• Korean Journal of Food Science and Technology
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• v.45 no.4
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• pp.515-520
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• 2013

Bacterial communities derived from cheonggukjang and raw rice straw collected from a Mireuksan farm and a Heungup cheonggukjang in Gangwon province were investigated using both culture-based method and denaturing gradient gel electrophoresis (DGGE) analysis. Pure cultures, which were isolated from raw rice straw and cheonggukjang and cultured on tryptic soy agar plates (53-76 colonies per plate), were identified by analysis of 16S rRNA sequences. The traditional culture-based method and analysis of PCR-amplified 16S rRNA by DGGE revealed that for samples collected from the Mireuksan farm, Pantoea agglomerans and Bacillus subtilis were the predominant species in the raw rice-straw and cheonggukjang, respectively. For samples collected from the Heungup cheonggukjang, Bacillus amyloliquefaciens was the predominant species in both raw rice straw and cheonggukjang. Other microorganisms, including members of Pantoea, Bacillus, Enterococcus, Enterobacter, Pseudomonas, Rhodococcus, and Acinetobacter, were also present in the raw rice-straw and cheonggukjang, as were bacteria that could not be cultured.

• Korean Journal of Microbiology
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• v.46 no.2
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• pp.177-182
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• 2010

The bacterial community structure of two marine sponges, Spirastrella abata and Cinachyrella sp. collected from Jeju Island, in April 2009, was analyzed by 16S rDNA-denaturing gradient gel electrophoresis (DGGE). DGGE banding patterns indicated 8 and 7 bands for Spirastrella abata and Cinachyrella sp., respectively. Comparative sequence analysis of variable DGGE bands revealed from 92% to 100% similarity to the known published sequences. The bacterial groups associated with Spirastrella abata were Alphaproteobacteria and Deltaproteobacteria. The bacterial community of Cinachyrella sp. consisted of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria. Alphaproteobacteria was common and predominant in both the sponge species. Deltaproteobacteria was found only in Spirastrella abata while Actinobacteria and Gammaproteobacteria were found only in Cinachyrella sp. The results revealed that though the common bacterial group was found in both the sponges, the bacterial community profiles differed between the two sponge species obtained from the same geographical location.

• Journal of Korean Society on Water Environment
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• v.29 no.4
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• pp.459-465
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• 2013

A sequencing batch reactor was operated under different pH conditions to see the influence of pH to microbial community in enhanced biological phosphorus removal (EBPR) systems. Long term influences of different steady-state pH conditions on the microbial community composition were evaluated by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). The shift in populations from polyphosphate-accumulating organisms (PAOs) to Alphaproteobacteria was observed when pH was changed from 7.5 to 7.0. Alphaproteobacteria with the typical morphological traits of tetrad-forming organisms (TFOs) eventually became dominant members. The alphaproteobacterial TFOs were the phenotype expected for glycogen-accumulating organisms (GAOs), which accumulate large amount of glycogen into the cell. The results strongly suggested that low operational pH condition encourages the appearance of the GAOs in EBPR process, significantly reducing the EBPR capacity.

• Environmental Engineering Research
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• v.15 no.1
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• pp.3-7
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• 2010

To better understand the ecology of tetrade forming organisms (TFOs) floating in a large amount of dairy wastewater treatment plant (WWTP) effluent (sequencing batch reactor [SBR]) during the inefficient phosphorus (P) removal process of an enhanced biological P removal system, the TFOs from the effluent of a full scale WWTP were separated and attempts made to culture the TFOs in presence/absence of oxygen. The intact TFOs only grew aerobically in the form of unicellular short-rods. Furthermore, to identify the intact TFOs and unicellular short-rods the DNAs of both were extracted, analyzed using their denaturing gradient gel electrophoresis (DGGE)-profiles and then sequenced. The TFOs and unicellular short-rods exhibited the same banding pattern in their DGGE-profiles, and those sequencing data resulted in their identification as Acinetobacter sp. The intact TFOs appeared in clumps and packages of tetrade cells, and were identified as Acinetobacter sp., which are known as strict aerobes and efficient P-removers. The thick layer of extracellular polymeric substance surrounding Acinetobacter sp. may inhibit phosphate uptake, and the cell morphology of TFOs might subsequently be connected with their survival strategy under the anaerobic regime of the SBR system.

• Food Science and Biotechnology
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• v.17 no.4
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• pp.892-894
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• 2008

During dongchimi fermentation at 5 and $25^{\circ}C$, the pH lowered slowly and reached 4.03 at $5^{\circ}C$ after 30 days, whereas it lowered dramatically and reached 3.59 at $25^{\circ}C$ after 2 days. The predominant bacteria were Leuconostoc (Leu.) mesenteroides at $25^{\circ}C$ until day 2 which changed into Lactobacillus (Lb.) plantarum at day 3, analyzed by a culture dependent method with partial 16S rRNA gene sequencing, whereas Leu. mesenteroides occupied predominantly at $5^{\circ}C$ until day 7. In a culture-independent method using a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) with partial 16S rRNA gene sequencing, Lb. algidus was predominant at $5^{\circ}C$ until day 7 and Lb. plantarum occupied predominantly at $25^{\circ}C$ until day 3, which is different from the results of the culture based method, indicating the both methods need to be combined for accuracy. Based on the culture-dependent method, Leu. mesenteroides might be responsible for the early and mid-phase of dongchimi fermentation.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2004.04a
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• pp.332-336
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• 2004

An anaerobic PCE(tetrachloroethylene) dechlorinating bacterial culture from a landfill soil was enriched and characterized. The enrichment culture could dechlorinate 60$\mu$mol/$m\ell$ of PCE during a month of incubation and cis-DCE(cis-dichloroethylene) was observed as a main product of PCE dechlorination. Microbial analysis of the dechlorinating enrichment culture by rising PCR-DGGE (Polymerase chain reaction-Denaturing gradient gel electrophoresis) method showed that at least three microorganisms were related to the anaerobic PCE dechlorination.

