• Korean journal of applied entomology
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• v.45 no.3 s.144
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• pp.301-307
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• 2006

A ligniolytic bacterial strain was isolated from the digestive tract of a red dragonfly, Sympetrum dopressiusculum. It was identified as a Serratia marcescens HY-5 by 16S rDNA sequence analysis and physiological and biochemical analysis. The isolated strain showed proportional increase of ligninolytic activity to the cell growth in the culture media which include lignin compounds. It showed about 25-45% decomposition of lignin compound by 48 hr incubation especially, showed effective decomposition of monomer lignin compounds, vanillin and guaiacol, and a dimer, dealkaline lignin. PCR amplification of 16S rDNA followed by denaturing gradient gel electrophoresis analysis showed high density of S. marcescens HY-5 in the gut of the S. depressiusculum at both gut samples which collected at different site.

• Journal of Korean society of Dental Hygiene
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• v.13 no.5
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• pp.889-900
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• 2013

Objectives : Molecular biology techniques were employed to assess diversity of bacterial in children's dental caries. Methods : DNA of germs was extracted and the diversity of the 16S rRNA clones was analyzed by amplified rDNA restriction analysis and sequencing. The experimental samples were pit and fissure caries (PC), deep dentinal caries (DC), smooth surface caries (SC), and supragingival plaque (PQ) from 50 children of age less than 12 years old. The control group was healthy teeth supragingival plaque (HT). Thirty clones from each 16S rRNA clone library of 5 samples were randomly selected, thus a total of 150 clones were analyzed. Results : Amplified rDNA restriction analysis uncovered 18, 20, 11, 17, and 22 phylotypes from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and supragingival plaque, respectively. Sequencing analysis found the dominance of Actinomycs naeslundii and Fusobacterium nucleatum in the healthy teeth; Leptotrichia sp. in the pit and fissure caries; Actinomyces sp., Streptococcus mutans, and Rahnella aquatilis in the deep dentinal caries; Streptococcus mutans and Actinomyces sp. in the smooth surface caries; Enterobacter hormaechei and Streptococcus sanguinis in the supragingival plaque. Conclusions : Clonal analysis identified 6 phyla, 20 genera, and 51 species.

• Korean journal of applied entomology
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• v.39 no.1
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• pp.5-12
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• 2000

The sweetpotato whiteflies, Bemisia tabaci(Gennadius), were found recently in Korea on Glycine max, Euphorbia pulcherrima, and Rosa hybrida. The biotype identity of Bemisia tabaci in Korea was determined by several DNA markers including the random amplified polymorphic DNAs, and restriction fragments length polymorphism of mitochondrial 12S and 16S rRNA genes. The electromorph profiles of DNA fragments from the rose(Jincheon) and poinsettia(Seoul) populations in Korea are both identical to those of B biotypes distributed in Australia, Israel, and Japan. The populations of B. tabaci collected on Glycine max, Ipomea batatas, and Perilla frutescens in different localities retained the same DNA markes with the population from Lonicera japonica and shikoku of Japan. These populations are non-B biotype and considered as an indigenous type in the Far Eastern Asia Region including Korea and Japan, Morphological Characteristics of B. Tabaci were also observed by the scanning electron microscope and described with the comparison to the other important whitefly pest, Trialeurodes vaporariorum (Westwood).

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.643-650
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• 2000

A new aniline-utilizing microorganism, strain HY1 obtained from an orchard soil, was characterized by using the BIOLOG system, an analysis of the total cellular fatty acids, and a 16S rDNA sequence. Strain HY1 was identified as a Burkholderia species, and was designated Burkholderia sp. HY1. GC and HPLC analyses revealed that Burkholderia sp. HY1 was able to degrade aniline to produce catechol, which was subsequently converted to cis,cis-muconic acid through an ortho-ring fission pathway under aerobic conditions. Strain HY1 exhibited a drastic reduction in the rate of aniline degradation when glucose was added to the aniline media. However, the addition of peptone or nitrate to the aniline media dramatically accelerated the rate of aniline degradation. A fatty acid analysis showed that strain HY1 was able to produce lipids 16:0 2OH, and 11 methyl 18:1 ${\omega}7c$ approximately 3.7-, 2.2-, and 6-fold more, respectively, when grown on aniline media than when grown on TSA. An analysison the alignment of a 1,435 bp fragment. A phylogenetic analysis of the 16S rDNA sequence based on a 1,420 bp multi-alignment sowed of the 16s rDNA sequence revealed that strain HY1 was very closely related to Burkholderia graminis with 95% similarity based that strain HY1 was placed among three major clonal types of $\beta$-Proteobacteria, including Burkholderia graminis, Burkholderia phenazinium, and Burkholderia glathei. The sequence GAT(C or G)${\b{G}}$, which is highly conserved in several locations in the 16S rDNA gene among the major clonal type strains of $\beta$-Proteobacteria, was frequently replaced with GAT(C or G)${\b{A}}$ in the 16S rDNA sequence from strain HY1.

