mannheimia glucosida sp. nov. corresponds to [P.] haemolytica biogroups 3A-3H and the β-glucosidase and meso-inositol-positive strains of [P.] haemolytica biogroup 9. All typable strains within M. glucosida belong to serotype 11. Mannheimia ruminalis sp. nov. consists of strains previously classified as Bisgaard taxon 18 and [P.] haemolytica biogroup 8D. Finally, Mannheimia varigena sp. nov. includes [P.] haemolytica biogroup 6 as well as Bisgaard taxon 15 and Bisgaard taxon 36. The type strains are NCTC 9380T (M. haemolytica), ATCC 49244T (M. granulomatis), CCUG 38457T = P925T (M. glucosida). CCUG 38470T = HPA92T (M. ruminalis) and CCUG 38462T = 177T (M. varigena).
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Ignavigranum ruoffiae sp. nov., isolated from human clinical specimens
Two strains of a hitherto undescribed Gram-positive catalase-negative, facultatively anaerobic coccus isolated from human sources were characterizec by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated the unknown strains were genealogically identical, and constitute a new line close to, but distinct from, the genera Facklamia and Globicatella. The unknown bacterium was readily distinguished from Facklamia species and Globicatella sanguinus by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classifiec as lgnavigranum ruoffiae gen. nov., sp. nov. The type strain of lgnavigranum ruoffiae is CCUG 37658T.
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Haloanaerobacter salinarius sp. nov., a novel halophilic fermentative bacterium that reduces glycine-betaine to trimethylamine with hydrogen or serine as electron donors; emendation of the genus Haloanaerobacter
A novel halophilic fermentative bacterium has been isolated from the black sediment below a gypsum crust and a microbial mat in hypersaline ponds of Mediterranean salterns. Morphologically, physiologically and genetically this organism belongs to the genus Haloanaerobacter. Haloanaerobacter strain SG 3903T (T = type strain) is composed of non-sporulating long flexible rods with peritrichous flagella, able to grow in the salinity range of 5–30% NaCI, with an optimum at 14–15%. The strain grows by fermenting carbohydrates or by using the Stickland reaction with either serine or H2 as electron donors and glycine-betaine as acceptor, which is reduced to trimethylamine. The two species described so far in the genus Haloanaerobacter are not capable of Stickland reaction with glycine-betaine + serine; however, Haloanaerobacter chitinovorans can use glycine-betaine with H2 as electron donor. Strain SG 3903T thus represents the first described strain in the genus Haloanaerobacter capable of the Stickland reaction with two amino acids. Although strain SG 3903T showed 67% DNA-DNA relatedness to H. chitinovorans, it is physiologically sufficiently different from the two described species to be considered as a new species which has been named Haloanaerobacter salinarius sp. nov.
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Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll a production from hypersaline Ekho Lake
Eight Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and daughter cells could be motile. Bacteriochlorophyll a was sometimes produced, but production was repressed by constant dim light. The strains tolerated a wide range of temperature, pH, concentrations of artificial seawater and NaCI, but had an absolute requirement for sodium ions. Glutamate was metabolized with and without an additional source of combined nitrogen. The dominant fatty acid was C18:1; other characteristic fatty acids were C18:2, C12:0 2-OH, C12:1 3-OH, C16:1 C16:0 and C18:0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C base composition was 62–64 mol%. 16S rRNA gene sequence comparisons showed that the isolates were phylogenetically close to the genera Antarctobacter, ‘Marinosulfonomonas’, Octadecabacter, Sagittula, Sulfitobacter and Roseobacter. Morphological, physiological and genotypic differences to these previously described and distinct genera support the description of a new genus and a new species, Roseovarius tolerans gen. nov., sp. nov. The type strain is EL-172T ( = DSM 11457T).
