• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2005.04a
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• pp.28-30
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• 2005

Because of high population diversity in soil microbial communities, it is difficult to accurately assess the capability of biodegradation of toxicant by microbes in soil and sediment. Identifying biodegradative microorganisms is an important step in designing and analyzing soil bioremediation. To remove non-important noise information, it is necessary to selectively enrich genomes of biodegradative microorganisms fromnon-biodegradative populations. For this purpose, a stable isotope probing (SIP) technique was applied in selectively harvesting the genomes of biphenyl-utilizing bacteria from soil microbial communities. Since many biphenyl-using microorganisms are responsible for aerobic PCB degradation In soil and sediments, biphenyl-utilizing bacteria were chosen as the target organisms. In soil microcosms, 13C-biphenyl was added as a selective carbon source for biphenyl users, According to $13C-CO_2$ analysis by GC-MS, 13C-biphenyl mineralization was detected after a 7-day of incubation. The heavy portion of DNA(13C-DNA) was separated from the light portion of DNA (12C-DNA) using equilibrium density gradient ultracentrifuge. Bacterial community structure in the 13C-DNAsample was analyzed by t-RFLP (terminal restriction fragment length polymorphism) method. The t-RFLP result demonstates that the use of SIP efficiently and selectively enriched the genomes of biphenyl degrading bacteria from non-degradative microbes. Furthermore, the bacterial diversity of biphenyl degrading populations was small enough for environmental genomes tools (metagenomics and DNA microarrays) to be used to detect functional (biphenyl degradation) genes from soil microbial communities, which may provide a significant progress in assessing microbial capability of PCB bioremediation in soil and groundwater.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.4
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• pp.254-261
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• 2014

The scientific information between microbial activities and chemical properties of reclaimed tidal soil is not enough to apply for reclamation projects. This study was conducted to investigate the relation between chemical properties and microbial activities of reclaimed tidal lands located at western coastal area (25 samples from Nampo, Ewon, Sukmoon and Shihwa sites). Most of the reclaimed soils showed chemical characteristics as salinity soil except Nampo site. The major component influenced the salinity of reclaimed soil was identified as a sodium from the relationship between EC and exchangeable cation. With an increase in EC of soil, the population of mesophilic bacteria decreases whereas halotolerant and halophilic bacteria increases. The population of mesophilic bacteria increased with an increase in both organic matter and dehydrogenase activity. However, the population of halotolerant and halophilic bacteria decreased with an increase in organic matter. Based on the relation between chemical property and microbial activity of reclaimed tidal soil, electrical conductivity and organic matter as chemical properties of soil, population of mesophilic bacteria, halotolerant and halophilic bacteria and dehydrogenase activity as microbial activities could be the major parameters for reclamation process.

• Clinical and Experimental Pediatrics
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• v.55 no.6
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• pp.193-201
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• 2012

Atopic dermatitis (AD) is an immune disorder that is becoming increasingly prevalent throughout the world. The exact etiology of AD remains unknown, and a cure for AD is not currently available. The hypothesis that appropriate early microbial stimulation contributes to the establishment of a balanced immune system in terms of T helper type Th1, Th2, and regulatory T cell (Treg) responses has led to the use of probiotics for the prevention and treatment of AD in light of various human clinical studies and animal experiments. Meta-analysis data suggests that probiotics can alleviate the symptoms of AD in infants. The effects of balancing Th1/Th2 immunity and enhancing Treg activity via the interaction of probiotics with dendritic cells have been described in vitro and in animal models, although such an effect has not been demonstrated in human studies. In this review, we present some highlights of the immunomodulatory effects of probiotics in humans and animal studies with regard to their effects on the prevention of AD.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.1
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• pp.28-35
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• 2014

