• Food Engineering Progress
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• v.15 no.4
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• pp.370-375
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• 2011

In this study the polymerase chain reaction (PCR) combined with denaturing gradient gel electrophoresis (DGGE) was evaluated as a method permitting the rapid detection of pathogens in fresh originally grown vegetables. A universal primer (341GCf/534r) was selected for its ability to amplify the V3 region of 16S-rRNA genes in their target pathogens (Salmonella typhimurium, Pseudomonas fluorescens, Bacillus cereus, Listeria monoytogenes, Staphyloocus aureus, E. coli). The 194 bp fragments in PCR were successfully duplicated as expected. The amplified fragments of the same size from six different pathogens also showed good separation upon DGGE. The detection limit of PCR-DGGE for six pathogens in fresh-cut lettuces were over $10^{5}$ CFU/g when sampled by stomaching. However, when the sampling method was changed from stomaching to shaking, the detection limit of six pathogens in organic vegetables was shown to increase by over $10^{1}$ CFU/g, but only those of B. cereus were over $10^{3}$ CFU/g. Therefore, PCR-DGGE was shown to be a reliable method for the detection of pathogens in fresh-cut vegetables.

• Korean Journal of Microbiology
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• v.41 no.4
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• pp.281-286
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• 2005

In this study, the anaerobic enrichment cultivation was performed with the sediments and the dredged soils from the cities of Ulsan, Masan, Yeosu, Gwangyang, Ansan and Seongnam. Acetate as an electron donor and PCE (perchloroethylene) or TCE (trichloroethylene) as an electron acceptor were injected into the serum bottle with an anaerobic medium. After the incubation of 12 weeks, the removal efficiency of PCE was highest at $70\%$ in the treatment with the sediment of Ulsan. Also, the bacterial community structure was analyzed by D-DGGE (double denatured gradient gel electrophoresis) through PCR-based 16S rDNA approaches. The dominant species id the anaerobic enrichment were found to belong to the genus of Desulfovibrio.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.225-235
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• 2011

The change of microbial communities during cyanobacterial bloom was comparatively analyzed by 16S rDNA PCR-DGGE in Daechung Reservoir during 2003~2005. Morphological analysis showed that Cyanophyceae dominated algal community in the bloom. Dominant cyanobacteria were Microcystis, Planktothrix (Oscillatoria), Phormidium and Anabaena. We used 16S rDNA-denaturing gradient gel electrophoresis (DGGE) profiles and phylogenetic affiliations of the DGGE bands to analyze the community structure and diversity of the predominant microbial community. The DGGE band patterns demonstrated that the most frequent bands were identified as Microcystis during the monitoring periods, Planktothrix also dominated on September 2003 and 2004, whereas Anabaena was showed a peak on September 2005 and Aphanizomenon on August 2003. DGGE and phylogenetic analysis provided us new information that could not be obtained by traditional, morphological analysis. The relationship between cyanobacteria and other aquatic bacteria can be traced and their genetic diversity also identified in detail.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.21-29
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• 2010

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from the 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

• Journal of Life Science
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• v.27 no.11
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• pp.1290-1298
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• 2017

Intestinal microbiota is an important factor in the development of immune defense mechanisms in the human body. Treatments with anticancer agents, such as 5-Fluorouracil, Cisplatin, and Oxaliplatin, significantly change the temporal stability and environment of intestinal bacterial flora. The anticancer treatment chemotherapy often depresses the immune system and induces side effects, such as diarrhea. This study investigated the effects anticancer agents have on the intestinal microbial ecosystems of patients with gastric cancer. An exploration of the diversity and temporal stability of the dominant bacteria was undertaken using a DGGE with the 16S rDNA gene. Researchers collected stool samples from patients zero, two and eight weeks after the patients started chemotherapy. After the treatment with anticancer agents, the bacteria strains Sphingomonas paucimobilis, Lactobacillus gasseri, Parabacteroides distasonis and Enterobacter sp. increased. This study focused on the survival of the beneficial microorganisms Bifidobacterium and Lactobacillus in the intestines of cancer patients. The administration of antigastric cancer agents significantly decreased Lactobacillus and Bifidobacterium populations and only moderately affected the main bacterial groups in the patients' intestinal ecosystems. The results showed the versatility of a cultivation independent-PCR DGGE analysis regarding the visual monitoring of ecological diversity and anticancer agent-induced changes in patients' complex intestinal microbial ecosystems.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.398-406
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• 2015

Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene 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 rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. 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.