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Desulfocella halophila gen. nov., sp. nov., a halophilic, fatty-acid-oxidizing, sulfate-reducing bacterium isolated from sediments of the Great Salt Lake
More LessA new halophilic sulfate-reducing bacterium, strain GSL-But2T, was isolated from surface sediment of the Southern arm of the Great Salt Lake, UT, USA. The organism grew with a number of straight-chain fatty acids (C4–C16), 2-methylbutyrate, l-alanine and pyruvate as electron donors. Butyrate was oxidized incompletely to acetate. Sulfate, but not sulfite or thiosulfate, served as an electron acceptor. Growth was observed between 2 and 19% (w/v) NaCl with an optimum at 4–5% (w/v) NaCl. The optimal temperature and pH for growth were around 34 °C and pH 6·5–7·3, respectively. The generation time under optimal conditions in defined medium was around 28 h, compared to 20 h in complex medium containing yeast extract. The G+C content was 35·0 mol%. 16S rRNA gene sequence analysis revealed that strain GSL-But2T belongs to the family Desulfobacteriaceae within the delta-subclass of the Proteobacteria and suggested that strain GSL-But2T represents a member of a new genus. The name Desulfocella halophila gen. nov., sp. nov. is proposed for this organism. The type strain of D. halophila is strain GSL-But2T (= DSM 11763T = ATCC 700426T).
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Rubrimonas cliftonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from a saline lake
More LessPhenotypic and phylogenetic studies were performed with two strains (OCh 317Tand OCh 318; T = type strain) of aerobic chemoheterotrophic bacteriochlorophyll-containing bacteria isolated from water of a saline lake located on the west coast of Australia. Both strains were Gram-negative, short rods and were motile by means of polar flagella. Catalase, oxidase, nitrate reductase, phosphatase and urease were produced. The cells utilized d-glucose, citrate, glycolate, pyruvate and ethanol. Acids were produced from l-arabinose, d-fructose, d-galactose, d-glucose, d-ribose and d-xylose. The strains could grow in media containing 0·5–7·5% NaCl. Bacteriochlorophyll a was synthesized under aerobic conditions. The results of 16S rRNA gene sequence comparisons revealed that strain OCh 317Trepresented a new lineage in the α-3 group of the class Proteobacteria. Strains OCh 317Tand OCh 318 were identified as strains of the same species because of their very similar phenotypic characteristics and their previously described high DNA-DNA homology. Therefore, it was concluded that the two strains should be assigned to a new genus and species, for which the name Rubrimonas cliftonensis is proposed. The type strain is OCh 317T(= JCM 10189T).
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Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen
More LessStrain 130ZT was isolated from the bovine rumen. It is a facultatively anaerobic, pleomorphic, Gram-negative rod. It exhibits a ‘Morse code’ form of morphology, which is characteristic of the genus Actinobacillus. Strain 130ZT is a capnophilic, osmotolerant succinogen that utilizes a broad range of sugars. It accumulates high concentrations of succinic acid (> 70gl-1). Strain 130ZT is positive for catalase, oxidase, alkaline phosphatase and β-galactosidase, but does not produce indole or urease. Acid but no gas is produced from d-glucose and d-fructose. 16S rRNA sequence analysis places strain 130ZT within the family Pasteurellaceae; the most closely related members of the family Pasteurellaceae have 16S rRNA similarities of 95.5% or less with strain 130ZT. Strain 130ZTwas compared with Actinobacillus lignieresii and the related Bisgaard Taxa 6 and 10. Based upon morphological and biochemical properties, strain 130ZT is most similar to members of the genus Actinobacillus within the family Pasteurellaceae. It is proposed that strain 130ZT be classified as a new species, Actinobacillus succinogenes. The type strain of Actinobacillus succinogenes sp. nov. is ATCC 55618T.
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Reassessment of the taxonomic position of Vibrio iliopiscarius ( Onarheim et al. 1994 ) and proposal for Photobacterium iliopiscarium comb. nov.
More LessThe phylogenetic position of Vibrio iliopiscarius was inferred by the maximum-likelihood, maximum-parsimony and neighbour-joining methods on the basis of almost complete 16S rRNA gene sequences. The results showed that this species falls into the same cluster as Photobacterium species and is clearly distinct from other Vibrio species. Its nearest phylogenetic neighbour is Photobacterium phosphoreum. From these results, it is concluded that V. iliopiscarius should be reclassified as Photobacterium iliopiscarium comb. nov. the type strain of which is PS1T(= ATCC 51760T).
