International journal of systematic bacteriology最新文献

{"title":"A protein-based phylogenetic tree for gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene.","authors":"S Ahmad,&nbsp;A Selvapandiyan,&nbsp;R K Bhatnagar","doi":"10.1099/00207713-49-4-1387","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1387","url":null,"abstract":"<p><p>The dnaK operon from Bacillus subtilis and other Gram-positive bacteria with low G + C DNA content contains additional heat-shock genes, including hrcA. The hrcA gene encodes a transcription factor that negatively regulates heat-shock genes and is uniformly present in all Gram-positive bacteria studied to date. An hrcA homologue is also present in Synechocystis species, Leptospira interrogans, Chlamydia trachomatis, Caulobacter crescentus and Methanococcus jannaschii, organisms that diverged early on from the common ancestor of all Gram-positive bacteria and Proteobacteria, according to 16S rRNA phylogeny. A partial, protein-based phylogenetic tree, derived using amino acid sequence homology of hrcA proteins from Gram-positive bacteria, is presented here, and the results are compared with the phylogenetic trees generated from 16S rRNA, dnaK and dnaJ sequences. The location of the hrcA gene and the genome organization of the dnaK operon support the division of all Gram-positive bacteria into three major groups: one group contains high-G + C Gram-positive bacteria, and two others contain low-G + C Gram-positive bacteria. Among the Gram-positive bacteria with low G + C DNA content, the results indicate that there is a close phylogenetic relationship between Bacillus species and Clostridium species on the one hand and between Lactococcus lactis and Streptococcus mutans on the other. Streptomyces and Mycobacterium species also exhibited a close relationship. A hierarchical arrangement of Gram-positive bacteria based on HrcA sequences is proposed as an additional refinement of the phylogenetic relationships within this important bacterial group.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1387-94"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1387","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Streptomyces malaysiensis sp. nov., a new streptomycete species with rugose, ornamented spores.","authors":"A al-Tai,&nbsp;B Kim,&nbsp;S B Kim,&nbsp;G P Manfio,&nbsp;M Goodfellow","doi":"10.1099/00207713-49-4-1395","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1395","url":null,"abstract":"<p><p>The taxonomic position of a streptomycete strain isolated from Malaysian soil was established using a polyphasic approach. The organism, designated strain ATB-11T, was found to have chemical and morphological properties consistent with its classification in the genus Streptomyces. An almost complete 16S rRNA gene (rDNA) sequence determined for the test strain was compared with those of previously studied streptomycetes by using two treeing algorithms. The 16S rDNA sequence data not only supported classification of the strain in the genus Streptomyces but also showed that it formed a distinct phyletic line. At maturity, the aerial hyphae of strain ATB-11T differentiated into tight, spiral chains of rugose, cylindrical spores. The organism was readily distinguished from representatives of validly described Streptomyces species with rugose spores by using a combination of phenotypic features. It is proposed, therefore, that strain ATB-11T be classified in the genus Streptomyces as Streptomyces malaysiensis sp. nov.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1395-402"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1395","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clostridium frigidicarnis sp. nov., a psychrotolerant bacterium associated with 'blown pack' spoilage of vacuum-packed meats.","authors":"D M Broda,&nbsp;P A Lawson,&nbsp;R G Bell,&nbsp;D R Musgrave","doi":"10.1099/00207713-49-4-1539","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1539","url":null,"abstract":"<p><p>Two strains of a psychrotolerant Clostridium, isolated from vacuum-packed, temperature-abused beef, were characterized using a multiphasic approach. The strains were Gram-positive motile rods producing elliptical subterminal spores during early stationary growth phase. The strains were psychrotolerant. At pH 7.0, they grew between 3.8 and 40.5 degrees C; their optimum growth temperature was 30.0-38.5 degrees C. At 30 degrees C, the pH range for growth was between 4.7 and 9.5; the optimum pH for growth was 6.4-7.2. The organisms were proteolytic and saccharolytic, lecithinase-positive and hydrolysed gelatin. The fermentation products formed in peptone/yeast extract/glucose/starch broth were acetate, ethanol, butyrate, isovalerate, butanol, isobutyrate, oxalacetate, lactate, hydrogen and carbon dioxide. The DNA G + C compositions of the two meat strains were 27.3 and 28.4 mol%. Phylogenetic analyses indicated that the strains belong to Cluster I of the genus Clostridium (sensu Collins et al., 1994). The new strains differed from phylogenetically related clostridia in terms of cellular fatty acid composition, soluble protein profiles and phenotypic properties. On the basis of phenotypic and genotypic characterization data, the strains were assigned to a new species for which the name Clostridium frigidicarnis is proposed; strain SPL77AT (= DSM 12271T) is the type strain.