Sequence Length Variation of Internal Genic Space of 16S rDNA-23S rDNA in Bacterium with High Yield of Hydrogen Production

2011 ◽  
Vol 183-185 ◽  
pp. 1413-1416
Author(s):  
Yong Feng Li ◽  
Yi Xuan Wang ◽  
Lu Wang ◽  
Zhan Qing Wang
Keyword(s):  
16S Rdna ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
High Yield ◽  
23S Rrna ◽  
Sequence Length ◽  
Rrna Gene ◽  
Length Variation ◽  
Intergenic Spacer Region

To develop the identification of species for fermentative biohydrogen-producing bacterium, scholars have found a method which is based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions. In the study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2000 bases of the 23S rDNA, were polymerasechain reaction (PCR) amplified. The PCR amplification of the genomic DNA of Leptonema ilk strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA genes were linked via an intergenic spacer region. The sequencing of the intergenic spacer region indicated that it was 435 nucleotides in length and sequence similarity searches revealed that it bore no homology to any known sequences including tRNA available in databases.

scholarly journals Identification of Lactobacillus Isolates from the Gastrointestinal Tract, Silage, and Yoghurt by 16S-23S rRNA Gene Intergenic Spacer Region Sequence Comparisons

1999 ◽  
Vol 65 (9) ◽  
pp. 4264-4267 ◽  
Author(s):  
G. W. Tannock ◽  
A. Tilsala-Timisjarvi ◽  
S. Rodtong ◽  
J. Ng ◽  
K. Munro ◽  
...  
Keyword(s):  
Lactobacillus Rhamnosus ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Sequence Comparisons ◽  
Intergenic Spacer Region ◽  
23S Rrna Gene

Lactobacillus isolates were identified by PCR amplification and sequencing of the region between the 16S and 23S rRNA genes (spacer region). The sequences obtained from the isolates were compared to those of reference strains held in GenBank. A similarity of 97.5% or greater was considered to provide identification. To check the reliability of the method, the V2-V3 region of the 16S rRNA gene was amplified and sequenced in the case of isolates whose spacer region sequences were less than 99% similar to that of a reference strain. Confirmation of identity was obtained in all instances. Spacer region sequencing provided rapid and accurate identification ofLactobacillus isolates obtained from gastrointestinal, yoghurt, and silage samples. It had an advantage over 16S V2-V3 sequence comparisons because it distinguished between isolates ofLactobacillus casei and Lactobacillus rhamnosus.

scholarly journals Diversity of Salmonella Strains Isolated from the Aquatic Environment as Determined by Serotyping and Amplification of the Ribosomal DNA Spacer Regions

2000 ◽  
Vol 66 (4) ◽  
pp. 1544-1552 ◽  
Author(s):  
Julia Baudart ◽  
Karine Lemarchand ◽  
Anne Brisabois ◽  
Philippe Lebaron
Keyword(s):  
Pathogenic Bacteria ◽  
Natural Waters ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Natural Environments ◽  
Storm Events ◽  
Intergenic Spacer Region ◽  
Coastal Watershed

ABSTRACT Salmonella species are pathogenic bacteria often detected in sewage, freshwater, marine coastal water, and groundwater.Salmonella spp. can survive for long periods in natural waters, and the persistence of specific and epidemic strains is of great concern in public health. However, the diversity of species found in the natural environment remains unknown. The aim of this study was to investigate the diversity of Salmonellastrains isolated from different natural aquatic systems within a Mediterranean coastal watershed (river, wastewater, and marine coastal areas). A total of 574 strains isolated from these natural environments were identified by both conventional serotyping and the ribosomal spacer-heteroduplex polymorphism (RS-HP) method (M. A. Jensen and N. Straus, PCR Methods Appl. 3:186–194, 1993). More than 40 different serotypes were found, and some serotypes probably mobilized from widespread animal-rearing activities were detected only during storm events. These serotypes may be good indicators of specific contamination sources. Furthermore, the RS-HP method based on the PCR amplification of the intergenic spacer region between the 16S and 23S rRNA genes can produce amplicon profiles allowing the discrimination of species at both serotype and intraserotype levels. This method represents a powerful tool that could be used for rapid typing of Salmonella isolates.

Genomic fingerprinting ofFrankiamicrosymbionts fromCeanothuscopopulations using repetitive sequences and polymerase chain reactions

1999 ◽  
Vol 77 (9) ◽  
pp. 1220-1230 ◽  
Author(s):  
Soon-Chun Jeong ◽  
David D Myrold
Keyword(s):  
Dna Sequencing ◽  
Dna Analysis ◽  
Repetitive Sequences ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Genomic Fingerprinting ◽  
Chain Reactions ◽  
Intergenic Spacer Region ◽  
Polymerase Chain

Specificity between Ceanothus species and their microsymbionts, Frankia, were investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequencing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyzed by genomic fingerprinting using repetitive sequences and PCR. A newly designed direct repeat (DR) sequence and a BOX sequence were used as PCR primers after justification that these primers can generate Frankia-specific fingerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR showed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geographic separation plays a more important role for divergence of Ceanothus-microsymbiotic Frankia than host plant.Key words: Frankia, Ceanothus, rep-PCR, diversity.