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Sodalis gen. nov. and Sodalis glossinidius sp. nov., a microaerophilic secondary endosymbiont of the tsetse fly Glossina morsitans morsitans
More LessA secondary intracellular symbiotic bacterium was isolated from the haemolymph of the tsetse fly Glossina morsitans morsitans and cultured in Aedes albopictus cell line C6/36. Pure-culture isolation of this bacterium was achieved through the use of solid-phase culture under a microaerobic atmosphere. After isolation of strain M1T, a range of tests was performed to determine the phenotypic properties of this bacterium. Considering the results of these tests, along with the phylogenetic position of this micro-organism, it is proposed that this intracellular symbiont from G. m. morsitans should be classified in a new genus Sodalis gen. nov., as Sodalis glossinidius gen. nov., sp. nov. Strain M1Tis the type strain for this new species.
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Paracoccus carotinifaciens sp. nov., a new aerobic Gram-negative astaxanthin-producing bacterium
More LessThe strain E-396T, isolated from soil, was Gram-negative, aerobic, orangepigmented, rod-shaped, motile by peritrichous flagella and astaxanthin-producing. This organism produced carotenoids, mainly astaxanthin, and did not produce bacteriochlorophyll. The ubiquinone system was Q-10. Analysis of the 16S rRNA sequence of strain E-396T showed it to be a member of the α-3 subclass of the Proteobacteria, forming a cluster with the species of the genus Paracoccus. On the basis of the production of orange pigments and motility by peritrichous flagella, together with DNA-DNA reassociation data, it is concluded that the new isolate should be classified into a new species of the genus Paracoccus, Paracoccus carotinifaciens sp. nov. The type strain is E-396T (= IFO 16121T).
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Bartonella alsatica sp. nov., a new Bartonella species isolated from the blood of wild rabbits
Bartonella species are considered as emerging human pathogens, with at least six different species pathogenic or possibly pathogenic for humans. However, little is known about Bartonella distribution, species polymorphism and pathogenicity in mammalian species. The objective of this work was to determine the presence, the frequency and the distribution of Bartonella species in wild rabbits (Oryctolagus cuniculus) caught in warrens in Alsace, France. Humans may come into contact with wild rabbits when hunting, especially when they are picked up with bare hands and at time of evisceration. Of 30 blood samples collected and cultured from wild rabbits, nine (30%) were positive for organisms morphologically similar to Bartonella spp. The bacteria appeared as small, fastidious, aerobic, oxidase-negative. Gram-negative rods which could be localized within erythrocytes. Their biochemical properties were similar to those of the genus Bartonella. The sequence of the 16S rRNA gene obtained from the rabbit isolates was highly related to the sequences of the different Bartonella species (97·8-99·3% similarity). The high DNA hybridization rate (81–90% similarity) between the three strains isolated from rabbit blood confirmed that they belong to the same bacterial species. Hybridization values, obtained with the nuclease-TCA method, when testing type strains of recognized Bartonella species (9-14% similarity), support the creation of a new species for the rabbit isolates. The name Bartonella alsatica is proposed for these strains isolated from the blood of wild rabbits. The type strain is IBS 382T(= CIP 105477T).
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A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov.
The taxonomic position of a yellow-pigmented group of bacteria, isolated from the phyilosphere of grasses was investigated. Results obtained from restriction analysis of amplified 16S rDNA with seven endonucleases (CfoI, HaeIII, AluI, HinfI, MspI, Sau3A and ScrFI) showed identical restriction patterns for each enzyme of all isolates studied, which suggests that all strains belong to the same species. The grass isolates displayed the characteristics of the genus Pseudomonas. They were Gram-negative, aerobic and rod-shaped with polar flagella. Isolates were catalase-positive and oxidase-negative, and unable to oxidize or ferment glucose with the production of acid. The isolates did not reduce nitrate to nitrite but were able to utilize a wide range of compounds individually as a sole carbon source, with preference being given to the utilization of monosaccharides. The disaccharides tested were not utilized as substrates. The DNA base compositions of the tested strains ranged from 60 to 61 mol% G+C. The major isoprenoid quinone of each was ubiquinone Q-9 and hydroxy fatty acids were represented by 3-hydroxydodecanoic acid and 2-hydroxydodecanoic acid. Comparison of 16S rDNA sequences showed that the bacteria were members of the genus Pseudomonas, with similarity values between 91·5 and 97·7%. DNA–DNA hybridization studies with closely related neighbours revealed a low level of homology (< 27%), indicating that the isolates represent an individual species. On the basis of phenotypic and phylogenetic analyses a new species, Pseudomonas graminis sp. nov. (type strain DSM 11363T), is proposed.