• Journal of Life Science
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• v.24 no.4
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• pp.393-402
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• 2014

Culture-dependent and culture-independent denaturing gradient gel electrophoresis (DGGE) analyses were employed to investigate the bacterial community associated with a natural dye wastewater treatment facility. A total of 104 (influent water, 48 strains; aeration tank, 25; settling tank, 31) bacterial strains were isolated. Based on the 16S rRNA gene sequences comparison analysis, the isolates belonged to four phyla: Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes. Seventeen DGGE bands representing dominant taxa in each sample were cloned and partially sequenced. The same four phyla were detected by DGGE fingerprinting. The most dominant taxon retrieved by both methods was the member of the phylum Proteobacteria with Alphaproteobacteria as the predominant class. The bacterial community associated with the natural dye wastewater treatment facility is composed of parasites of animals and plants, decomposers of polysaccharides and dyes, and producers of extracellular polysaccharides.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.35 no.5
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• pp.490-496
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• 2002

In order to detect the DNA heteropolymorphism of chum salmon, selected essential genes were examined in different regional chum salmons, i.e., Korean, Japanese and American by denaturing gradient gel electrophoresis (DGGE) and real time PCR methods. From the promoter regions and introns of growth hormone, mtDNA NDI region, D-loop region, IGF-I, histone H3 and MCH2 several representative primer pairs were obtained and employed for the DGGE with the PCR products from the genomic DNAs of the different regional chum salmons. mtDNA NDI, D-loop region and IGE-I genes showed marked heteropolymorphism between Korean and American chum salmons. Intron C of growth hormone also showed a heteropolymorphism between Korean and Japanese chum salmons. Whereas heteropolnnorphism of histone liH and MCH2 genes was detected among in Korean, Japanese and Asnerican chum salmons in the examined region. The real time PCR disclosed the characteristic incremental production of target DNAs dependent on the heteropolymorphic conditions of genomic DNAa of chum salmons, thus the different regional chum salmons could be grouped by the variable incremental curies. Although the DGGE and real time PCR did not produce the identical results in this study, we suggest that the DGGE and real time PCR could be used for the primary screening of the DNA heteropolymorphism of different animal genome.

• Analytical Science and Technology
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• v.17 no.1
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• pp.53-59
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• 2004

Up to now, methods for the detection of genetic alterations as single strand conformation polymorphism (SSCP) or denaturing gradient gel electrophoresis (DGGE) have been used. It is too labor-intensive and expensive to serve for routine analysis. Moreover, lower in its sensitivity and specificity being also strongly dependent on the experience of the investigater. To improve these problems, we analysed mutation of ${\beta}_2$-adrenergic receptor gene that controls bronchial asthma by denaturing high performance liquid chromatography (DHPLC) according to ion-pair reversed phase chromatography (IP-RPC). We extracted genomic DNA from 80 asthma patients and then amplified DNA using PCR and analysed PCR product by SSCP and DHPLC. As a result, we analysed mutation frequency is 19 (23.75%) on SSCP and 25 (31.25%) on DHPLC in ${\beta}_2$-adrenergic receptor gene. We conclude that DHPLC is a fast and simple screening method rather than SSCP analysis.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.678-684
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• 2017

The aim of this study was to elucidate the changes in the microbial community and biochemical properties of a traditional sweet paste during fermentation. PCR-denaturing gradient gel electrophoresis (DGGE) analysis showed that Aspergillus oryzae was the predominant species in the koji (the fungal mixture), and the majority of the fungi isolated belonged to two Zygosaccharomyces species in the mash. The bacterial DGGE profiles revealed the presence of Bacillus subtilis during fermentation, and Lactobacillus acidipiscis, Lactobacillus pubuzihii, Lactobacillus sp., Staphylococcus kloosi, and several uncultured bacteria were also detected in the mash after 14 days of main fermentation. Additionally, during main fermentation, amino-type nitrogen and total acid increased gradually to a maximum of $6.77{\pm}0.25g/kg$ and $19.10{\pm}0.58g/kg$ (30 days) respectively, and the concentration of reducing sugar increased to $337.41{\pm}3.99g/kg$ (7 days). The 180-day fermented sweet paste contained $261.46{\pm}19.49g/kg$ reducing sugar and its pH value remained at around 4.65. This study has used the PCR-DGGE technique to demonstrate the microbial community (including bacteria and fungi) in sweet paste and provides useful information (biochemical properties) about the assessment of the quality of sweet paste throughout fermentation.