• Korean Journal of Microbiology
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• v.51 no.1
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• pp.31-38
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• 2015

The bacterial community structures of two marine sponges, Cinachyrella sp. and Plakortis sp., collected from Chuuk in the South Pacific in February 2012 were analyzed by PCR-DGGE (Denaturing Gradient Gel Electrophoresis) fingerprinting. After isolation of the total genomic DNAs from the sponges, the V3 regions of the 16S rRNA genes were amplified and subjected to DGGE profiling. The two species of sponges displayed different DGGE band patterns. The sequences derived from the DGGE bands revealed 85-100% similarities to known bacterial species in the public database. The bacterial community of Cinachyrella sp. was composed of 6 classes: Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria (Alpha-, Gamma-, Delta-). The bacterial community of Plakortis sp. included 7 classes: Actinobacteria, Chloroflexi, Firmicutes, Spirochaetes, and Proteobacteria (Alpha-, Gamma-, Delta-). Though Actinobacteria, Chloroflexi and Proteobacteria were commonly found in both sponges, the predominant bacterial communities differed between the two. Namely, the predominant bacterial groups in Cinachyrella sp. and Plakortis sp. were Proteobacteria and Chloroflexi, respectively. The sponge-associated bacteria are sponge host-specific, as each of the tested sponges from the same geographical location had different predominant bacterial diversity.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1561-1569
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• 2006

Denaturing gradient gel electrophoresis (DGGE) is one of the most frequently used methods for analysis of soil microbial community structure. Unbiased PCR amplification of target DNA templates is crucial for efficient detection of multiple microbial populations mixed in soil. In this study, DGGE profiles were compared using different pairs of primers targeting different hypervariable regions of thirteen representative soil bacteria and clones. The primer set (1070f-1392r) for the E. coli numbering 1,071-1,391 region could not resolve all the 16S rDNA fragments of the representative bacteria and clones, and moreover, yielded spurious bands in DGGE profiles. For the E. coli numbering 353-514 region, various forward primers were designed to investigate the efficiency of PCR amplification. A degenerate forward primer (F357IW) often yielded multiple bands for a certain single 16S rDNA fragment in DGGE analysis, whereas nondegenerate primers (338f, F338T2, F338I2) differentially amplified each of the fragments in the mixture according to the position and the number of primer-template mismatches. A forward primer (F352T) designed to have one internal mismatch commonly with all the thirteen 16S rDNA fragments efficiently produced and separated all the target DNA bands with similar intensities in the DGGE profiles. This primer set F352T-519r consistently yielded the best DGGE banding profiles when tested with various soil samples. Touchdown PCR intensified the uneven amplification, and lowering the annealing temperature had no significant effect on the DGGE profiles. These results showed that PCR amplification bias could be much improved by properly designing primers for use in fingerprinting soil bacterial communities with the DGGE technique.

• Korean Journal of Environmental Biology
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• v.24 no.3
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• pp.221-229
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• 2006

The effects of ultrasonication on phytoplankton were investigated in two ponds in which physicochemical and biological water quality was similar, one as a treatment and the other as a control. The samples were collected from August 18 to September 30 in 2003. Traditional morphological analysis showed that Bacillariophyceae dominated phytoplankton community in both ponds. The abundance of Cyanophyceae was lower in the phytoplankton community of the sonicated pond than that of control pond. We used DGGE (denaturing gradient gel electrophoresis) to analyze the diversity and change of phytoplankton community in two ponds. The DGGE banding patterns of 16S rRNA gene and sequence analysis demonstrated that Oscillatoria acuminata and CFB (Cytophaga-Flavobacterium-Bacteroides) group bacterium appeared in the treated pond, and the control pond was dominated by Synechococcus sp. and Aphanizomenon flos-aquae. Especially, Pseudanabaena sp. dominated during the ultrasonic cessation in the treated pond. The DGGE profiles of 18S rRNA gene and sequence analysis showed that the treated pond was dominated by Chlamydomonas reinhardtii and the control pond by C. reinhardtii and Pteromonas protracta. In conclusion, the ultrasonication affected the reduced growth of cyanobacteria, particularly Pseudanabaena.

• Korean Journal of Microbiology
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• v.51 no.2
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• pp.133-140
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• 2015

We have examined the correlation between the physicochemical and microbiological environment variables for the different layers of oak forest soil in Mt. Gyeryong, Korea. The result shows that there is a high correlation in the environment variables between the soil parameters of the fermented (F) layer and humus (H) layer. In particular, the pH level in the F layer shows a high correlation with C and N, while the various organic acids of the H layer turns out to be closely correlated with soil bacteria density. As we evaluated phylogenetic characteristics of bacterial populations by DGGE analysis with DNA extracted. Total of 175 bands including 43 bands from litter (L) layer, 42 bands from F layer, 43 bands from H layer and 47 bands from rhizosphere (A) layer were selected as the major DGGE band of oak forest soil. Based on the 16S rRNA gene sequences, 175 DGGE bands were classified into 32 orders in 7 phylum. The heat map was analyzed in order to compare the quantity of the base sequences of each order and based on the clustering of the different layers of oak forest soil, the result confirms that the F layer and H layer belong to a different cluster from that of L layer and A layer. Furthermore, it also showed that approximately 50% of the total microbial population in different layers is ${\alpha}$-proteobacteria, which indicates that they belong to the dominant system group. In particular, Rhizobiales, Burkholderiales and Actinobacteriales were observed in all the seasons and layers of oak forest soil, which confirms that they are the indigenous soil bacterial community in oak forest soil.