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1539-50"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov.","authors":"R Howarth,&nbsp;R F Unz,&nbsp;E M Seviour,&nbsp;R J Seviour,&nbsp;L L Blackall,&nbsp;R W Pickup,&nbsp;J G Jones,&nbsp;J Yaguchi,&nbsp;I M Head","doi":"10.1099/00207713-49-4-1817","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1817","url":null,"abstract":"<p><p>The relationship of mixotrophic and autotrophic Thiothrix species to morphologically similar chemoorganotrophic bacteria (e.g. Leucothrix species, Eikelboom type 021N bacteria) has been a matter of debate for some years. These bacteria have alternatively been grouped together on the basis of shared morphological features or separated on the basis of their nutrition. Many of these bacteria are difficult to maintain in axenic culture and, until recently, few isolates were available to allow comprehensive phenotypic and genotypic characterization. Several isolates of Thiothrix spp. and Eikelboom type 021N strains were characterized by comparative 16S rRNA sequence analysis. This revealed that the Thiothrix spp. and Eikelboom type 021N isolates formed a monophyletic group. Furthermore, isolates of Eikelboom type 021N bacteria isolated independently from different continents were phylogenetically closely related. The 16S rRNA sequence-based phylogeny was congruent with the morphological similarities between Thiothrix and Eikelboom type 021N. However, one isolate examined in this study (Ben47) shared many morphological features with the Thiothrix spp. and Eikelboom type 021N isolates, but was not closely related to them phylogenetically. Consequently, morphology alone cannot be used to assign bacteria to the Thiothrix/type 021N group. Comparative 16S rRNA sequence analysis supports monophyly of the Thiothrix/type 021N group, and phenotypic differences between the Thiothrix spp. and Eikelboom type 021N bacteria are currently poorly defined. For example, both groups include heterotrophic organisms that deposit intracellular elemental sulfur. It is therefore proposed that the Eikelboom type 021N bacteria should be accommodated within the genus Thiothrix as a new species, Thiothrix eikelboomii sp. nov., and three further new Thiothrix species are described: Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1817-27"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1817","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic analysis of Fusobacterium alocis and Fusobacterium sulci based on 16S rRNA gene sequences: proposal of Filifactor alocis (Cato, Moore and Moore) comb. nov. and Eubacterium sulci (Cato, Moore and Moore) comb. nov.","authors":"J Jalava,&nbsp;E Eerola","doi":"10.1099/00207713-49-4-1375","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1375","url":null,"abstract":"<p><p>Genes encoding the 16S rRNA of Fusobacterium alocis ATCC 35896T and Fusobacterium sulci ATCC 35585T were sequenced. These sequences did not have any affinity with the 16S rRNA gene sequences of members of the genus Fusobacterium. Fusobacterium alocis ATCC 35896T and Fusobacterium sulci ATCC 35585T belonged to Clostridium cluster XI; the species most closely related to these strains were Filifactor villosus NCTC 11220T and Eubacterium infirmum W1471, respectively. Two new combinations are proposed: Filifactor alocis (Cato, Moore and Moore) comb. nov. (type strain ATCC 35896T) and Eubacterium sulci (Cato, Moore and Moore) comb. nov. (type strain ATCC 35585T).</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1375-9"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1375","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eubacterium minutum is an earlier synonym of Eubacterium tardum and has priority.","authors":"W G Wade,&nbsp;J Downes,&nbsp;M A Munson,&nbsp;A J Weightman","doi":"10.1099/00207713-49-4-1939","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1939","url":null,"abstract":"<p><p>The recently proposed species Eubacterium minutum and Eubacterium tardum appeared to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of strains of both species to clarify their taxonomic position. The type strains of E. minutum and E. tardum exhibited identical biochemical and protein profiles and their 16S rRNA gene sequences displayed 99.9% similarity. The G + C content of the DNA of both strains was estimated at 45 mol%. It is concluded that E. minutum and E. tardum are synonyms; E. minutum has priority. An emended description of E. minutum is given.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1939-41"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1939","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brevibacterium avium sp. nov., isolated from poultry.","authors":"C Pascual,&nbsp;M D Collins","doi":"10.1099/00207713-49-4-1527","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1527","url":null,"abstract":"<p><p>Two strains of a Brevibacterium-like bacterium originating from bumble-foot lesions of domestic fowls were subjected to a polyphasic taxonomic study. The phenotypic characteristics of the bacterium were consistent with its assignment to the genus Brevibacterium although comparative 16S rRNA gene sequencing showed that the organism represents a distinct subline within the genus. Chromosomal DNA-DNA pairing studies confirmed that the unidentified bacterium was genomically distinct and worthy of separate species status. Based on the phenotypic and genotypic distinctiveness of the bacterium from poultry, a new species, Brevibacterium avium, is proposed. The type strain of Brevibacterium avium is NCIMB 703055T.