scholarly journals Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.

2004 ◽  
Vol 54 (3) ◽  
pp. 929-933 ◽  
Author(s):  
Jung-Sook Lee ◽  
Yu-Ryang Pyun ◽  
Kyung Sook Bae
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Pcr Primers ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Paenibacillus Ehimensis

The taxonomic status of Bacillus ehimensis and Bacillus chitinolyticus was examined, based on their 16S rDNA sequences, DNA–DNA hybridization and other taxonomic characteristics. A phylogenetic analysis using 16S rDNA sequences revealed that the two species belong to the genus Paenibacillus. In particular, B. ehimensis KCTC 3748T and B. chitinolyticus KCTC 3791T were found to be phylogenetically closely related to Paenibacillus koreensis YC300T (98·3 % sequence similarity) and Paenibacillus chinjuensis WN9T (95·2 % sequence similarity), respectively. DNA–DNA hybridization values between B. ehimensis KCTC 3748T and P. koreensis YC300T were less than 26 %. An experiment using Paenibacillus-specific PCR primers, PAEN515F and 1377R, revealed that B. ehimensis and B. chitinolyticus had the same amplified 16S rDNA fragment as members of the genus Paenibacillus. Accordingly, it is proposed that B. ehimensis and B. chitinolyticus be transferred to the genus Paenibacillus as Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov., respectively.

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3423 (1) ◽  
pp. 61 ◽  
Author(s):  
JERZY A. LIS ◽  
PAWEŁ LIS ◽  
DARIUSZ J. ZIAJA ◽  
ANNA KOCOREK
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Sister Group ◽  
Systematic Position ◽  
Bayesian Phylogenetic Analysis ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Affinity ◽  
The Moment

Mitochondrial 12S and 16S rDNA sequences of five species of Dinidoridae Stål, 1868, a largely Paleotropical family, and 16 other shield bugs (Pentatomoidea) were studied. This was the first molecular examination of the systematic position of this family within the superfamily Pentatomoidea using more than a single dinidorid species. Phylogenetic trees obtained from the Bayesian inference of 12S and 16S sequences of these mitochondrial DNA, identified Dinidoridae as the monophylum and a sister group to the Tessaratomidae. Moreover, results of the study suggested a close molecular affinity of the genus Eumenotes to representatives of the subfamily Dinidorinae, which contradicts all previous morphological analyses that placed it within the subfamily Megymeninae. We suggest restoring taxonomic status of the tribe Eumenotini and removing it from the synonymy of Megymenini, leaving the genus with no subfamilial assignment for the moment.

scholarly journals Comparison of Different DNA Fingerprinting Techniques for Molecular Typing of Bartonella henselaeIsolates

1998 ◽  
Vol 36 (10) ◽  
pp. 2973-2981 ◽  
Author(s):  
Anna Sander ◽  
Michael Ruess ◽  
Stefan Bereswill ◽  
Markus Schuppler ◽  
Bernhard Steinbrueckner
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Dna Fingerprinting ◽  
Genetic Heterogeneity ◽  
Bartonella Henselae ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Specific Amplification ◽  
Clear Differentiation

Seventeen isolates of Bartonella henselae from the region of Freiburg, Germany, obtained from blood cultures of domestic cats, were examined for their genetic heterogeneity. On the basis of different DNA fingerprinting methods, including pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic consensus (ERIC)-PCR, repetitive extragenic palindromic (REP) PCR, and arbitrarily primed (AP)-PCR, three different variants were identified among the isolates (variants I to III). Variant I included 6 strains, variant II included 10 strains, and variant III included only one strain. By all methods used, the isolates could be clearly distinguished from the type strain, Houston-1, which was designated variant IV. A previously published type-specific amplification of 16S rDNA differentiated two types of the B. henselaeisolates (16S rRNA types 1 and 2). The majority of the isolates (16 of 17), including all variants I and II, were 16S rRNA type 2. Only one isolate (variant III) and the Houston-1 strain (variant IV) comprised the 16S rRNA type 1. Comparison of the 16S rDNA sequences from one representative strain from each of the three variants (I to III) confirmed the results obtained by 16S rRNA type-specific PCR. The sequences from variant I and variant II were identical, whereas the sequence of variant III differed in three positions. All methods applied in this study allowed subtyping of the isolates. PFGE and ERIC-PCR provided the highest discriminatory potential for subtypingB. henselae strains, whereas AP-PCR with the M13 primer showed a very clear differentiation between the four variants. Our results suggest that the genetic heterogeneity of B. henselae strains is high. The methods applied were found useful for typing B. henselae isolates, providing tools for epidemiological and clinical follow-up studies.

Molecular bacterial diversity and distribution in waste from a steel plant

2008 ◽  
Vol 54 (12) ◽  
pp. 996-1005 ◽  
Author(s):  
Dulcecleide B. Freitas ◽  
Mariana P. Reis ◽  
Leandro M. Freitas ◽  
Paulo S. Assis ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Partial Length ◽  
16S Rdna Sequences ◽  
Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

scholarly journals Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

2004 ◽  
Vol 54 (2) ◽  
pp. 487-491 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Phenotypic Properties ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Isoprenoid Quinones ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

scholarly journals Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

2004 ◽  
Vol 54 (3) ◽  
pp. 851-855 ◽  
Author(s):  
Wan-Taek Im ◽  
Hee-Sung Bae ◽  
Akira Yokota ◽  
Sung Taik Lee
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
The Novel ◽  
Comamonas Testosteroni ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
Degrading Bacterium ◽  
16S Rdna Sequences ◽  
Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

scholarly journals Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

1998 ◽  
Vol 64 (11) ◽  
pp. 4333-4339 ◽  
Author(s):  
Daniel H. Buckley ◽  
Joseph R. Graber ◽  
Thomas M. Schmidt
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
Soil Samples ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Long Term Ecological Research

ABSTRACT Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilicCrenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.

scholarly journals Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree

2004 ◽  
Vol 54 (2) ◽  
pp. 533-536 ◽  
Author(s):  
Raúl Rivas ◽  
Martha E. Trujillo ◽  
P. F. Mateos ◽  
E. Martínez-Molina ◽  
Encarna Velázquez
Keyword(s):  
Phylogenetic Analysis ◽  
Cell Wall ◽  
Dna Hybridization ◽  
Type Strain ◽  
Cell Wall Composition ◽  
Physiological Data ◽  
Fatty Acid Profiles ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Motile Bacterium

A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99·0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11T in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA–DNA hybridization with C. humilata ATCC 25174T, in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11T should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11T (=LMG 21723T=CECT 5729T) as the type strain.

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