• Journal of Korean Society of Environmental Engineers
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• v.30 no.12
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• pp.1239-1244
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• 2008

In this study, PCR-DGGE was conducted to investigate the variations of microbial community according to pH conditions from pH 3 to pH 10 during anaerobic fermentation process of hydrogen production. Maximum hydrogen yield was 1.8 mol $H_2$/mol substrate at pH 5. The microbial growth rate was not proportional to the hydrogen production rate at each pH. Variations of microbial community was observed at each condition from PCR-DGGE experiment of 16s rDNA. Klebsiella was main species of the microbial community. Streptococcus and Clostridium were mainly contributed for hydrogen production.

• Microbiology and Biotechnology Letters
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• v.32 no.1
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• pp.91-95
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• 2004

For the detection of the oil-degrading bacterium, Nocardia sp. Hl7-1, inoculated during the bioremediation of oil-contaminated soil, a species-specific primer was constructed based on the 16S rDNA sequence of this strain. Two forward primers and two reverse primers were designed and tested against both closely and distantly related bacterial strains. All the primers designed were specific to the Nocardia sp. H17-1. Particularly, primer sets NH169F-NH972R and NH575F-NH972R could be used to detect 50 fg of template DNA and TEX>$1.2${\times}$10^4$ CFU/g of sandy soil. These two PCR primer sets successfully detected the H 17-1 strain in the oil-con-laminated soil samples containing heterogeneous DNA. We also conformed the primer specificity by restriction-enzyme cleavage of the PCR products and denaturing gradient gel electrophoresis.

• Journal of Korean Society of Environmental Engineers
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• v.31 no.2
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• pp.139-146
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• 2009

In this study, characteristics of biological hydrogen production and microbial distribution were investigated with the wastewater of Tofu manufacturing process. Comparison of hydrogen production was conducted with acid or base pre-treatment of the wastewater. Maximum hydrogen production was acquired with combination of heat and acid treatment. Hydrogen production ($P_h$) and maximum hydrogen production rate ($R_h$) was calculated 661.01 mL and 12.21 mL/g dry wt biomass/hr from the modified Gompartz equation. Most of microbial community was analyzed as Streptococcus sp. from PCR-DGGE experiment of 16S rDNA. It was concluded that most significant microorganism for hydrogen production was Streptococcus gallolyticus sub sp. in this experiment.

• Journal of Microbiology and Biotechnology
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• v.23 no.5
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• pp.614-622
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• 2013

Daqu, a traditional fermentation starter, has been used to produce attractively flavored foods such as vinegar and Chinese liquor for thousands of years. Although Bacillus spp. are one of the dominant microorganisms in Daqu, more precise information is needed to reveal why and how Bacillus became dominant in Daqu, and next, to assess the impact of Bacillus sp. on Daqu and its derived products. We combined culture-dependent and culture-independent methods to study the ecology of Bacillus during Daqu incubation. Throughout the incubation, 67 presumptive Bacillus spp. isolates were obtained, 52 of which were confirmed by 16S rDNA sequencing. The identified organisms belonged to 8 Bacillus species: B. licheniformis, B. subtilis, B. amyloliquefaciens, B. cereus, B. circulans, B. megaterium, B. pumilus, and B. anthracis. A primer set specific for Bacillus and related genera was used in a selective PCR study, followed by a nested DGGE PCR targeting the V9 region of the 16S rDNA. Species identified from the PCR-DGGE fingerprints were related to B. licheniformis, B. subtilis, B. amyloliquefaciens, B. pumilus, B. benzoevorans, and B. foraminis. The predominant species was found to be B. licheniformis. Certain B. licheniformis strains exhibited potent antimicrobial activities. The greatest species diversity occurred at the Liangmei stage of Daqu incubation. To date, we lack sufficient knowledge of Bacillus distribution in Daqu. Elucidating the ecology of Bacillus during Daqu incubation would enable the impact of Bacillus on Daqu to be accessed, and the quality and stabilization of Daqu-derived products to be optimized.