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1527-30"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1527","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21415627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic re-evaluation of 'Nocardiopsis' sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov.","authors":"S Chiba,&nbsp;M Suzuki,&nbsp;K Ando","doi":"10.1099/00207713-49-4-1623","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1623","url":null,"abstract":"<p><p>Re-evaluation of the taxonomic position of strain K-252T, which produces the compound K-252a, showed that the strain does not belong to the genus Nocardiopsis suggested previously. Strain K-252T formed aerial mycelia with long spore chains, and hyphal fragmentation was not observed. The cell wall chemotype of the strain was III/B, the major menaquinone was MK-9 (III, VIII-H4), the phospholipid pattern was PIV and the major cellular fatty acids were 10Me-C17:0, iso-C16:0 and C16:0. Phylogenetic analysis of the 16S rRNA sequence showed that strain K-252T was clustered in the Nonomuraea group. Furthermore, on the basis of DNA-DNA reassociation and phenotypic data, strain K-252T (= NRRL 15532T) was classified as a new species of the genus Nonomuraea. This strain is proposed as Nonomuraea longicatena sp. nov.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1623-30"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21414928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Burkholderia species and genomovars from cystic fibrosis patients by AFLP fingerprinting.","authors":"T Coenye,&nbsp;L M Schouls,&nbsp;J R Govan,&nbsp;K Kersters,&nbsp;P Vandamme","doi":"10.1099/00207713-49-4-1657","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1657","url":null,"abstract":"<p><p>AFLP is a genomic fingerprinting technique based on the selective amplification of restriction fragments from a total double-digest of genomic DNA. The applicability of this method to differentiate between species and genomovars of the genus Burkholderia was tested, with particular emphasis on taxa occurring in cystic fibrosis patients. In this study, 78 well-characterized strains and field isolates were investigated by two methods of AFLP fingerprinting. In the manual procedure, a radioactively labelled primer was used, amplified fragments were separated by conventional PAGE and the patterns were revealed by autoradiography. In the automated procedure, a fluorescently labelled primer was used in combination with electrophoresis and on-line data collection by means of an automated DNA sequencer. Overall, there was good agreement between the two AFLP procedures and the data were mostly consistent with results obtained from SDS-PAGE of whole-cell proteins and DNA-DNA hybridization experiments. The automated AFLP procedure has considerable technical advantages compared with the manual AFLP procedure, but a thorough visual analysis of the DNA profiles was required to avoid misidentification of some Burkholderia cepacia genomovar III strains.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1657-66"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1657","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21414931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of three different types of 'Tropheryma whippelii' directly from clinical specimens by sequencing, single-strand conformation polymorphism (SSCP) analysis and type-specific PCR of their 16S-23S ribosomal intergenic spacer region.","authors":"H P Hinrikson,&nbsp;F Dutly,&nbsp;S Nair,&nbsp;M Altwegg","doi":"10.1099/00207713-49-4-1701","DOIUrl":"https://doi.org/10.1099/00207713-49-4-1701","url":null,"abstract":"<p><p>The 16S-23S rDNA intergenic spacer region of organisms identical with or closely related to 'Tropheryma whippelii', the uncultivated causative agent of Whipple's disease, was analysed directly from 38 clinical specimens of 28 patients using a specific nested PCR followed by direct sequencing. As compared to the reference sequence in public databases, two novel 'T. whippelii' spacer types were recognized. In the absence of DNA-DNA hybridization data it is uncertain whether the three types found represent subtypes of a single species or three different but closely related species. Methods were developed to detect all three variants by single-strand conformation polymorphism analysis and by type-specific PCR assays, thus allowing the screening of large numbers of specimens. Further studies may provide a clue to the possible associations between the type of infecting strain and the various clinical presentations of Whipple's disease.</p>","PeriodicalId":14428,"journal":{"name":"International journal of systematic bacteriology","volume":"49 Pt 4 ","pages":"1701-6"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1099/00207713-49-4-1701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21414935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}