Due to recent interest of the consumers on safe farm products and the government's political support for eco-friendly agriculture, organic fruit production has been growing continuously. This research was conducted in order to study the effect of cover plants on soil microbial community on cover plants and establish an organic fruit cultivation method through choosing optimal cover plant. As a result of investigating soil microbial population density, the bacterial density in soil showed an increasing trend in June compared to April, and there was a decreasing trend in bacterial density of the soil in August compared to June. The density of actinomycetes in soil increased around 1.6 times in June compared to April when the soil was covered with hairy vetch. The increase of filamentous fungus in crimson clover group was 6.1 times higher in June compared to April and in hairy vetch group, the increase was 4.9 times higher in June compared to April. As a result of analyzing DNA extracted from the soil categorized by different types of cover plants using DGGE method, soil collected from April had higher number of bands detected from different locations according to different types of cover plants. Diversity of the bands from the soil collected from August showed higher range of reduction. As a result of analyzing soil microbial community by different period and the types of cover plants using Pyrosequencing method, microbes were detected in the order of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Firmicutes. Distribution rate of Firmicutes increased in the soil collected in August compared to June and this was shown in all types of cover plants by twice the amount.

• Journal of Microbiology and Biotechnology
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• v.26 no.7
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• pp.1303-1310
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• 2016

Although many studies on the effects of genetically modified (GM) crops on soil microorganisms have been carried out over the past decades, they have provided contradictory information, even for the same GM crop, owing to the diversity of the soil environments in which they were conducted. This inconsistency in results suggests that the effects of GM crops on soil microorganisms should be considered from many aspects. In this study, we investigated the effects of the GM drought-tolerant rice MSRB2-Bar-8, which expresses the CaMSRB2 gene, on soil microorganisms based on the culture-dependent and culture-independent methods. To this end, rhizosphere soils of GM and non-GM (IM) rice were analyzed for soil chemistry, population densities of soil microorganisms, and microbial community structure (using pyrosequencing technology) at three growth stages (seedling, tillering, and maturity). There was no significant difference in the soil chemistry between GM and non-GM rice. The microbial densities of the GM soils were found to be within the range of those of the non-GM rice. In the pyrosequencing analyses, Proteobacteria and Chloroflexi were dominant at the seedling stage, while Chloroflexi showed dominance over Proteobacteria at the maturity stage in both the GM and non-GM soils. An UPGMA dendrogram showed that the soil microbial communities were clustered by growth stage. Taken together, the results from this study suggest that the effects of MSRB2-Bar-8 cultivation on soil microorganisms are not significant.

• Journal of Microbiology and Biotechnology
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• v.17 no.4
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• pp.560-570
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• 2007

The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the l6S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.

• Proceedings of the Korean Society of Food Hygiene and Safety Conference
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• 1996.06a
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• pp.33-33
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• 1996

Interests in the field of rapid methods and automation in microbiology have been growing steadily on an international scale in recent years. International meetings concerned this problem have been held in elsewhere in the world countries since the past twenty years. But, unfortunately in the field of microbial examination in food hygiene, this problem have not yet been developed so much as in the field of clinical microbiology. Today, I would like to introduce you here present aspects of rapid and automation technologies, those which are manly carrying in milk and meats industries. My illustration will be given recent improved technologies using automatic apparatus and instruments along with process of microbial count procedure. Recent direct microbiological counting system (ChemeScan \ulcorner) as real time ultrasensitive analysis created by Cheminex Ltd., France is now most evolutional instrument to provide direct microbial counts, down to one cell, within 30 minutes. The results from these evaluations how a good correlation between the ChemScan system and the standard plate count method. This system will be successful application for not only in the field of pharmacology but also food microbiology. In addition, current identification of microbes by sophisticated instruments suitable for food microbiology, one of which Biology is manual system (BIOLOG\ulcorner), provides reference-level capability at a modes price. For the manual system, the color reactions in the microplate are read by eye and manually keyed into personal computer. Species identification appears on the computer screen within seconds, along with biotype patterns, a list of closely related species, and other useful statistics. In present this is useful application for microbial ecology and epidemiological survey. RiboPrinter system newly produced by DuPont is now focusing among microbiologists in the world, and is one of the biggest microbial characterization system using a DNA-based approach. The technology analyzer is bacterial culture for its genetic fingerprint or riboprint pattern. Finally Bio-cellTracer system for automatic measurement of fungal growth and Fukitori-Maseter, a Surface Hygiene Monitoring Kit by using swabe procedure in food processing environment are briefly illustrated in this presentation.

