• 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.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.812-822
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• 2014

Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.

• Biomedical Science Letters
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• v.18 no.3
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• pp.299-306
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• 2012

Recently, the prevalence of 16S rRNA methylase conferring high-level resistance to aminoglycosides has been increasing in Gram-negative bacilli globally. We determined the prevalence and genotype of these methylase-producing bacteria, and characterized the co-resistance to ${\beta}$-lactam antibiotics and quinolone in Gram-negative clinical isolates collected in 2010 at a hospital in Korea. Among 65 amikacin-resistant isolates screened from 864 Gram-negative bacilli (GNB), 16S rRNA methylase genes were detected from 49 isolates, including Acinetobacter baumannii (43), Klebsiella pneumoniae (2), Proteus mirabilis (2) and Serratia marcescens (1), Empedobacter brevis (1). All of the 16S rRNA methylase genotype was armA and no variant sequences of amplified PCR products for armA were noted. The 16S rRNA methylase producing bacteria showed much higher resistance to aminoglycoside for Enterobacteriaceae and glucose non-fermenting (NF)-GNB and to imipenem for glucose NF-GNB, than the non-producing isolates. All of the 16S rRNA methylase producing Enterobacteriaceae had the extended-spectrum-${\beta}$-lactamase. In addition, two K. pneumoniae concurrently produced both plasmid-mediated AmpC ${\beta}$-lactamase and qnrB gene. All of the amikacin-resistant A. baumannii (43) co-harbored armA 16S rRNA methylase and $bla_{OXA-23}$ carbapenemase. In conclusion, 16S rRNA methylase producing bacteria were very prevalent among GNB in South Korea, and were commonly associated with co-resistance, including carbapenem and quinolone.

• Journal of fish pathology
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• v.17 no.2
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• pp.91-98
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• 2004

This study was performed for the identification of Streptococcus sp. from cultured flounders (Paralichthys olivaceus) showing streptococcosis in the Jeju island. We isolated 10 strains of Streptococcus iniae from the cultured olive flounders with streptococcosis. Isolated strains were identified in S. iniae since they have formed the expected band through performing PCR assay using specific primers, Sin-1 (5'-CTAGAGTACACATGTACT(AGCT)AAG-3') and Sin-2 (5'-GGATTTTCCACTCCCATTAC-3'). In addition to 16S-23S rRNA intergenic spacers (ISR), operon structure of isolated strains showed that all strains had three 16S-23S rRNA ISR band patterns. The 16S-23S rRNA ISR sequence of isolated strains showed 96% sequence identity with S. iniae (GenBank accession number AF 048773). This paper is the first report that S. iniae is associated with streptococcosis of Olive flounder in Korea.

• 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.

• Journal of Naturopathy
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• v.8 no.2
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• pp.71-77
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• 2019

Purpose: The purpose of this study was to investigate the far-infrared emissivity of patented ocher quilt cotton fabrics and to investigate the microorganisms that survived the washing of cotton fabrics up to 20 times. Methods: A 16S rRNA assay was performed using a far-infrared radiometer and a single colony in which microorganisms grew in nutrient media. Results: The far-infrared emissivity of ocher quilt was 0.902 (90.2%) at 5~20 ㎛ at 40℃, and the radiation energy was 3.63 × 10² w/m². The number of viable cells was 2.0 × 10² cells/ml in ocher duvet cotton fabric, and no viable bacteria found in regular cotton fabric. The base sequence of 16S rRNA of B-2 strain isolated into single colonies was 1,419 bases, and the base sequence of strain A-4 was 1,284 bases. The base sequence of 16S rRNA of these two strains showed high homology with Bacillus spp. The B-2 bacteria showed high homology with 99.0% of the 16S rRNA sequence of B. aryabhattai EF114313 and 99.0% of the A-4 bacteria of B. bingmayongensis AKCS01000011. Consequently the colony strain B-2 finally identified as B. aryabhattai BJ-2 and A-4 as B. bingmayongensis BJ-4 strain. Concusions: Soil Bacillus strains survived in ocher quilt cotton fabric after 20 washing. The material can be useful because quilt cotton fabric emits a large amount of far-infrared and far-infrared radiation energy.

• Korean Journal of Food Science and Technology
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• v.35 no.3
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• pp.470-474
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• 2003

DNA sequence information on small-subunit rRNA gene (16S rDNA) obtained from food-poisoning bacterial culture was used to investigate the presence of bacterial pathogens in food. By reverse dot blot detection method, presence of food-poisoning bacteria could be confirmed on hybridization of digoxigenin-labeled 16S rDNA Polymerase Chain Reaction (PCR) primer product and biotin-labeled specific oligonucleotide probe. Escherichia coli, Bacillus cereus. and Salmonella sp. were used as the representative food-poisoning bacterial microorganisms. An oligonucleotide probe, based on the variable region of 16S rRNA gene, was used as the specific probe. These tools may be more useful than classic biochemical method for rapid identification of contaminated food.

• 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.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.12
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• pp.1816-1821
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• 2003

Reliable PCR based identification of lactobacilli has been described utilizing the sequence of 16S-23S rRNA intergenic spacer region. Those sequence comparisons showed a high degree of difference in homology among the strains of L. rhamnosus, L. casei, L. acidophilus and L. helveticus whose 16S-23S rRNA intergenic small SR's sizes were 222 bp, 222 bp, 206 bp and 216 bp respectively. The sequence of 16S-23S rRNA intergenic spacer region of L. rhamnosus ATCC 53103 revealed the close relatedness to those of L. casei strains by the homology ranges from 95.4% to 97.2%. 16S-23S rRNA intergenic spacer region nucleotide sequence of L. acidophilus showed some distant relatedness with L. rhamnosus ATCC 53103 with the homology ranges from 40.3% to 41.8% and that with L. helveticus was shown to be 30% of homology, which exists at the most distant phylogenetic relatedness. The identification of species and strain of lactobacilli was possible on the basis of these results. The common sequences among the 17 strains were CTAAGGAA located in the initiating position of the DNA and some discrepancies were found between the same strains based on these results.