• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1983-1992
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• 2016

Pseudomonas strains isolated from the heavily contaminated Lubin copper mine and Zelazny Most post-flotation waste reservoir in Poland were screened for the presence of integrons. This analysis revealed that two strains carried homologous DNA regions composed of a gene encoding a DNA_BRE_C domain-containing tyrosine recombinase (with no significant sequence similarity to other integrases of integrons) plus a three-component array of putative integron gene cassettes. The predicted gene cassettes encode three putative polypeptides with homology to (i) transmembrane proteins, (ii) GCN5 family acetyltransferases, and (iii) hypothetical proteins of unknown function (homologous proteins are encoded by the gene cassettes of several class 1 integrons). Comparative sequence analyses identified three structural variants of these novel integron-like elements within the sequenced bacterial genomes. Analysis of their distribution revealed that they are found exclusively in strains of the genus Pseudomonas.

• Journal of Korean society of Dental Hygiene
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• v.24 no.2
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• pp.131-139
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• 2024

Objectives: Oral bacterial samples included subgingival, supragingival, and saliva plaques. As the diversity and number of microorganisms deffer depending on the area of the oral cavity and the method used, an appropriate and reliable collection method is important. The present study investigated oral bacterial sampling methods. Methods: Supragingival dental plaque was collected from the buccal and lingual tooth surfaces of study participants using sterilized cotton swabs. Plaques were collected from the subgingival area using a sterilized curette. Bacterial genomic DNA was extracted using MagNA Pure 96 DNA and Viral NA low-volume kits. Real-time polymerase chain reaction (PCR) was performed using the PowerCheck^TM Periodontitis Pathogens Multiplex Real-time PCR kit. Results: Aggregatibacter actinomycetemcomitans, Prevotella intermedia, and Fusobacterium nucleatum of the orange complex were not observed in the subgingival biofilms of all study participants. For Porphyromonas. gingivalis, a significant correlation was observed between supragingival, subgingival, and total tooth surface biofilms. Compared to the supragingival and subgingival biofilmss, total tooth surface biofilm exhibited the highest bacterial count when the inswabbing method was used. Conclusions: Based on these findings, the supragingival swab method is recommended for oral bacterial research.

• International Journal of Oral Biology
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• v.41 no.4
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• pp.199-208
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• 2016

The aim of this study was to identify the non-Aggregatibacter actinomycetemcomitans bacteria grown on the tryptic soy-serum-bacitracin-vancomycin (TSBV) medium, an A. actinomycetemcomitans selective medium. A total of 82 unidentified bacterial isolates from the oral cavities of a Korean population were kindly provide by the Korean Collection for Oral Microbiology. All the clinical isolates were grown on TSBV medium and bacterial DNA purified from each isolate was subjected to PCR with universal primers specific for bacterial 16S rRNA genes (16S rDNAs) sequence. The each bacterial 16S rDNA was amplified by PCR and the nucleotide sequences of it was determined by the dideoxynucleotide chain termination method. They were identified by 16S rDNA sequence comparison method at the specie-level. The data showed that Neisseria spp. (42 strains), Fusobacterium spp. (10 strains), Capnocytophaga spp. (8 strains), Propionibacterium acnes (5 strains), Aggregatibacter aprophilus (4 strains), Campylobacter spp. (5 strains), Veillonella dispar (3 strains), Streptococcus sp. (1 strain), Haemophilus parainfluenzae (1 strain), Leptotrichia wadei (1 strain), Morococcus sp./Neisseria sp. (1 strain), and Staphylococcus sp. (1 strain) were identified. These results could be used to develop a new A. actinomycetemcomitans-selective medium which is more effective than the TSBV medium in future studies.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.272-276
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• 2003

Sapgyo Lake is an artificial freshwater reservoir which is located to the midwest of Korea and is the main water reservoir for industry and agriculture of the region. In this study we investigated environmental factors and the change of bacterial community with the influence of surrounding inflow water and the seasonal variation using the molecular ecological approach. Water samples were collected at front of the dike in May and August, 2001. Bacterial genomic DNAs were extracted directly and purified for the amplification of bacterial 16S rDNA. Clone libraries of the 16S rDNA were constructed using pGEM-T easy vector and RFLP analysis was performed to make a group as OTUs with 4 base recognizing enzymes (MspI and HaeIII). The estimated values of richness in August sample was higher than in May. Thirty-three of 153 clones in May and thirty-eight of 131 clones in August were sequenced from forward region of bacterial 16S rDNA for about 600~800 bp. Proteobacteria, Cytophaga, gram positive bacteria and Verrucomicrobia were observed both months. Especially, Planctomyces, cyanobacteria and chloroplast appeared in August when algal bloom occurred. On the whole investigation, Sapgyo lake showed a typical community structure of estuarine and was influenced by heterochthonous organic matters from the surrounding stream.