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- New Taxa - Gram-Positive Bacteria
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Classification of thermophilic streptomycetes, including the description of Streptomyces thermoalcalitolerans sp. nov.
A polyphasic taxonomic study was undertaken to clarify relationships within and between representative thermophilic alkalitolerant streptomycetes isolated from soil and appropriate marker strains. The resultant data, notably those from DNA–DNA relatedness studies, support the taxonomic integrity of the validly described species Streptomyces thermodiastaticus, Streptomyces thermoviolaceus and Streptomyces thermovulgaris. However, the genotypic and phenotypic data clearly show that Streptomyces thermonitrificans Desai and Dhala 1967 and S. thermovulgaris ( Henssen 1957 ) Goodfellow et al. 1987 represent a single species. On the basis of priority, S. thermonitrificans is a later subjective synonym of S. thermovulgaris. Similarly, 10 out of the 11 representative thermophilic alkalitolerant isolates had a combination of properties consistent with their classification as S. thermovulgaris. The remaining thermophilic alkalitolerant isolate, Streptomyces strain TA56, merited species status. The name Streptomyces thermoalcalitolerans sp. nov. is proposed for this strain. A neutrophilic thermophilic isolate, Streptomyces strain NAR85, was identified as S. thermodiastaticus.
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A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care centre
Scotochromogenic mycobacterial isolates from water-damaged parts of indoor building materials of a children’s day care centre represented a phenetically and genetically distinct group of strains. A 16S rDNA dendrogram (1243 bp) showed that the closest species to the new strain MA112/96Twas Mycobacterium abscessus. Phylogenetic and phenetic analyses (100 characteristics) grouped the new isolates with M. abscessus, Mycobacterium vaccae, Mycobacterium aurum and Mycobacterium austroafricanum. Ribotyping with Pvull restriction distinguished the 5 isolates from the other 12 most closely related species by the major bands at 6·5–7 kb and 13–15 kb. The cell morphology of the new isolates was typical of mycobacteria, electron microscopy revealed a triple-layered cell wall with an irregular electron-dense outer layer. They grew at 10–37 °C with no growth at 45 °C in 5 d. The gene encoding the secreted 32 kDa protein, specific to mycobacteria, was detected by PCR. The main whole-cell fatty acids were characterized by high tuberculostearic acid 10Me-C18:0 (17% at 28 °C), which increased with increasing growth temperature (22% at 37 °C). The other main fatty acids were C18:1 cis9 and C16:0 (21–20% each), followed by, C17:1 cis9 (14%), C16:1 cis10 (8%) and also a high amount of C20 alcohol (9%). α-Mycolic acids, keto-mycolates and wax esters were present (C60–C90), MK-9(H2) (90%) and MK-8(H2) were the main menaquinones. The cellular phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidyl inositolmannosides and diphosphatidylglycerol. Polyamine content was low. G+C content was 72·9 mol%. The new isolates are proposed as a new species, Mycobacterium murale sp. nov. The type strain is MA112/96T(= DSM 44340T).
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Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia)
Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksár tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68Tand TAGA27Twas supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68Tand TAGA27Tis 69·4 and 69·6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925Tand Kocuria rhizophila, type strain DSM 11926T.
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Reclassification of Brevibacterium oxydans (Chatelain and Second 1966) as Microbacterium oxydans comb. nov.
More LessPhylogenetic and chemoteaxonomic analyses indicate that Brevibacterium oxydans is closely related to species of the genus Microbacterium, namely Microbacterium liquefaciens, Microbacterium luteolum and Microbacterium saperdae. DNA-DNA reassociation values of less than 60% between Brevibacterium oxydans and these three Microbacterium species support the distinctness of this miclclassified Brevibacterium species, which is reclassified as Microbacterium oxydans comb. nov.
