• Food Science and Industry
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• v.50 no.1
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• pp.2-10
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• 2017

Human have eaten various traditional fermented foods for a numbers of million years for health benefit as well as survival. The beneficial effects of fermented foods have been resulted from complex microbial communications within the fermented foods. Therefore, the holistic approaches for individual identification and complete microbial profiling involved in their communications have been of interest to food microbiology fields. Microbiome is the ecological community of microorganisms that literally share our environments including foods as well as human body. However, due to the limitation of culture-dependent methods such as simple isolations of just culturable microorganisms, the culture-independent methods have been consistently developed, resulting in new light on the diverse non-culturable and hitherto unknown microorganisms, and even microbial communities in the fermented foods. For the culture-independent approaches, the food microbiome has been deciphered by employing various molecular analysis tools such as fluorescence in situ hybridization, quantitative PCR, and denaturing gradient gel-electrophoresis. More recently, next-generation-sequencing (NGS) platform-based microbiome analysis has been of interest, because NGS is a powerful analytical tool capable of resolving the microbiome in respect to community structures, dynamics, and activities. In this overview, the development status of analysis tools for the fermented food microbiome is covered and research trend for NGS-based food microbiome analysis is also discussed.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.135-141
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• 2000

Global Biodiversity is common interest of humans for better health and sustainable development of the society. To provide access and analysis on microbial diversity information, Bacteriology Insight Orienting System (BIOS) has been developed. BIOS contains 6402 species and subspecies names of bacteria and archaea, 2606 names of cyanobacteria by March 2000. BIOS of which web based analytical tool provides windows to compare the results of phylogenetic analysis based on 16S rDNA sequence and the results of cluster analysis on proteome profiling. The sequence data and 2 dimensional gel electrophoresis analysis data were accumulated in BIOS database content for cyanobacteria reclassification and taxonomy. (BIOS URL: http.://www-sp2000ao.nies.go.jp/bios/index.html).

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.2
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.4
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• pp.307-316
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• 2009

Soil microbial activity and diversity are affected by organic sources applied to improve soil quality and fluctuate seasonally. We investigated the effects of municipal compost (MC), poultry litter (PL), and cover crops of spring oats and red clover (RC) on soil enzyme activities, and soil bacterial community-level physiological profiling (CLPP) in a Mexico silt loam in North Central Missouri, USA. Temporal patterns of these parameters were observed by periodic five soil sampling from spring to fall over a two year period. MC increased soil dehydrogenase (DH) activity consistently beginning about three months after MC application; fluorescein diacetate (FDA) hydrolytic activity significantly began to increase by the September of the first year but fluctuated during the following period. DH activity responded more directly to the amount or properties of organic residues in soils while FDA hydrolysis and CLPP were generally influenced by composition of organic sources, and enzyme activities and CLPP showed seasonal variation, which depended on organic sources and soil moisture. MC and cover crops may be useful organic sources for enhancing general soil microbial activity and altering soil microbial diversity, respectively. Because microbial activities and diversity are dynamic and subject to seasonal changes, the effects of organic amendments on these parameters should be investigated frequently during a growing season.

• Korean Journal of Organic Agriculture
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• v.23 no.2
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• pp.323-334
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• 2015

This study was conducted to develop environment-friendly agricultural products with anti-microbial activity against Acidovorax avenae subsp. citrulli as a pathogen of bacterial fruit blotch in cucurbit. Schlechtendalia chinensis was extracted by MeOH and solvent fraction. The hexane fraction, which showed highest value of anti-microbial activity, was analyzed by GC-MS. Each mass spectra, corresponding to each peak of chromatogram, was compared to MS database of Wiley library. As a result, myristic acid, palmitic acid and 3-n-pentadecylphenol were identified as maine compounds showing antimicrobial activity against A. avenae subsp. citrulli. Bioassay using commercial myristic acid, palmitic acid and 3-n-pentadecylphenol to test for the anti-microbial activity conformed the anti-microbial activity of potential active compounds, and myristic acid and 3-n-pentadecylphenol showed strong activity. In conclusion, myristic acid and 3-n-pentadecylphenol identified from S. chinensis were anti-microbial chemicals.