• Korean Journal of Microbiology
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• v.39 no.1
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• pp.36-39
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• 2003

The rapid and reliable 16S rDNA multiplex polymerase chain reaction (PCR) assay was established to characterize bacterial etiologies of middle ear effusion. These etiologies included Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumonia, which were detected in middle-ear effusion (MEE) samples taken from patient with otitis media. A total of 39 MEE samples were aspirated from 26 patients. DNA was extracted from MEE samples, and PCR was done with DNA extracts by using the common primers, which is localized at C4 region in the 16S rDNA gene of all bacterial species, and species-specific primers: (i) Haemophilus-specific primer, (ii) Moraxella- specific primer, and (iii) Streptococcus-specific primer. Among 39 samples tested, 24 (61.5%) were positive for H. influenzae, 10 (25.6%) were positive for M. catarrhalis, 3(7.7%) were positive for S. pneumonia, and 11 (28%) were negative for 165 rDNA multiplex PCR reaction. Nine samples (28.6%) exhibited a mixed infection and were positive for both H. infuenzae and M. catarrhalis. We suggested that 16S rDNA multiplex PCR is a useful method to identify rapidly for rapid identification of the pathogenic bacteria and characterization of bacterial etiologies of middle ear effusion.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.207-218
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• 2008

The impacts of planted transgenic rice varieties on bacterial communities in paddy soils were monitored using both cultivation and molecular methods. The rice field plot consisted of eighteen subplots planted with two genetically modified (GM) rice and four non-GM rice plants in three replicates. Analysis with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes revealed that the bacterial community structures were quite similar to each other in a given month, suggesting that there were no significant differences in bacterial communities between GM and non-GM rice soils. The bacterial community structures appeared to be generally stable with the seasons, as shown by a slight variation of microbial population levels and DGGE banding patterns over the year. Comparison analysis of 16S rDNA clone libraries constructed from soil bacterial DNA showed that there were no significant differences between GM and non-GM soil libraries but revealed seasonal differences of phyla distribution between August and December. The composition profile of phospholipid fatty acids (PLFA) between GM and non-GM soils also was not significantly different to each other. When soil DNAs were analyzed with PCR by using primers for the bar gene, which was introduced into GM rice, positive DNA bands were found in October and December soils. However, no bar gene sequence was detected in PCR analysis with DNAs extracted from both cultured and uncultured soil bacterial fractions. The result of this study suggested that, in spite of seasonal variations of bacterial communities and persistence of the bar gene, the bacterial communities of the experimental rice field were not significantly affected by cultivation of GM rice varieties.

• Journal of Oral Medicine and Pain
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• v.47 no.1
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• pp.10-26
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• 2022

Purpose: The purpose of this study was to investigate whether various saliva collection methods affect the observed salivary microbiome and whether microbiomes of stimulated and unstimulated saliva and plaque differ in richness and diversity. Methods: Seven sampling methods for unstimulated saliva, stimulated saliva, and plaque samples were applied to six orally and systemically healthy participants. Bacterial 16S ribosomal RNA genes of 10 major oral bacterial species, namely, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia, Prevotella nigrescens, Streptococcus mitis, Streptococcus sobrinus, and Lactobacillus casei, were analyzed by real-time polymerase chain reaction. We comprehensively examined the dependence of the amount of bacterial ribosomal DNA (rDNA), bacterial-community composition, and relative abundance of each species on sample collection methods. Results: There were significant differences in the bacterial rDNA copy number depending on the collection method in three species: F. nucleatum, P. nigrescens, and S. mitis. The species with the highest richness was S. mitis, with the range from 89.31% to 100.00%, followed by F. nucleatum, P. nigrescens, T. denticola, T. forsythia, and P. intermedia, and the sum of the proportions of the remaining five species was less than 1%. The species with the lowest observed richness was P. gingivalis (<0.1%). The Shannon diversity index was the highest in unstimulated saliva collected with a funnel (4.449). The Shannon diversity index was higher in plaque samples (3.623) than in unstimulated (3.171) and stimulated (3.129) saliva and in mouthwash saliva samples (2.061). Conclusions: The oral microbial profile of saliva samples can be affected by sample collection methods, and saliva differs from plaque in the microbiome. An easy and rapid technique for saliva collection is desirable; however, observed microbial-community composition may more accurately reflect the actual microbiome when unstimulated saliva is assayed.

• BMB Reports
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• v.38 no.1
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• pp.97-103
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• 2005

Under the condition of expression of $\lambda$ P protein at lethal level, the oriC DNA-binding activity is significantly affected in wild-type E. coli but not in the rpl mutant. In purified system, the $\lambda$ P protein inhibits the binding of both oriC DNA and ATP to the wild-type DnaA protein but not to the rpl DnaA protein. We conclude that the $\lambda$ P protein inhibits the binding of oriC DNA and ATP to the wild-type DnaA protein, which causes the inhibition of host DNA synthesis initiation that ultimately leads to bacterial death. A possible beneficial effect of this interaction of $\lambda$ P protein with E. coli DNA initiator protein DnaA for phage DNA replication has been proposed.

• 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.

• Microbiology and Biotechnology Letters
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• v.36 no.2
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• pp.115-120
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• 2008

Bacterial populations from the rhizosphere were obtained and the efficacy of the bacterial wilt suppression, root colonizing ability and resistance to three kinds of chemical pesticides were assayed. According to these results, SKU48-2 was selected as a potential biological agent to control the bacterial wilt caused by Ralstonia solanacearum. SKU48-2 strain at $10^8CFU/ml$ inoculum was able to suppress the bacterial wilt up to 60% in greenhouse trials. Also, the resistance of SKU48-2 to chemical pesticides make possible to use in combination with chemical pesticides for the control of bacterial wilt. Three different powder formulations of SKU48-2 were developed. The shelf-life of powder formulations was effective up to 6 months of storage. Unformulated bacterial suspension could not be stored for 2 weeks, at which time cell viability was completely lost. According to 16S rDNA sequence data, the SKU48-2 stain was identified as Bacillus subtilis.