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Reclassification of Brevibacterium incertum ( Breed 1953 ) as Desemzia incerta gen. nov., comb. nov.
More LessPhylogenetic analysis of 16S rDNA indicates that Brevibacterium incertum is not a member of the genus Brevibacterium but related to species of the genus Carnobacterium. Hence, Brevibacterium incertum is not a member of the class Acrinobactena but belongs to the phylogenetically defined broad Bacillus-Lactobacillus cluster. Based upon properties that taxonomically clearly distinguishes Brevibacterium incertum from species of the phylogenetic sister genus Carnobacterium, Brevibacterium incertum is reclassified as Desemzia incerta gen. nov., comb. nov.
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Phenotypic and phylogenetic characterization of a novel Lactobacillus species from human sources: description of Lactobacillus iners sp. nov.
More LessEleven strains of a hitherto undescribed Gram-positive, catalase-negative, facultatively anaerobic rod-shaped bacterium from human sources and medical care products were characterized by phenotypic and molecular taxonomic methods. The phenotypic properties of the bacterium were consistent with its assignment to the genus Lactobacillus but it was readily distinguished from all currently described species of this genus by its biochemical characteristics and by SDS-PAGE analysis of its cellular proteins. Comparative 16S rRNA gene sequence analysis demonstrated that the unknown bacterium was a member of rRNA group I Lactobacillus which includes Lactobacillus delbrueckii, the type species of the genus, and close relatives. Lactobacillus gasseri and Lactobacillus johnsonii were the nearest phylogenetic relatives of the unknown bacterium, but 16S rRNA sequence divergence values of >4% clealy showed that it represents a distinct species. Based on both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium should be classified in the genus Lactobacillus, as Lactobacillus iners sp. nov. The type strain of Lactobacillus iners is CCUG 28746T.
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Corynebacterium terpenotabidum sp. nov., a bacterium capable of degrading squalene
More LessThe taxonomic status of Arthrobacter sp. Y-11T, which was described as a squalene-degrading bacterium, was investigated by chemotaxonomic and genetic methods. The strain possesses wall chemotype IV, MK-9(H2) as the predominant menaquinone, mycolic acids, and straight-chain, saturated and monounsaturated fatty acids, with considerable amounts of tuberculostearic acid. The DNA G+C content is 67·5 mol%. 16S rRNA gene sequence analysis and quantitative DNA-DNA hybridization experiments provided strong evidence that strain Y-11Trepresents a new species within the genus Corynebacterium, for which the name Corynebacterium terpenotabidum sp. nov. is proposed. The type strain of C. terpenotabidum is strain Y-11T(= IFO 14764T).
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Paenibacillus dendritiformis sp. nov., proposal for a new pattern-forming species and its localization within a phylogenetic cluster
More LessA new strain capable of forming distinctive patterns during colony development was identified by using a combination of phenotypic characterization, fatty acid analysis and analysis of the 16S rRNA gene sequence. The strain formed either a branched, tip-splitting colony morphology (referred to as the T morphotype) or a chiral pattern exhibiting thinner branches with distinctive curling patterns (referred to as the C morphotype). Isolates of the T morphotype exhibited sequence identities greater than 97% to Paenibacillus thiaminolyticus JCM 7540. Phylogenetic analysis placed the T morphotype within the Paenibacillus cluster on a phylogenetic tree. On the basis of unique colony morphology and distinctive phenotypic characteristics, it is proposed that the pattern-forming isolates should be placed within a new species of Paenibacillus, Paenibacillus dendritiformis sp. nov., the type strain of which is T168T(= 30A1T).
