• Food Science and Biotechnology
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• 제17권4호
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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.

• 상하수도학회지
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• 제20권3호
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• pp.461-467
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• 2006

The seasonal change in attached algae and microbial community structure at sedimentation basin of water treatment plant was investigated by using quinone profiles and denaturing gel gradient electrophoresis (DGGE). The photosynthetic bacteria and algae contains PQ-9 and VK-1 as major quinone are major component of the total quinone fraction in attached algae and microorganisms on sedimentation basin trough. The microorganisms containing menaquinones appear to be sensitivity to the change in temperature than those containing ubiquinones. The plot of the mole fraction of dominant quinone species ($f_d$) to the DQ values showed higher sensitivity to the seasonal change in the microbial community structure. The results indicated that quinone and DGGE are useful tool for the evaluation of the changes in the microbial community structure.

• Journal of Microbiology and Biotechnology
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• 제23권1호
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• pp.76-84
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• 2013

A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique followed by sequencing of the 16S rDNA fragments eluted from the bands of interest on denaturing gradient gels was used to monitor changes in the bacterial microflora of two commercial kimchi, salted cabbage, and ingredient mix samples during 30 days of fermentation at $4^{\circ}C$ and $10^{\circ}C$. Leuconostoc (Lc.) was the dominant lactic acid bacteria (LAB) over Lactobacillus (Lb.) species at $4^{\circ}C$. Weissella confusa was detected in the ingredient mix and also in kimchi samples throughout fermentation in both samples at $4^{\circ}C$ and $10^{\circ}C$. Lc. gelidum was detected as the dominant LAB at $4^{\circ}C$ in both samples. The temperature affected the LAB profile of kimchi by varing the pH, which was primarily caused by the temperature-dependent competition among different LAB species in kimchi. At $4^{\circ}C$, the sample variations in pH and titratable acidity were more conspicuous owing to the delayed growth of LAB. Temperature affected only initial decreases in pH and initial increases in viable cell counts, but affected both the initial increases and final values of titratable acidity. The initial microflora in the kimchi sample was probably determined by the microflora of the ingredient mix, not by that of the salted cabbage. The microbial distributions in the samples used in this study resembled across the different kimchi samples and the different fermentation temperatures as the numbers of LAB increased and titratable acidity decreased.

• 미생물학회지
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• 제41권4호
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• pp.281-286
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• 2005

울산, 여수 등 공단지역의 토양, 하천의 저니, 해양의 준설토 둥을 이용하여 난분해성 염소화합물인 PCE (perchloroethylene)및 TCE (trichloroethylene)의 혐기성 탈염소화에 관련하는 미생물을 탐색하고 이들의 탈염소화 효율을 조사하였다. 혐기성 상호대사에 의한 탈염소화 효율을 조사하기 위해 전자공여체로 acetate를 사용하여 혐기성 회분식 실험을 실시하였으며, 이와 병행하여 분자생물학적인 기법인 16S rDNA의 PCR-Double Gradient DGGE (DG-DGGE)를 이용하여 미생물의 군집을 분석하였다. 그 결과 울산 태화강 및 여수 하남천의 저니를 접종한 경우 PCE는 $70\%,\;65\%$, TCE는 $50\%,\;45\%$의 높은 탈염소화 효율을 나타내었다. 또한 16S rDNA의 PCR을 이용한 DG-DGGE로 미생물 군집을 분석한 결과, 탈염소화 효율이 높은 지역의 저니에는 Desulfovibrio sup.의 미생물이 주로 존재함을 확인하였다.

• Journal of Microbiology and Biotechnology
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• 제23권7호
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• pp.993-1003
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• 2013

Methanotrophs are the most important sink of $CH_4$, which is a more highly potent greenhouse gas than $CO_2$. Methanotrophic abundance and community diversity in cover soils from two typical semi-aerobic landfills (SALs) in China were detected using real-time polymerase chain reaction (real-time-PCR) and denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA genes, respectively. Real time-PCR showed that Type I methanotrophs ranged from $1.07{\times}10^6$ to $2.34{\times}10^7$ copies/g soil and that of Type II methanotrophs from $1.51{\times}10^7$ to $1.83{\times}10^8$ copies/g soil. The ratio of Type II to Type I methanotrophic copy numbers ranged from 5.61 to 21.89, indicating that Type II methanotrophs dominated in SAL. DGGE revealed that Type I methanotrophs responded more sensitively to the environment, changing as the community structure varied with different soil types and locations. Methylobacter, Methylosarcina, and Methylomicrobium for Type I, and Methylocystis for Type II were most prevalent in the SAL cover layer. Abundant interflow $O_2$ with high $CH_4$ concentration in SALs is the reason for the higher population density of methanotrophs and the higher enrichment of Type II methanotrophs compared with anaerobic landfills and other ecosystems, which proved a conclusion that increasing the oxygen supply in a landfill cover layer would greatly improve $CH_4$ mitigation.

• Journal of Microbiology and Biotechnology
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• 제18권5호
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• pp.815-820
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• 2008

Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.

