scholarly journals Phylogenetic Analysis of Salmonella spp. Isolated from Clinical Samples of Tehran's Hospitals Based on 23S rRNA Gene Sequence

2018 ◽  
Vol 12 (4) ◽  
pp. 239-247
Author(s):  
Mercedeh Tajbakhsh ◽  
Mohammad reza Zali ◽  
Fatemeh Fallah ◽  
◽  
◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Sequence ◽  
23S Rrna ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Salmonella Spp ◽  
23S Rrna Gene

scholarly journals T2182C Mutation in 23S rRNA Is Associated with Clarithromycin Resistance in Helicobacter pylori Isolates Obtained in Bangladesh

2004 ◽  
Vol 48 (9) ◽  
pp. 3567-3569 ◽  
Author(s):  
Rasel Khan ◽  
Shamsun Nahar ◽  
Jinath Sultana ◽  
Mian Mashhud Ahmad ◽  
Motiur Rahman
Keyword(s):  
Helicobacter Pylori ◽  
Gene Sequence ◽  
Point Mutations ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Clarithromycin Resistance ◽  
Gene Sequence Analysis ◽  
23S Rrna Gene ◽  
Transition Mutation

ABSTRACT Twelve clarithromycin-resistant (MIC, ≥1 μg/ml) Helicobacter pylori isolates were analyzed for point mutations in the 23S rRNA gene. Sequence analysis of all of the resistant isolates revealed a T-to-C transition mutation at position 2182. Transformation experiments confirmed that a single T-to-C transition mutation at position 2182 is associated with clarithromycin resistance.

scholarly journals Kushneria sinocarnis sp. nov., a moderately halophilic bacterium isolated from a Chinese traditional cured meat

2010 ◽  
Vol 60 (8) ◽  
pp. 1881-1886 ◽  
Author(s):  
Zhengzhong Zou ◽  
Gejiao Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Sequence ◽  
Halophilic Bacterium ◽  
23S Rrna ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium ◽  
Cured Meat

A Gram-negative, aerobic, moderately halophilic bacterium, designated strain Z35T, was isolated from a Chinese traditional cured meat produced in Wuhan. The isolate grew with 1–20 % NaCl (optimum 10 %), at 4–42 °C (optimum 37 °C) and at pH 4.5–8.5 (optimum pH 7.0). Cells of strain Z35T were not motile and were rod or oval shaped. The genomic DNA G+C content was 59.1 mol%. The isoprenoid quinones were Q-9 (88.96 %), Q-8 (9.46 %) and Q-10 (1.58 %). The major fatty acids were C19 : 0 cyclo ω8c, C16 : 0 and C17 : 0 cyclo. Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that strain Z35T was closely related to the type strains of Kushneria species with 93.7–95.3 % sequence similarities. Phylogenetic analysis based on 23S rRNA gene sequence similarity values also confirmed the phylogenetic position of the isolate. Therefore, based on the phenotypic, chemotaxonomic and phylogenetic evidence, strain Z35T is affiliated to Kushneria, but is clearly differentiated from other species of this genus and represents a new member, for which the name Kushneria sinocarnis sp. nov. is proposed. The type strain is Z35T (=CCTCC AB 209027T =NRRL B-59197T =DSM 23229T).

Identification ofGluconobacter strains isolated in Thailand based on 16S–23S rRNA gene ITS restriction and 16S rRNA gene sequence analyses

2008 ◽  
Vol 58 (4) ◽  
pp. 741-747 ◽  
Author(s):  
Jintana Kommanee ◽  
Ancharida Akaracharanya ◽  
Somboon Tanasupawat ◽  
Taweesak Malimas ◽  
Pattaraporn Yukphan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
23S Rrna Gene

scholarly journals Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics

2005 ◽  
Vol 187 (17) ◽  
pp. 6106-6118 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Zeli Shen ◽  
Michael S. Scimeca ◽  
Lauren N. Stokes ◽  
Tahani Boumenna ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
23S Rrna Gene ◽  
23S Rrna Genes

ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

Identification ofAcetobacter strains isolated in Thailand based on 16S–23S rRNA gene ITS restriction and 16S rRNA gene sequence analyses