• 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 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.

• Microbiology and Biotechnology Letters
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• v.38 no.4
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• pp.448-454
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• 2010

This study investigated the effect of PCE and TCE as electron acceptors on the bacterial composition of dechlorinating communities. The enrichment cultures reductively dechlorinating PCE and TCE were developed from three environment samples using acetate as electron donor. The cultures were prepared by sequential enrichment, which was seeded with sediment and dredged soil. Denatured gradient gel electrophresis (DGGE) of 16S rRNA gene fragment was used to compare the microbial communities of these three enrichment cultures. After incubation for 4 weeks, the removal efficiencies of PCE and TCE were highest from Yeocheon site (87.37% and 84.46%, respectively). PCE and TCE as electron acceptors affected the bacterial diversity and community profiles in the enrichment cultures. DGGE analysis showed that the dominant bacteria in PCE and TCE enrichment were belonged to Clostridium sp., Desulfotomaculum sp., and uncultured bacteria.

• Journal of Korean Society of Environmental Engineers
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• v.32 no.8
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• pp.780-786
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• 2010

The bacterial community structure in biological reactor in wastewater treatment system was investigated by denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH). Samples were collected at different three points in wastewater treatment system. Through treatment processes, BOD (biochemical oxygen demand) and COD (chemical oxygen demand) of was removal efficiency was 83.1~98.6%, 67.2~85.2% respectively. Microbial community of aerobic tank and oxic tank were similar but anoxic tank was different (RRP group was increased about tripple) by DGGE and FISH in sludge (2007 October and 2008 January). Samples in 2007 October and 2008 January were dominant ${\alpha}$-Proteobacteria and CF group respectively. Sludge in 2008 April were different comparing former results dominant others as 65~80%. Others group was dominant. Eubacteria by FISH with the probe EUB338 was about $1.7{\sim}7.6{\times}10^9\;cells/mL$. It could be successfully observed bacterial community in biological wastewater system.

• Journal of Microbiology and Biotechnology
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• v.28 no.1
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• pp.32-39
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• 2018

Samples of Laru (a fermentation starter) obtained from the upper part of Borneo Island were analyzed for their lactic acid bacteria (LAB) and fungal diversity using both a culture-independent method (PCR-DGGE) and culture-dependent methods (SDS-PAGE and MALDI-TOF MS). Pediococcus pentosaceus, Lactobacillus brevis, Saccharomycopsis fibuligera, Hyphopichia burtonii, and Kodamaea ohmeri were detected by all three methods. In addition, Weissella cibaria, Weissella paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Lactococcus lactis, Rhizopus oryzae/Amylomyces rouxii, Mucor indicus, and Candida intermedia were detected by PCR-DGGE. In contrast, Lactobacillus fermentum, Lactobacillus plantarum, Pichia anomala, Candida parapsilosis, and Candida orthopsilosis were detected only by the culture-dependent methods. Our results indicate that the culture-independent method can be used to determine whether multiple laru samples originated from the same manufacturing region; however, using the culture-independent and the two culture-dependent approaches in combination provides a more comprehensive overview of the laru microbiota.

• Journal of Microbiology and Biotechnology
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• v.25 no.10
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• pp.1670-1679
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• 2015

Two hollow fiber membrane biofilm reactors (HF-MBfRs) were operated for autotrophic nitrification and hydrogenotrophic denitrification for over 300 days. Oxygen and hydrogen were supplied through the hollow fiber membrane for nitrification and denitrification, respectively. During the period, the nitrogen was removed with the efficiency of 82-97% for ammonium and 87-97% for nitrate and with the nitrogen removal load of 0.09-0.26 kg NH₄⁺-N/m³/d and 0.10-0.21 kg NO₃^--N/m³/d, depending on hydraulic retention time variation by the two HF-MBfRs for autotrophic nitrification and hydrogenotrophic denitrification, respectively. Biofilms were collected from diverse topological positions in the reactors, each at different nitrogen loading rates, and the microbial communities were analyzed with partial 16S rRNA gene sequences in denaturing gradient gel electrophoresis (DGGE). Detected DGGE band sequences in the reactors were correlated with nitrification or denitrification. The profile of the DGGE bands depended on the NH₄⁺ or NO₃^- loading rate, but it was hard to find a major strain affecting the nitrogen removal efficiency. Nitrospira-related phylum was detected in all biofilm samples from the nitrification reactors. Paracoccus sp. and Aquaspirillum sp., which are an autohydrogenotrophic bacterium and an oligotrophic denitrifier, respectively, were observed in the denitrification reactors. The distribution of microbial communities was relatively stable at different nitrogen loading rates, and DGGE analysis based on 16S rRNA (341f /534r) could successfully detect nitrate-oxidizing and hydrogen-oxidizing bacteria but not ammonium-oxidizing bacteria in the HF-MBfRs.