- Volume 49, Issue 2, 1999
Volume 49, Issue 2, 1999
- New Taxa - Yeasts
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Cystofilobasidiales, a new order of basidiomycetous yeasts
More LessThe order Cystofilobasidiales is described for teleomorphic basidiomycetous yeasts with holobasidia and teliospores. Their septa have dolipores, but lack parenthesomes. d-Glucuronate, nitrate and nitrite are assimilated and myo-inositol is usually assimilated. Coenzyme Q has 8 or 10 isoprenologues. 25S and 18S rDNA sequence analysis indicates a monophyletic branch within the Tremellomycetidae of the Hymenomycetes. Cystofilobasidium is the type genus.
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic position of Chitinophaga pinensis in the Flexibacter–Bacteroides–Cytophaga phylum
L. I. Sly, M. Taghavi and M. FeganComparison of the 16S rRNA gene sequence determined for Chitinophaga pinensis showed that this species is most closely related to Flexibacter filiformis in the Flexibacter–Bacteroides–Cytophaga phylum. These two chitinolytic bacteria, which are characterized by transformation into spherical bodies on ageing, belong to a strongly supported lineage that also includes Cytophaga arvensicola, Flavobacterium ferrugineum and Flexibacter sancti. The lineage is distinct from the microcyst-forming species Sporocytophaga myxococcoides.
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The phylogenetic relationships of Caulobacter, Asticcacaulis and Brevundimonas species and their taxonomic implications
More LessThe phylogenetic relationships among the species of Caulobacter, Asticcacaulis and Brevundimonas were studied by comparison of their 16S rDNA sequences. The analysis of almost complete sequences confirmed the early evolutionary divergence of the freshwater and marine species of Caulobacter reported previously [Stahl, D. A., Key, R., Flesher, B. & Smit, J. (1992). J Bacteriol 174, 2193-2198]. The freshwater species formed two distinct clusters. One cluster contained the species Caulobacter bacteroides, Caulobacter crescentus, Caulobacter fusiformis and Caulobacter henricii. C. bacteroides and C. fusiformis are very closely related (sequence identity 99.8%). The second cluster was not exclusive and contained the species Caulobacter intermedius, Caulobacter subvibrioides and Caulobacter variabilis, as well as Brevundimonas diminuta and Brevundimonas vesicularis. The marine species Caulobacter halobacteroides and Caulobacter maris were very closely related, with a sequence identity of 99.7%. These two species were most closely but distantly related to the marine hyphal/budding bacteria Hyphomonas jannaschiana and Hirschia baltica, which formed a deep phylogenetic line with Rhodobacter sphaeroides and Rhodobacter capsulatus. Caulobacter leidyia is unrelated to the other species of Caulobacter and belongs to the alpha-4 subclass of the Proteobacteria, forming a distinct cluster with Asticcacaulis excentricus and Asticcacaulis biprosthecium. The taxonomic implications of the polyphyletic nature of the genus Caulobacter and the absence of a type culture for the type species of the genus, Caulobacter vibrioides, are discussed.
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Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli
More LessSequence heterogeneities of variable positions located at regions V1 and V6 of 56 cloned 16S rRNA genes were determined from six Escherichia coli strains. These nucleotides were involved in secondary structure base-pairing of stem-loops. Compensatory and single mutations have occurred but secondary structure was conserved. Eight different sequences were found in the stem at region V1 indicating that in these sites mutation rates are higher than those of homogenization processes. Region V6 showed two different structures (V6-I and V6-II) although heterogeneities were determined in nine sites. Strains ECOR52 and ECOR56 only showed the V6-I sequence, ECOR35 showed V6-II, whereas clones from ECOR42 and ECOR49 showed both types of V6 structures. Results were confirmed by PCR using V6 sequence-specific probes. Stem V6-II was also found in 16S rRNA sequences deposited in the RDP (Ribosomal Database Project) belonging to distantly related taxa; ancestral sequence V6-II seems to be homogenized in all rrn operons of the multigene family of strain ECOR35 producing effects of distortion in the molecular clock, similar to those that homoplasies could produce. V6 sequence-specific probes were applied to the 72 ECOR strains: half showed both V6-I and V6-II, and the rest had one or another. Only strain ECOR24 did not yield products in the PCR test and sequencing of 12 cloned 16S rRNA genes revealed a third form, V6-III, also found in the RDP. Concerted evolution by homogenization of the rRNA family may induce chronometric distortions responsible for a loss of ultrametricity in phylogenetic trees, particularly, of very closely related micro-organisms.