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- New Taxa - Yeasts
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Kodamaea nitidulidarum, Candida restingae and Kodamaea anthophila, three new related yeast species from ephemeral flowers
Three new yeast species were discovered during studies of yeasts associated with ephemeral flowers in Brazil, Australia and Hawaii. Their physiological and morphological similarity to Kodamaea (Pichia) ohmeri suggested a possible relationship to that species, which was confirmed by rDNA sequencing. Kodamaea nitidulidarum and Candida restingae were found in cactus flowers and associated nitidulid beetles in sand dune ecosystems (restinga) of Southeastern Brazil. Over 350 strains of Kodamaea anthophila were isolated from Hibiscus and morning glory flowers (lpomoea spp.) in Australia, and from associated nitidulid beetles and Drosophila hibisci. A single isolate came from a beach morning glory in Hawaii. Expansion of the genus Kodamaea to three species modified the existing definition of the genus only slightly. The type and isotype strains are as follows: K. nitidulidarum strains UFMG96-272T(h+; CBS 8491T) and UFMG96-3941(h–; CBS 84921); Candida restingae UFMG96-276T(CBS 8493T); K. anthophila strains UWO(PS)95-602.1T(h+; CBS 8494T), UWO(PS)91-893.2I(h–; CBS 84951) and UWO(PS)95-725.1I(h–; CBS 8496I).
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Zygosaccharomyces lentus sp. nov., a new member of the yeast genus Zygosaccharomyces Barker
Unusual growth characteristics of a spoilage yeast, originally isolated from spoiled wholeorange drink and previously identified as Zygosaccharomyces bailii, prompted careful re-examination of its taxonomic position. Small-subunit rRNA gene sequences were determined for this strain and for four other strains also originally described as Z. bailii but which, in contrast to other strains of this species, grew poorly or not at all under aerobic conditions with agitation, failed to grow in the presence of 1 % acetic acid and failed to grow at 30 °C. Comparative sequence analysis revealed that these strains represented a phylogenetically distinct taxon closely related to, but distinct from, Z. bailii and Zygosaccharomyces bisporus. Furthermore, sequence analysis of the internal transcribed spacer (ITS) region showed that, while all five strains had identical ITS2 sequences, they could be subdivided into two groups based on ITS1 sequences. Despite such minor inter-strain sequence variation, these yeasts could readily be distinguished from all other currently described Zygosaccharomyces species by using ITS sequences. On the basis of the phylogenetic results presented, a new species comprising the five strains, Zygosaccharomyces lentus sp. nov., is described and supporting physiological data are discussed, including a demonstration that growth of this species is particularly sensitive to the presence of oxygen. The type strain of Z. lentus is NCYC D2627T.
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization
More LessThe phylogenetic relationships of 49 Acinetobacter strains, 46 of which have previously been classified into 18 genomic species by DNA–DNA hybridization studies, were investigated using the nucleotide sequence of gyrB, the structural gene for the DNA gyrase B subunit. The phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus). 2 (Acinetobacter baumannii), 3 and TU13; genomic species 6, BJ15, BJ16 and BJ17; genomic species 5, BJ13 (synonym of TU14) and BJ14; genomic species 7 (Acinetobacter johnsonii), 10 and 11; and genomic species 8 and 9. The phylogenetic grouping of Acinetobacter strains based on gyrB genes was almost congruent with that based on DNA–DNA hybridization studies. Consequently, gyrB sequence comparison can be used to resolve the taxonomic positions of bacterial strains at the level of genomic species. However, minor discrepancies existed in the grouping of strains of genomic species 8, 9 and BJ17. The phylogenetic tree for these strains was reconstructed from the sequence of rpoD, the structural gene for the RNA polymerase σ 70 factor. The latter tree was 100% congruent with the grouping based on DNA–DNA hybridization. The reliability of DNA–DNA hybridization may be superior to that of sequence comparison of a single protein-encoding gene in resolving closely related organisms since the former method measures the homologies between the nucleotide sequences of total genomic DNAs. Three strains that have not been characterized previously by DNA-DNA hybridization seem to belong to two new genomic species, one including strain ATCC 33308 and the other including strains ATCC 31012 and MBIC 1332.