• Asian-Australasian Journal of Animal Sciences
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• 제20권12호
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• pp.1887-1894
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• 2007

In this paper, a rapid and reliable gene-targeted species-specific polymerase chain reaction (PCR) technique based on a two-step process was established to identify bifidobacteria in dairy products. The first step was the PCR assay for genus Bifidobacterium with genus specific primers followed by the second step, which identified the species level with species-specific primer mixtures. Ten specific primer pairs, designed from nucleotide sequences of the 16-23S rRNA region, were developed for the Bifidobacterium species including B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. infantis, B. longum, B. minimum, B. subtile, and B. thermophilum. This technique was applied to the identification of Bifidobacterium species isolated from 6 probiotic products, and four different Bifidobacterium spp. (B. bifidum, B. longum, B. infantis, and B. breve) were identified. The findings indicated that the 16S-23S rDNA gene-targeted species-specific PCR technique is a simple and reliable method for identification of bifidobacteria in probiotic products. PCR combined with Denaturing Gradient Gel Electrophoresis (DGGE) for identification of the bifidobacteria was also evaluated and compared with the gene-targeted species-specific technique. Results indicated that for fermented milk products consistency was found for both species-specific PCR and PCR-DGGE in detecting species. However, in some lyophilized products, the bands corresponding to these species were not visualized in the DGGE profile but the specific PCR gave a positive result.

• 한국식품과학회지
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• 제45권4호
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• pp.515-520
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• 2013

전통적인 방법으로 제조한 청국장과 볏짚시료로부터 배양방법과 비배양방법인 DGGE를 이용한 청국장의 발효미생물 군집을 분석하였다. 배양방법에서는 미륵산농원의 볏짚과 청국장 시료에서 P. agglomerans (65%)와 B. subtilis (60%)가 우점미생물로 나타내었고, 흥업토속 청국장의 볏짚과 청국장 시료에서는 B. amyloliquefaciens (57%와 52%)가 우점미생물로 확인하였다. DGGE 분석에서는 미륵산농원의 볏짚과 청국장 시료에서 P. agglomerans (Band intensity 20.6%)와 B. subtilis (Band intensity 25.7%)가 우점미생물로 나타내었고 흥업토속 청국장의 볏짚과 청국장 시료에서는 B. amyloliquefaciens (Band intensity 27.3%, 26.4%)가 우점미생물로 확인하였다. 그 외에도 볏짚에서는 Pantoea sp. Enterococcus durans, Enterobacter sp, P. ananatis, Bacillus sp., Rhodococcus sp. Pseudomonas fulva, Acinetobacter sp., B. licheniformis, B. amyloliquefaciens 등의 미생물을 확인하였고 청국장에서는 B. licheniformis, B. subtilis, Bacillus sp., B. circulans, Acinetobacter sp. 등의 미생물을 확인이 되었으며, 비배양 방법을 이용한 청국장 발효미생물 균총 조사는 배양이 불가능한 미생물을 확인할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제27권6호
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• pp.898-906
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• 2014

The objective of this study was to investigate differences in the faecal microbial composition among Lantang, Bama, Erhualian, Meishan, Xiaomeishan, Duroc, Landrace, and Yorkshire sows and to explore the possible link of the pig breed with the gut microbial community. Among the sows, the Meishan, Landrace, Duroc, and Yorkshire sows were from the same breeding farm with the same feed. Fresh faeces were collected from three sows of each purebred breed for microbiota analysis and volatile fatty acid (VFA) determination. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that samples from Bama, Erhualian, and Xiaomeishan sows, which from different farms, were generally grouped in one cluster, with similarity higher than 67.2%, and those from Duroc, Landrace, and Yorkshire sows were grouped in another cluster. Principal component analysis of the DGGE profile showed that samples from the foreign breeds and the samples from the Chinese indigenous breeds were scattered in two different groups, irrespective of the farm origin. Faecal VFA concentrations were significantly affected by the pig breed. The proportion of acetate was higher in the Bama sows than in the other breeds. The real-time PCR analysis showed that 16S rRNA gene copies of total bacteria, Firmicutes and Bacteroidetes were significantly higher in the Bama sows compared to Xiaomeishan and Duroc sows. Both Meishan and Erhualian sows had higher numbers of total bacteria, Firmicutes, Bacteroidetes and sulphate-reducing bacteria as compared to Duroc sows. The results suggest that the pig breed affects the composition of gut microbiota. The microbial composition is different with different breeds, especially between overseas breeds (lean type) and Chinese breeds (relatively obese type).

• 생명과학회지
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• 제27권11호
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• pp.1290-1298
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• 2017

인체의 장내에 존재하는 장내 미생물은 서로 공생 또는 길항 관계를 유지하며 우리 몸의 면역 방어 기전에 중요한 요소로 작용한다. 본 연구는 항암제가 위암 환자의 장내 미생물 생태계에 미치는 영향을 조사 하였다. 항암치료를 받는 환자의 분변에서 genomic DNA를 추출하고, 16S rDNA 유전자에 대한 denaturing gradient gel electrophoresis (DGGE)를 수행하였다. 분석된 균주는 개체간의 차이가 있었으나, 대부분 사람의 장내에 살고 있는 normal flora로 동정되었다. 모든 분변에 존재하는 5 개 밴드의 서열 분석 결과에 의하면 Faecalibacterium prausnitzii, Morganella morganii 및 Uncultured bacterium sp.가 나타났고, 항암제 처리 후 Sphingomonas paucimobilis, Lactobacillus gasseri, Parabacteroides distasonis 및 Enterobacter sp.가 증가하였다. 이 연구에서 probiotic으로 알려진 Bifidobacterium과 Lactobacillus를 특이적 PCR primer를 이용하여 동정한 결과, 항암제 투여로 인해 Bifidobacterium과 Lactobacillus의 개체군이 현저하게 줄어들어 diarrhea와 같은 부작용의 원인을 예상하게 하며, 장내 생태계의 주요 박테리아 집단에도 중요한 영향을 미치는 것을 알 수 있었다. 이러한 결과는 항암제 투여와 같이 시간의 흐름에 따른 균총의 변화를 시각적으로 모니터링하기 위하여 PCR-DGGE 분석법이 유용하다는 것을 나타낸다.