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Polar lipids of four listeria species containing L-lysylcardiolipin, a novel lipid structure, and other unique phospholipids
More LessThe membrane lipids of Listeria innocua, Listeria monocytogenes, Listeria seeligeri and Listeria welshimeri were fractionated on DEAE-cellulose and purified by chromatography on silica gel and/or preparative TLC. The lipid structures were elucidated by chemical and chromatographic means. The polar lipid composition of the four listeria species was similar. Phospholipids predominated. They consisted of phosphatidylglycerol, l-lysylphosphatidylglycerol, cardiolipin [bis(phosphatidyl)glycerol] and l-lysylcardiolipin. A phospholipid more polar than cardiolipin, possibly two l-lysyl derivatives of it, sn-glycero-1-phosphoglycolipid, its d-alanyl derivative, and polyprenol phosphate were also detected. Towards the end of exponential growth, the relative amounts of cardiolipin and l-lysylcardiolipin increased, approaching 47–78% lipid phosphorus with a ratio of l-lysylcardiolipin to cardiolipin of 0·25–1·6. As shown by fast atom bombardment-mass spectrometry, cardiolipin and l-lysylcardiolipin consisted of five molecular species due to various fatty acid combinations. l-Lysylcardiolipin has so far not been found in nature. It belongs to the recently discovered class of substituted cardiolipins. Its occurrence in the four listeria species tested shows that it is a characteristic lipid component of the L. monocytogenes line of descent. Further studies on the lipid pattern of members of the other descent line are required to decide whether lysylcardiolipin can serve as a genus-specific chemotaxonomic marker for listeriae.
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Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales
The 16S rDNA sequences of 20 novel isolates of members of the order Planctomycetales were compared to those of the type strains of described planctomycete species and 22 planctomycete isolates for which the 16S rDNA sequences had been previously determined. The novel isolates could be assigned to several phylogenetically broad groups, four of which are defined by the genera Gemmata, Isosphaera, Planctomyces and Pirellula. To evaluate polyamines as a chemotaxonomic marker within this order, the polyamine pool was determined for six planctomycete reference species and for 20 planctomycete isolates. All analysed members of the order Planctomycetales contained significant amounts of polyamines. sym-Homospermidine (HSPD) is present in all strains except Planctomyces limnophilus and related strains, which had high amounts of putrescine (PUT) as the dominant polyamine component. The distribution of PUT, HSPD and spermidine reflects the phylogenetic diversity within the Planctomycetales as closely related representatives of the phylogenetic groups defined by described species and novel isolates exhibit similar polyamine patterns. Determination of the DNA base composition revealed G+C contents of >60 mol% for members of Gemmata and Isosphaera whereas, except for two isolates, strains which are phylogenetically associated with Planctomyces and Pirellula had G+C contents of 51-57 mol%.
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NOTE
More LessThe nucleotide sequences of the 16S rRNA gene (rDNA) in 38 taxa of the genus Staphylococcus were compared phylogenetically. Based on phylogenetic tree analysis, staphylococcal species were divided into 12 cluster groups. These cluster groups were in very good agreement with species groups determined by DNA–DNA reassociation studies. These genealogical classifications were consistent with the results of the production of coagulase or oxidase and with resistance to novobiocin. These suggest that the phylogenetic relationship of the genus Staphylococcus is accurately represented by the results obtained from the sequence analysis of 16S rDNA.
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- Methods
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Rapid identification of hyperthermophilic methanococci isolated from deep-sea hydrothermal vents
More Less16S rDNAs amplified by PCR from 22 hyperthermophilic methanococci isolated from deep-sea hydrothermal vents were compared with those of the six type strains of the genus Methanococcus by RFLP analysis. Restriction fragments obtained with Haelll enabled four of the type species to be distinguished. Restrictions with HhaI, BstUI and MspI were necessary to differentiate Methanococcus jannaschii and Methanococcus fervens. The results indicate that the 16S rDNA PCR-RFLP method provides a rapid and reliable tool for the identification of newly isolated hyperthermophilic Methanococcus spp.
