• Korean Journal of Microbiology
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• v.45 no.4
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• pp.430-434
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• 2009

Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

• Bulletin of the Korean Chemical Society
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• v.20 no.11
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• pp.1335-1339
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• 1999

The function of 5S rRNA, a constituent of a large subunit of ribosome, is not clearly known yet. To identify RNA motifs interacting with 5S rRNA, and thereby to get an insight into the function of 5S rRNA in the ribosome, a SELEX (Systematic Evolution of Ligands by Exponential Enrichment) experiment was performed. RNA molecules binding to Escherichia coli 5S rRNA were selected from a 48-mer random sequence library through 12 rounds of selection, cloned, and sequenced. Two groups of the selected RNA molecules had the consensus sequences GCGG and GUGAAA, respectively, which are present in the segment, G688 through A696, of E. coli 16S rRNA. The gel mobility shift assay showed that 5S rRNA interacted with the 16S rRNA fragment containing the GCGG and GUGAAA sequences. The enzymatic protection experiment shows that the A29CCUGA34 and G51AAGUG56 sequences of 5S rRNA and the C680AGG683 and G688CGG691 sequences of the 16S rRNA fragment are involved in the interaction between the two RNA molecules. On the basis of this observation, we suggest that 5S rRNA and 16S rRNA play a role for the association of two ribosomal subunits.

• The Plant Pathology Journal
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• v.18 no.2
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• pp.98-101
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• 2002

Using phytoplasma universal primer pair Pl and P7, a fragment of about 1.8 kb nucleotide sequences of 16S rRNA gene and 16S-23S rRNA intergenic spacer region, and a portion of 23S rRNA gene of jujube witches'broom (JWB) and mulberry dwarf(MD) phytoplasmas were determined. The nucleotide sequences of JWB and MD were 1,850 bp and 1,831 bp long, respectively. The JWB phytoplasma sequence was aligned with the homologous sequence of MD phytoplasma. Twenty-eight base insertions and nine base deletions were found in the JWB phytoplasma sequence compared with that of MD phytoplasma. The similarity of the aligned sequences of JWB and MD was 84.8%. The near-complete 16S rRNA gene DNA sequences of JWB and MD were 1,529 bp and 1,530 bp in length, respectively, and revealed 89.0% homology. The 16S-23S rRNA intergenic spacer region DNA sequences were 263 bp and 243 bp in lengths respectively, while homology was only 70% and the conserved tRNA-lle gene of JWB and MD was located into the intergenic space region between 16S-23S rRNA gene. The nucleotide sequences were 77 bp long in both JWB and MD, and showed 97.4% sequence homology. Based on the phylogenetic analysis of the two phytoplasmas, the JWB phytoplasma belongs to the Elm yellow phytoplasma group (16S rV), whereas, the MD phytoplasma belongs to the Aster yellow group (16S rI).

• Environmental Engineering Research
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• v.19 no.4
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• pp.317-329
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• 2014

The diversity of cyanobacteria in Sri Lanka was studied in different water reservoirs, paddy fields, brackish water and tsunami affected areas using light microcopy, 16S rRNA sequences, followed by phylogenetic analysis. Based on light microscopy, 24 genera were identified from environmental samples belonging to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. In cultures, 33 genera were identified from all five cyanobacterial orders, including Stigonematales. Based on 16S rRNA gene sequences and their morphology, two isolates were identified up to species level, 72 to genus level, one isolate up to family and 11 up to order level. Twelve isolates couldn't be assigned to any taxonomic level. The results of 16S rRNA gene sequences along with the phylogenetic analysis indicated that some cyanobacterial isolates could be accommodated to genus or order level. The 16S rRNA sequence analysis data in this study confirmed that order Nostocales and order Pleurocapsales cyanobacteria are monophyletic while orders Chroococcales, Oscillatoriales and Stigonematales cyanobacteria are polyphyletic. Polyphasic approach including the combination of light microscopy, cultures and the analysis of 16S rRNA gene sequences provide a promising approach to ascertain the diversity of cyanobacteria in different habitats.

• ALGAE
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• v.27 no.2
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• pp.75-82
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• 2012