Differentiation of group VIII Spiroplasma strains with sequences of the 16S–23S rDNA intergenic spacer region

2004 ◽  
Vol 50 (12) ◽  
pp. 1061-1067 ◽  
Author(s):  
Laura B Regassa ◽  
Kimberly M Stewart ◽  
April C Murphy ◽  
Frank E French ◽  
Tao Lin ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Analytical Models ◽  
23S Rrna ◽  
Rrna Gene ◽  
Group Viii ◽  
Similarity Coefficients ◽  
Intergenic Spacer Region ◽  
Intergenic Sequences ◽  
The Stability ◽  
The 16S Rrna Gene

Spiroplasma species (Mollicutes: Spiroplasmataceae) are associated with a wide variety of insects, and serology has classified this genus into 34 groups, 3 with subgroups. The 16S rRNA gene has been used for phylogenetic analysis of spiroplasmas, but this approach is uninformative for group VIII because the serologically distinct subgroups generally have similarity coefficients >0.990. Therefore, we investigated the utility of the 16S–23S rRNA spacer region as a means to differentiate closely related subgroups or strains. We generated intergenic sequences and detailed serological profiles for 8 group VIII Spiroplasma strains. Sequence analyses using Maximum Parsimony, Neighbor Joining, and Maximum Likelihood placed the strains into 2 clades. One clade consisted of strains BARC 2649 and GSU5367. The other clade was divided into clusters containing representatives of the 3 designated group VIII subgroups (EA-1, DF-1, and TAAS-1) and 3 previously unclassified strains. The stability of the positions of the strains in various analytical models and the ability to provide robust support for groupings tentatively supported by serology indicates that the 16S–23S intergenic rDNA sequence will prove useful in intragroup analysis of group VIII spiroplasmas.Key words: Mollicutes, Spiroplasma, phylogeny, Tabanidae.

scholarly journals Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array

2009 ◽  
Vol 58 (5) ◽  
pp. 596-605 ◽  
Author(s):  
Siou Cing Su ◽  
Mario Vaneechoutte ◽  
Lenie Dijkshoorn ◽  
Yu Fang Wei ◽  
Ya Lei Chen ◽  
...  
Keyword(s):  
Clinical Importance ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Oligonucleotide Array ◽  
Rrna Genes ◽  
Universal Primers ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nylon Membrane ◽  
Gram Negative

Many species of non-fermenting Gram-negative bacilli (non-fermenters) are important opportunistic and nosocomial pathogens. Identification of most species of non-fermenters by phenotypic characteristics can be difficult. In this study, an oligonucleotide array was developed to identify 38 species of clinically relevant non-fermenters. The method consisted of PCR-based amplification of 16S–23S rRNA gene intergenic spacer (ITS) regions using bacterial universal primers, followed by hybridization of the digoxigenin-labelled PCR products with oligonucleotide probes immobilized on a nylon membrane. A total of 398 strains, comprising 276 target strains (i.e. strains belonging to the 38 species to be identified) and 122 non-target strains (i.e. strains not included in the array), were analysed by the array. Four target strains (three reference strains and one clinical isolate) produced discrepant identification by array hybridization. Three of the four discordant strains were found to be correctly identified by the array, as confirmed by sequencing of the ITS and 16S rRNA genes, with the remaining one being an unidentified species. The sensitivity and specificity of the array for identification of non-fermenters were 100 and 96.7 %, respectively. In summary, the oligonucleotide array described here offers a very reliable method for identification of clinically relevant non-fermenters, with results being available within one working day.

scholarly journals rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira The GenBank accession numbers of the 16S rDNA gene sequences reported in this paper are AY038032–AY038037.

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 481-496 ◽  
Author(s):  
Isabelle Iteman ◽  
Rosmarie Rippka ◽  
Nicole Tandeau de Marsac ◽  
Michael Herdman
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Genomic Sequence ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Heterocystous Cyanobacteria

The taxonomic coherence and phylogenetic relationships of 11 planktonic heterocystous cyanobacterial isolates were examined by investigating two areas of the rRNA operon, the 16S rRNA gene (rrnS) and the internal transcribed spacer (ITS) located between the 16S rRNA and 23S rRNA genes. The rrnS sequences were determined for five strains, including representatives of Anabaena flos-aquae, Aphanizomenon flos-aquae, Nodularia sp. and two alkaliphilic planktonic members of the genera Anabaenopsis and Cyanospira, whose phylogenetic position was previously unknown. Comparison of the data with those previously published for individual groups of planktonic heterocystous cyanobacteria showed that, with the exception of members assigned to the genus Cylindrospermopsis, all the planktonic strains form a distinct subclade within the monophyletic clade of heterocystous cyanobacteria. Within this subclade five different phylogenetic clusters were distinguished. The phylogenetic groupings of Anabaena and Aphanizomenon strains within three of these clusters were not always consistent with their generic or specific assignments based on classical morphological definitions, and the high degree of sequence similarity between strains of Anabaenopsis and Cyanospira suggests that they may be assignable to a single genus. Ribotyping and additional studies performed on PCR amplicons of the 16S rDNA or the ITS for the 11 planktonic heterocystous strains demonstrated that they all contain multiple rrn operons and ITS regions of variable size. Finally, evidence is provided for intra-genomic sequence heterogeneity of the 16S rRNA genes within most of the individual isolates.

scholarly journals 16S–23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

2016 ◽  
Vol 7 ◽  
Author(s):  
Sima Tokajian ◽  
Nahla Issa ◽  
Tamara Salloum ◽  
Joe Ibrahim ◽  
Maya Farah
Keyword(s):  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Intergenic Spacer Region ◽  
23S Rrna Gene
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