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Identification of nine species of the Chlamydiaceae using PCR-RFLP
More LessThe family Chlamydiaceae contains two genera and nine species. Rapid and easy identification of these species is essential for taxonomic, epidemiological and clinical determinations. Currently, DNA sequence analysis is the only accepted method that decisively distinguishes all nine species. In this study, a simple and rapid PCR-RFLP procedure was developed by which laboratory-cultured chlamydial specimens could be identified. To accomplish this, conserved oligonucleotide primers and restriction sites were deduced from 16S and 23S rRNA sequence data from >50 chlamydial strains representing all nine species. DNA from 25 previously characterized chlamydial strains were tested with these primers and restriction enzymes. All nine chlamydial species were reliably distinguished in the tests. The procedure was optimized by adjusting the annealing temperature using both a standard and a heat-activated DNA polymerase to reduce mismatch PCR amplification of mycoplasmas and other bacteria. The result was that a PCR method for species identification of chlamydial isolates and for distinguishing mycoplasmas and chlamydiae was created. This method can be used to rapidly identify known species of the family Chlamydiaceae.
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AFLP fingerprinting for analysis of yeast genetic variation
More LessAmplified fragment length polymorphism (AFLP) was used to investigate genetic variation in commercial strains, type strains and winery isolates from number of yeast species. AFLP was shown to be effective in discriminating closely related strains. Furthermore, sufficient similarity in the fingerprints produced by yeasts of a given species allowed classification of unknown isolates. The applicability of the method for determining genome similarities between yeasts was investigated by performing cluster analysis on the AFLP data. Results from two species, Saccharomyces cerevisiae and Dekkera bruxellensis, illustrate that AFLP is useful for the study of intraspecific genetic relatedness. The value of the technique in strain differentiation, species identification and the analysis of genetic similarity demonstrates the potential of AFLP in yeast ecology and evolutionary studies.
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- International Committee On Systematic Bacteriology
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Recommended minimal standards for description of new staphylococcal species
More LessIn accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria, minimal standards are proposed for the genus Staphylococcus and the description of newly recognized species in this genus. Assignment of a strain to the genus Staphylococcus requires that it is a Gram-positive coccus that forms clusters, produces catalase, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and G+C content of DNA in a range of 30–40 mol%. The recommended minimal standards for describing a new Staphylococcus species are based on the results of phenotypic and genomic studies of at least five independently isolated strains. They include colony morphology and the results of the following conventional tests: pigment production, growth requirements, fermentative and oxidative activity on carbohydrates, novobiocin susceptibility, enzymic activities (nitrate reductase, alkaline phosphatase, arginine dihydrolase, ornithine decarboxylase, urease, cytochrome oxidase, staphylocoagulase in rabbit plasma, heat-stable nuclease, amidases, oxidases, clumping factor, and haemolytic activity on sheep or bovine blood agar). DNA–DNA hybridization experiments may distinguish species when the difference between the binding in the homologous reaction and the binding in the heterologous reaction expressed as a percentage is less than 70%. In addition, rRNA signature sequence criteria, ribotyping characterization of the nomenclature type strain and other strains of the species, and reference strains of other species is recommended to describe the strains of the new species with sets of genetic attributes and reveal possible grouping errors. This proposal has been endorsed by the members of the Subcommittee on the taxonomy of staphylococci and streptococci of the International Committee on Systematic Bacteriology.
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Revised Salmonella nomenclature: designation of Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 sp. nov. nom. rev. as the neotype species of the genus Salmonella Lignieres 1900 (Approv Lists 1980), rejection of the name Salmonella choleraesuis (Smith 1894) Weldin 1927 (Approved Lists 1980), and conservation of the name Salmonella typhi (Schroeter 1886) Warren and Scott 1930 (Approved Lists 1980). Request for an Opinion
More LessThe Request for an Opinion by Le Minor and Popoff 1987, proposing designation of ‘Salmonella enterica’ (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 as the type and only species of the genus Salmonella Lignieres 1900 (Approved Lists 1980), has not been positively decided upon by the Judicial Commission. However, many bacteriologists use the name ‘Salmonella enterica’. To avoid further confusion, it is requested to reject the name Salmonella choleraesuis (Smith 1894) Weldin 1927 (Approved Lists 1980), to recognize the species Salmonella enterica, to conserve the name Salmonella typhi (Schroeter 1886) Warren and Scott 1930 (Approved Lists 1980), and to emend the genus Salmonella with the establishment of a neotype species, Salmonella enterica.
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Replacement of ATCC 21273, the current type strain of Streptomyces rameus Shibata 1959, with IFO 3782
More LessIt is proposed that the type strain of Streptomyces rameus Shibata 1959 is IFO 3782 (= No. 43797), which is the originally designated type strain, and not ATCC 21273 as given in the Approved Lists. The level of DNA relatedness between IFO 3782 and ATCC 21273 is 30%, indicating that they are different species.
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- Errata
Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 34 (1984)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 12 (1962)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)