• International Journal of Oral Biology
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• v.44 no.3
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• pp.96-100
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• 2019

The purpose of this study was to develop Peptoniphilus mikwangii-specific quantitative real-time polymerase chain reaction (qPCR) primers based on the 16S ribosomal RNA (16S rDNA) gene. The specificity of the primers was determined by conventional PCR using 29 strains of 27 oral bacterial species including P. mikwangii. The sensitivity of the primers was determined by qPCR using the purified genomic DNA of P. mikwangii KCOM $1628^T$ (40 ng to 4 fg). The data showed that the qPCR primers (RTB134-F4/RTB134-R4) could detect P. mikwangii strains exclusively and as little as 40 fg of the genomic DNA of P. mikwangii KCOM $1628^T$. These results suggest that the developed qPCR primer pair can be useful for detecting P. mikwangii in epidemiological studies of oral bacterial infectious diseases.

• Food Engineering Progress
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• v.14 no.1
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• pp.7-13
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• 2010

A thermophilic microorganism, which is able to hydrolyze starch, was isolated from soil and compost in Korea. It was Gram-positive, rod-shaped, catalase positive, nonmotile, glucose and mannitol fermentative, xylose oxidative, and spore forming microorganism. It also has an ability to hydrolyze casein and gelatin. The color of colony was yellowish white. The sequence of 16S rDNA of strain 2719 showed 99.5% sequence homology with the sequence of 16S rDNA of Bacillus thermoglucosidasius. On the basis of biochemical and physiological properties and phylogenetic analysis, the isolated strain was named as Bacillus thermoglucosidasius 2719.

• International Journal of Oral Biology
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• v.31 no.1
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• pp.11-14
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• 2006

This study was undertaken to develop PCR primers for the identification and detection of Streptococcus anginosus using species-specific forward and reverse primers. These primers targeted the variable regions of the 16S ribosomal RNA coding gene(rDNA). The primer specificity was tested against 12 S. anginosus strains and 6 different species(10 strains) of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of S. anginosus ATCC $33397^T$. The data showed that species-specific amplicons were obtained from all the S. anginosus strains tested, but not in the six other species. The PCR could detect as little as 0.4pg of the chromosomal DNA from S. anginosus. This suggests that the PCR primers are highly sensitive and applicable to the detection and identification of S. anginosus.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.15-21
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• 2002

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.210-216
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• 2007

The principal objective of this study was to analyze 16S rDNA-ARDRA of the humus forest soil via an improved manual method and an ISOIL kit on the basis of the UPGMA clustering of the 16S rDNA combined profile, 44 ARDRA clusters of 76 clones via the ISOIL kit method and 45 ARDRA clusters of 136 clones via the improved manual method. On the basis of the 16S rDNA sequences, 44 clones from the ARDRA clusters by the ISOIL kit were classified into 3 phyla : ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria and Actinobacteria. Using the improved manual method, the specimens were classified into 6 phyla : the ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes and Gemmatomonadetes. As a result, the modified manual method indicated greater phylogenetic diversity than was detected by the ISOIL kit. Approximately 40 percent of the total clones were identified as ${\alpha}-Proteobacteria$ and 30 percent of the total clones were ${\gamma}-Proteobacteria$ and assigned to dominant phylogenetic groups using the ISOIL kit. Using the modified manual method, 41 percent of the total clones were identified as Acidobacteria and 28 percent of total clones were identified as ${\alpha}-proteobacteria$ and assigned to dominant phylogenetic groups.