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RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach
More LessIt has been established that 16S rRNA gene-based phytogeny gives a low resolution between members of the chemoautotrophic ammonia-oxidizing bacteria (AOB) belonging to the β-subclass of the Proteobacteria. In this study, 12 isolates of AOB were ribotyped, and the sequences of the 16S–23S rDNA intergenic spacer region (ISR) were determined and used in a phylogenetic study. 16S and 23S rDNA ribotyping revealed that the AOB studied contain only one rrn operon per genome, in contrast to most bacteria, which have 5–10 copies of the rRNA genes per genome. It is likely that the presence of only one set of rRNA genes is related to the slow growth of the AOB. The 16S and 23S rRNA genes of the AOB were shown to be arranged in the classical way: a 16S rRNA gene, an ISR and a 23S rRNA gene. Despite the close phylogenetic relationship among the AOB, the relative location of the rRNA genes in the genome appears to vary considerably. The size of the ISR was approximately 400 bp in the Nitrosomonas isolates and 645–694 bp in the Nitrosospira isolates, suggesting a species-specific size difference in the ISR. The ISR contained two potential tRNA genes in the 5′ end in all isolates studied. The similarity values between the ISR sequences of the AOB are low (42·9–96·2%) compared with the 16S rDNA sequence similarity values, and therefore the ISR sequences are valuable as a complementary phylogenetic tool in combination with 16S rRNA gene sequences. The phylogenetic analysis of the AOB based on ISR sequences confirms the 16S rRNA gene-based phytogeny but has the benefit of giving a higher resolution.
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Phylogeny of marine and freshwater Shewanella: reclassification of Shewanella putrefaciens NCIMB 400 as Shewanella frigidimarina
More LessDissimilatory Fe(III) reduction by Shewanella putrefaciens and related species has generated considerable interest in biochemical characterization of the pathways for anaerobic electron transfer in this organism. Two strains, MR-1 and NCIMB 400, have been extensively used, and several respiratory enzymes have been isolated from each. It has become apparent that significant sequence differences exist between homologous proteins from these strains. The 16S rRNA from NCIMB 400 was sequenced and compared to the sequences from MR-1 and other Shewanella strains. The results indicate that NCIMB 400 is significantly more closely related to the newly identified Shewanella frigidimarina than to the S. putrefaciens type strain. It is therefore proposed that NCIMB 400 should be reclassified as S. frigidimarina.
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Genetic structure of the genus Leptospira by multilocus enzyme electrophoresis
More LessThirty strains from the 11 species of the genus Leptospira were studied by multilocus enzyme electrophoresis at 12 enzyme loci, all of which were polymorphic. The mean number of alleles per locus was 6.5. Twenty-five electrophoretic types were distinguished. Grouping of the strains by cluster analysis was in general agreement with species delineation as determined by DNA-DNA hybridization, except for the strains of Leptospira meyeri and Leptospira inadai, which were scattered throughout the genus, reflecting previously recognized taxonomic uncertainties. Analysis of the clonality within Leptospira interrogans sensu stricto indicated that this population was relatively heterogeneous and a lack of gene linkage disequilibrium could not be excluded. There was a genetic discrimination between the pathogenic species and the saprophytic ones. The phenotypically intermediate species (L. inadai and Leptospira fainei) were also genetically separated and were probably closer to the saprophytes than to the pathogens.
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- Methods
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Application of temperature-gradient gel electrophoresis in taxonomy of coryneform bacteria
More LessStrains belonging to the Gram-positive coryneform soil bacteria were screened genotypically by temperature-gradient gel electrophoresis (TGGE). This method allows the sequence-specific separation of amplified fragments of 16S rRNA genes. A total of 115 reference strains representing the majority of the species of the genera Aeromicrobium, Agromyces, Arthrobacter, Aureobacterium, Cellulomonas, Curtobacterium, Nocardioides and Terrabacter were characterized. Depending on the genus investigated, the resolution limit of the technique appeared to be at the species or genus level or intermediate between the two. Aberrant TGGE profiles of strains within particular taxa revealed genomic heterogeneity and generic misclassification of nine strains studied. Beyond that, indications of 16S rRNA gene heterogeneity were found within the genomes of three Curtobacterium strains. The misclassifications revealed by TGGE were confirmed using whole-cell fatty acid methyl ester analysis and subsequent comparison with a database. TGGE has been demonstrated to be a useful tool in bacterial taxonomy.