$Arthrospira$ $platensis$ and $Arthrospira$ $maxima$ are species of cyanobacteria used in health foods, animal feed, food additives, and fine chemicals. This study conducted a comparison of the 16S rRNA gene and $cpcBA$-intergenic spacer ($cpcBA$-IGS) sequences in $Arthrospira$ strains from culture collections around the world. A cluster analysis divided the 10 $Arthrospira$ strains into two main genotypic clusters, designated I and II, where Group I contained $A.$ $platensis$ SAG 86.79, UTEX 2340, $A.$ $maxima$ KCTC AG30054, and SAG 49.88, while Group II contained $A.$ $platensis$ PCC 9108, NIES 39, NIES 46, and SAG 257.80. However, although $A.$ $platensis$ PCC 9223 belonged to Group II-2 based on its $cpcBA$-IGS sequence, this strain also belonged to Group I based on its 16S rRNA gene sequence. Phylogenetic analyses based on the 16S rRNA gene and $cpcBA$-IGS sequences showed no division between $A.$ $platensis$ and $A.$ $maxima$, plus the 16S rRNA gene and $cpcBA$-IGS sequence clusters did not indicate any well-defined geographical distribution, instead overlapping in a rather interesting way. Therefore, the current study supports some previous conclusions based on 16S rRNA gene and $cpcBA$-IGS sequences, which found that $Arthrospira$ taxa are monophyletic. However, when compared with 16S rRNA sequences, $cpcBA$-IGS sequences may be better suited to resolve close relationships and intraspecies variability.

• ALGAE
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• v.17 no.3
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• pp.153-159
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• 2002

Partial 16S rRNA gene sequences of seven cyanophycean strains from the National Instiute of Environmental Research of Korea - Microcystis aeruginosa, M. aeruginosa f. aeruginosa, M. ichthyoblade, M. viridis, Anabaena flos-aquae, and Oscillatoria sancta - were analyzed and the phylogenetic relationship of Microcystis among Cyanophyceae were evaluated. Based on sequence analysis results, Microcystis is monophyletic, the clade of which supported 100% bootstrap tress, and distinguished clearly from the other taxa. Therefore, the partial 16S rRNA gene sequences can be a useful and efficient tool for distinguishing Microcystis from other cyanophycean without axenic culture or cloning.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.218-223
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• 2004

Myxobacteria are Gram-negative soil bacteria known to be a rich source of potentially useful secondary metabolites. We have isolated 204 strains of bacteriolytic myxobacteria from soil samples collected in Korea and determined their 16S rRNA sequences. Sequence analysis of the partially determined 16S rRNA sequences has suggested that 132 isolates (65% of total isolates) belong to the genus Myxococcus and 59 isolates (29% of total isolates) belong to the genus Corallococcus. Meanwhile, 4 isolates appear to be Archangium spp. and the other 4 isolates appear to be Stigmatella spp. Genera of the remained 5 isolates have not been identified because their 16S rRNA sequences are distantly related to those of known myxobacteria.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.36 no.3
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• pp.239-246
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• 2003

We have examined the 16S-23S rRNA intergenic spacer region (ISR) of Vibrio vulnificus KCTC 2959. ISRs were amplified by primers complementary to conserved regions of 16S and 23S rRNA genes. ISR amplicons were cloned and sequenced. Analysis of the ISR sequences showed that V. vulnificus KCTC 2959 contains five types of polymorphic ISRs. Size of ISRs ranged from 424 to 741 bp in length and the number of tRNA genes ranged from one to four. The ISRs were designated as ISR-E $(tRNA^{Glu}),\;ISR-IA\;(tRNA^{Ile}-tRNA^{Ala})$, ISR-EKV $(tRNA^{Glu}-tRNA^{Lys}-tRNA^{Val})$, ISR-IAV $(tRNA^{Ile}-tRNA^{Ala}-tRNA^{val})$ and ISR-EKAV $(tRNA^{Glu}-tRNA^{Lys}-tRNA^{Ala}-tRNA^{Val})$ based on their tRNA genes. Multiple alignment of representative sequences from different Vibrio species revealed several domains of high sequence variability. We used the sequences of variable domains to design species-specific primer for detection PCR. Specificity of the primers was examined using genomic DNA prepared from 18 different Vibrio species. The results showed that the PCR using primers designed in this study can be used to detect V. vulnificus from other Vibrio species.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.1
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• pp.141-147
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• 2017

In this study, a meta-analysis of fecal bacteria in dogs was conducted using 16S rRNA gene sequences that have been recovered from cloning and Sanger sequencing. For this meta-analysis, we retrieved all 16S rRNA gene sequences recovered from fecal bacteria in dogs in the RDP database (Release 11, Update 3). A total of 420 sequences were identified from the RDP database, 42 of which were also recovered from cultured isolates. The 420 sequences were assigned to five phyla, of which Firmicutes was the most predominant phylum, accounting for 55.2% of all 420 sequences. Bacteroidetes was the second most predominant phylum, accounting for 32.1% of the 420 sequences, followed by Actinobacteria (6.4%), Fusobacteria (3.8%), and Proteobacteria (2.4%). The genus Bacteroides within Bacteroidetes was the largest, representing 30.0% of all 420 sequences, while the putative genus Clostridium XI within Firmicutes was the second largest, representing 27.4% of all 420 sequences. A total of 82 operational taxonomic units (OTUs) that are putative species were identified from the retrieved sequences. The results of this study will improve understanding of the diversity of fecal bacteria in dogs and guide future studies on the health and well-being of dogs.