2008 ◽  
Vol 58 (2) ◽  
pp. 319-324 ◽  
Author(s):  
Jintana Kommanee ◽  
Ancharida Akaracharanya ◽  
Somboon Tanasupawat ◽  
Taweesak Malimas ◽  
Pattaraporn Yukphan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
23S Rrna Gene

scholarly journals Helicobacter equorum sp. nov., a urease-negative Helicobacter species isolated from horse faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 213-218 ◽  
Author(s):  
H. Moyaert ◽  
A. Decostere ◽  
P. Vandamme ◽  
L. Debruyne ◽  
J. Mast ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Related Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Closely Related Species ◽  
23S Rrna Gene

Gram-negative, curved, motile bacteria (strains EqF1T and EqF2) were isolated from faecal samples from two clinically healthy horses. Both strains possessed a single, monopolar, sheathed flagellum and were urease-negative. The novel strains grew at 37 °C under microaerobic conditions and were positive for oxidase, catalase and alkaline phosphatase activities. The isolates reduced nitrate to nitrite, but γ-glutamyl transpeptidase activity was not detected. The novel isolates did not grow at 42 °C or on media containing 1 % glycine. They were resistant to cephalotin and nalidixic acid and susceptible to metronidazole. Analysis of the 16S and 23S rRNA gene sequences of the two novel strains identified them as representing a single species within the genus Helicobacter. In terms of 16S rRNA gene sequence similarity, Helicobacter pullorum and Helicobacter canadensis were the most closely related species (98 % similarity). 23S rRNA gene sequence analysis also classified strains EqF1T and EqF2 within the enterohepatic division of the genus Helicobacter, but only 94 % similarity was detected with H. pullorum and H. canadensis, which are helicobacters with unsheathed flagella. The most closely related species in terms of 23S rRNA gene sequence similarity was Helicobacter canis (95 %). Numerical analysis of whole-cell protein extracts by SDS-PAGE was performed and the novel isolates were clearly differentiated from H. pullorum, H. canadensis, H. canis and other species of the genus Helicobacter. This finding was also confirmed by sequence analysis of the hsp60 gene. On the basis of these genetic, biochemical and protein data, the isolates are classified as representing a novel species, for which the name Helicobacter equorum sp. nov. is proposed (type strain EqF1T=LMG 23362T=CCUG 52199T).

scholarly journals Denitratisoma oestradiolicum gen. nov., sp. nov., a 17β-oestradiol-degrading, denitrifying betaproteobacterium

2006 ◽  
Vol 56 (7) ◽  
pp. 1547-1552 ◽  
Author(s):  
Michael Fahrbach ◽  
Jan Kuever ◽  
Ruth Meinke ◽  
Peter Kämpfer ◽  
Juliane Hollender
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Municipal Wastewater ◽  
Treatment Plant ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence

A Gram-negative, motile, denitrifying bacterium (strain AcBE2-1T) was isolated from activated sludge of a municipal wastewater treatment plant using 17β-oestradiol (E2) as sole source of carbon and energy. Cells were curved rods, 0.4–0.8×0.8–2.0 μm in size, non-fermentative, non-spore-forming, oxidase-positive and catalase-negative. E2 was oxidized completely to carbon dioxide and water by reduction of nitrate to a mixture of dinitrogen monoxide and dinitrogen, with the intermediate accumulation of nitrite. Electron recoveries were between 90 and 100 %, taking assimilated E2 into account. With nitrate as the electron acceptor, the bacterium also grew on fatty acids (C2 to C6), isobutyrate, crotonate, dl-lactate, pyruvate, fumarate and succinate. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain AcBE2-1T represents a separate line of descent within the family Rhodocyclaceae (Betaproteobacteria). The closest relatives are the cholesterol-degrading, denitrifying bacteria Sterolibacterium denitrificans DSM 13999T and strain 72Chol (=DSM 12783), with <93.9 % sequence similarity. The G+C content of the DNA was 61.4 mol%. Detection of a quinone system with ubiquinone Q-8 as the predominant compound and a fatty acid profile that included high concentrations of C16 : 1 ω7c/iso-C15 : 0 2-OH and C16 : 0, in addition to C18 : 1 ω7c and small amounts of C8 : 0 3-OH, supported the results of the phylogenetic analysis. On the basis of 16S rRNA gene sequence data in combination with chemotaxonomic and physiological data, strain AcBE2-1T (=DSM 16959T=JCM 12830T) is placed in a new genus Denitratisoma gen. nov. as the type strain of the type species Denitratisoma oestradiolicum gen. nov., sp. nov.

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