• 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 Korean Dental Science
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• v.16 no.1
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.995-1004
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• 2017

Culture-dependent methods, such as heterotrophic plate counting (HPC), are usually applied to evaluate the bacteriological quality of hemodialysis water. However, these methods cannot detect the uncultured or viable but non-culturable (VBNC) bacteria, both of which may be quantitatively predominant throughout the hemodialysis water treatment system. Therefore, propidium monoazide (PMA)-qPCR associated with HPC was used together to profile the distribution of the total viable bacteria in such a system. Moreover, high-throughput sequencing of 16S rRNA gene amplicons was utilized to analyze the microbial community structure and diversity. The HPC results indicated that the total bacterial counts conformed to the standards, yet the bacteria amounts were abruptly enhanced after carbon filter treatment. Nevertheless, the bacterial counts detected by PMA-qPCR, with the highest levels of $2.14{\times}10^7copies/100ml$ in softener water, were much higher than the corresponding HPC results, which demonstrated the occurrence of numerous uncultured or VBNC bacteria among the entire system before reverse osmosis (RO). In addition, the microbial community structure was very different and the diversity was enhanced after the carbon filter. Although the diversity was minimized after RO treatment, pathogens such as Escherichia could still be detected in the RO effluent. In general, both the amounts of bacteria and the complexity of microbial community in the hemodialysis water treatment system revealed by molecular approaches were much higher than by traditional method. These results suggested the higher health risk potential for hemodialysis patients from the up-to-standard water. The treatment process could also be optimized, based on the results of this study.

• Journal of Korean Medicine for Obesity Research
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• v.15 no.2
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• pp.123-130
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• 2015

Objectives: Samjung-hwan (SJH), a well-known traditional fermented herb formula recorded in Dongui Bogam, has been commonly used for prolonging life for four hundred years in Eastern Asia. However, fermented SJH has not been investigated in terms of microbial ecology until present time. Methods: SJH was fermented for five weeks and fermentation characteristics during SJH fermentation were performed including pH, acidity and microbial profiling. Also, we measured total polyphenol and total flavonoid contents and 1,1-Diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity. In order to select starter candidate, several lactic acid bacteria were isolated from fermented SJH. Results: pH of fermented SJH was decreased from 4.7 to 3.0 and acidity was increased from 0.45% to 1.72%. Also, fermented SJH increased antioxidant indicator such as total polyphenol and total flavonoid as well as DPPH free radical scavenging activity. Lactobacillus brevis was increased, Pseudanabaena sp. was decreased, and Lactococcus lactis subsp. lactis was stable during 5-week fermentation of SJH. L. brevis and L. plantarum were isolated from fermented SJH. Conclusions: Fermented SJH for four weeks had optimal effect on antioxidant and fermentation characteristics such as pH, acidity and microbial profile. Further studies are required to develop starter and analyze functional compounds in oder to produce standardized SJH.

• Journal of Microbiology and Biotechnology
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• v.26 no.1
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• pp.120-129
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• 2016

An industrial complex in Wonju, contaminated with trichloroethene (TCE), was one of the most problematic sites in Korea. Despite repeated remedial trials for decades, chlorinated ethenes remained as sources of down-gradient groundwater contamination. Recent efforts were being made to remove the contaminants of the area, but knowledge of the indigenous microbial communities and their dechlorination abilities were unknown. Thus, the objectives of the present study were (i) to evaluate the dechlorination abilities of indigenous microbes at the contaminated site, (ii) to characterize which microbes and reductive dehalogenase genes were responsible for the dechlorination reactions, and (iii) to develop a PCE-to-ethene dechlorinating microbial consortium. An enrichment culture that dechlorinates PCE to ethene was obtained from Wonju stream, nearby a trichloroethene (TCE)-contaminated industrial complex. The community profiling revealed that known organohalide-respiring microbes, such as Geobacter, Desulfuromonas, and Dehalococcoides grew during the incubation with chlorinated ethenes. Although Chloroflexi populations (i.e., Longilinea and Bellilinea) were the most enriched in the sediment microcosms, those were not found in the transfer cultures. Based upon the results from pyrosequencing of 16S rRNA gene amplicons and qPCR using TaqMan chemistry, close relatives of Dehalococcoides mccartyi strains FL2 and GT seemed to be dominant and responsible for the complete detoxification of chlorinated ethenes in the transfer cultures. This study also demonstrated that the contaminated site harbors indigenous microbes that can convert PCE to ethene, and the developed consortium can be an important resource for future bioremediation efforts.