• Journal of Korean Medicine for Obesity Research
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• v.18 no.2
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• pp.64-73
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• 2018

Objectives: This study investigated the effect on microbial ecology, fermentation characteristics and anti-obesity of Platycodon grandiflorum (PG) fermentation with salt. Methods: PG was fermented for four weeks with 2.5% salt and the characteristics of fermented PG were performed by measuring pH, total sugar content, viable bacteria number and microbial profiling. Also, we measured total polyphenol, flavonoid and the percent of inhibition of lipase activity and lipid accumulation. Results: Salt added to PG for fermentation had an effect on pH, total sugar, total and the number of lactic acid bacteria. Total sugar and pH were reduced and number of total and lactic acid bacteria were increased after fermentation. The majority of bacteria for fermentation were Lactobacillus plantarum, Leuconostoc psedomesenteroides and Lactococcus lactis subspecies lactis regardless of salt addition. However, microbial compositions were altered by added salt and additional bacteria including Weissella koreensis, W. viridescens, Lactobacillus sakei and Lactobacillus cuvatus were found in fermented PG with salt. Total flavonoid was increased in fermented PG and lipid accumulation on HepG2 cells treated with fermented PG was reduced regardless of salt addition. Moreover, fermented PG without salt suppressed lipase activity. Conclusions: Addition of salt for PG fermentation had influence on fermentation characteristics including pH and sugar content as well as number of bacteria and microbial composition. In addition, fermented PG showed anti-obesity effect by increasing flavonoid content and inhibition of lipase activity and lipid accumulation.

• Journal of Ecology and Environment
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• v.41 no.3
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• pp.99-106
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• 2017

Background: Plants over-expressing Arabidopsis ABF3 (abscisic acid-responsive element-binding factor 3) have enhanced tolerance to various environmental stresses, especially drought. Using terminal restriction fragment length polymorphism (T-RFLP) analysis, we compared the rhizosphere-associated structures of microbial communities for transgenic potato containing this gene and conventional "Jopoong" plants. Results: During a 2-year field experiment, fungal richness, evenness, and diversity varied by year, increasing in 2010 when a moderate water deficit occurred. By contrast, the bacterial richness decreased in 2010 while evenness and diversity were similar in both years. No significant difference was observed in any indices for either sampling time or plant line. Although the composition of the microbial communities (defined as T-RF profiles) changed according to year and sampling time, differences were not significant between the transgenic and control plants. Conclusions: The results in this study suggest that the insertion of ABF3 into potato has no detectable (by current T-RFLP technique) effects on rhizosphere communities, and that any possible influences, if any, can be masked by seasonal or yearly variations.

• Molecular & Cellular Toxicology
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• v.2 no.1
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• pp.11-14
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• 2006

In this study we attempted to develop a novel genomic method to selectively isolate target functional microbial genomes from environmental samples. For this purpose, stable isotope probing (SIP) was applied in selectively isolating organic pollutant-assimilating populations. When soil microbes were fed with $^{13}C-labeled $ biphenyl, biphenyl-utilizing cells were incorporated with the heavy carbon isotope. The heavy DNA portion was successfully separated by CsCl equilibrium density gradient. And the diversity in the heavy DNA was sufficiently reduced, being suitable for the current DNA microarray techniques to detect biphenyl-utilizing populations in the soil. In addition, we proposed a new way to get more genetic information by combining this SIP method with selective metagenomic approach. The increased selective power of these new DNA isolation methods will be expected to provide a good quality of new genetic information, which, in turn, will result in development of a variety of biomarkers that may be used in assessing ecotoxicology issues including the impacts of organic hazards, and antibiotic-resistant pathogens on human and ecological systems.