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New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora
More LessMembers of the family Pseudonocardiaceae are difficult to identify on the basis of their micromorphology only. The biochemical characterization of each new isolate is a painstaking and time-consuming task which cannot always be undertaken when handling large numbers of strains as is the case in natural product screening programmes. In this study, two sets of genus-specific oligonucleotides were designed which allow rapid detection of members of the genera Pseudonocardia and Saccharopolyspora by means of PCR-specif ic amplification. The genus specificity of these primers was validated on a wide range of collection strains and the primers were subsequently used to study a group of 106 wild-type isolates that possessed morphological characteristics of the family. Out of this group, 51 strains could be identified as members of the genus Pseudonocardia and only nine isolates could be assigned to the genus Saccharopolyspora. The diversity indicated by whole-cell fatty acid profiles of both wild-type and reference strains was compared with that identified using the oligonucleotide primers. The partial 16S rDNA sequencing of representative wild-type strains was used to validate their genus assignment by PCR-specif ic amplification. This study shows the industrial usefulness of the application of these direct identification tools as well as the complementary use of two sources of data, PCR-specif ic amplification results and fatty acid composition, to assess the diversity of a microbial population.
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Novel characteristic for distinguishing Lactococcus lactis subsp. lactis from subsp. cremoris
More LessLactococcus lactis strains were examined for their ability to produce γ-aminobutyric acid (GABA). Results showed that strains of L. lactis subsp. lactis were able to produce this acid, whereas L. lactis subsp. cremoris were not. GABA production thus represents another effective characteristic for distinguishing L. lactis subsp. lactis from L. lactis subsp. cremoris.
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Polyamine profiles within genera of the class Actinobacteria with ll-diaminopimelic acid in the peptidoglycan
More LessPolyamine patterns of coryne-and nocardioform representatives of the class Actinobacteria with ll-diaminopimelic acid in the peptidoglycan, comprising strains of the genera Aeromicrobium, Nocardioides, Intrasporangium, Terrabacter, Terracoccus, Propioniferax, Friedmanniella, Microlunatus, Luteococcus and Sporichthya, were analysed. The different polyamine patterns were in good agreement with the phylogenetic heterogeneity within this group of actinomycetes. Strains of the closely related genera Nocardioides and Aeromicrobium were characterized by the presence of cadaverine. The second cluster, consisting of the type strains of the species Friedmanniella antarctica, Propioniferax innocua, Microlunatus phosphovorus and Luteococcus japonicus displayed as a common feature the presence of the two predominant compounds spermidine and spermine. The presence of putrescine was common to the type strains of the species Intrasporangium calvum, Terrabacter tumescens and Terracoccus luteus. Sporichthya polymorpha, which is a representative of a separate line of descent, displayed spermidine as the predominant polyamine. These data indicate that polyamine patterns are suitable for the classification of actinomycetes with ll-diaminopimelic acid in the peptidoglycan.
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Identification of yeasts by RFLP analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers
More LessThe identification and classification of yeasts have traditionally been based morphological, physiological and biochemical traits. Various kits have been developed as rapid systems for yeast identification, but mostly for clinical diagnosis. In recent years, different molecular biology techniques have been developed for yeast identification, but there is no available database to identify a large number of species. In the present study, the restriction patterns generated from the region spanning the internal transcribed spacer (ITS1 and ITS2) and the 5.8S rRNA gene were used to identify a total of 132 yeast species belonging to 25 different genera, including teleomorphic and anamorphic ascomycetous and basidiomycetous yeasts. In many cases, the size of the PCR products and the restriction patterns obtained with endonucleases CfoI, HaeIII and HinfI yielded a unique profile for each species. Accordingly, the use of this molecular approach is proposed as a new rapid and easy method of routine yeast identification.
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- International Committee On Systematic Bacteriology: Opinions
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Rejection of Clostridium putrificum and conservation of Clostridium botulinum and Clostridium sporogenes - Opinion 69
The Judicial Commission rejected the name Clostridium putrificum while conserving Clostridium botulinum for toxigenic strains and conserving Clostridium sporogenes for non-toxigenic strains.
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Volumes and issues
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