• Korean Journal of Environmental Agriculture
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• v.30 no.4
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• pp.466-472
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• 2011

BACKGROUND: Soybean [Glycine max (L.) Merrill] is a legume and an important oil crop worldwide. This study was conducted to evaluate the possible impact of transgenic soybean cultivation on the soil microbial community. METHODS AND RESULTS: Microorganisms were isolated from the rhizosphere soils. Microbial community was identified based on the culture-dependent and molecular biology methods. The total numbers of bacteria, fungi, and actinomycete in the rhizosphere soils cultivated with transgenic and non-transgenic soybeans were similar to each other, and there was no significant difference between transgenic and non-transgenic soybeans. Dominant bacterial phyla in the rhizosphere soils cultivated with transgenic or non-transgenic soybeans were Actinobacteria, Firmicutes, and Proteobacteria. The microbial communities in transgenic and non-transgenic soybean soils were characterized using the denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed the different patterns, but didn't show significant difference to each other at 0.05 significance level. DNAs were isolated from soils cultivating transgenic or non-transgenic soybeans and analyzed for persistence of transgenes in the soil by using PCR. PCR analysis revealed that there were no amplified ${\gamma}$-tmt and bar gene in soil DNA. CONCLUSION(S): The results of this study suggested that microbial community of soybean field were not significantly affected by cultivation of the transgenic soybeans.

• Journal of Microbiology and Biotechnology
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• v.32 no.6
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• pp.761-767
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• 2022

EHT1 and EEB1 are the key Saccharomyces cerevisiae genes involved in the synthesis of ethyl esters during wine fermentation. We constructed single (Δeht1, Δeeb1) and double (Δeht1Δeeb1) heterogenous mutant strains of the industrial diploid wine yeast EC1118 by disrupting one allele of EHT1 and/or EEB1. In addition, the aromatic profile of wine produced during fermentation of simulated grape juice by these mutant strains was also analyzed. The expression levels of EHT1 and/or EEB1 in the relevant mutants were less than 50% of the wild-type strain when grown in YPD medium and simulated grape juice medium. Compared to the wild-type strain, all mutants produced lower amounts of ethyl esters in the fermented grape juice and also resulted in distinct ethyl ester profiles. ATF2, a gene involved in acetate ester synthesis, was expressed at higher levels in the EEB1 downregulation mutants compared to the wild-type and Δeht1 strains during fermentation, which was consistent with the content of acetate esters. In addition, the production of higher alcohols was also markedly affected by the decrease in EEB1 levels. Compared to EHT1, EEB1 downregulation had a greater impact on the production of acetate esters and higher alcohols, suggesting that controlling EEB1 expression could be an effective means to regulate the content of these aromatic metabolites in wine. Taken together, the synthesis of ethyl esters can be decreased by deleting one allele of EHT1 and EEB1 in the diploid EC1118 strain, which may modify the ester profile of wine more subtly compared to the complete deletion of target genes.

• Journal of Microbiology and Biotechnology
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• v.18 no.4
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• pp.624-630
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• 2008

Terminal restriction fragment length polymorphism (T-RFLP) is a method that has been frequently used to survey the microbial diversity of environmental samples and to monitor changes in microbial communities. T-RFLP is a highly sensitive and reproducible procedure that combines a PCR with a labeled primer, restriction digestion of the amplified DNA, and separation of the terminal restriction fragment (T-RF). The reliable identification of T-RF requires the information of nucleotide sequences as well as the size of T-RF. However, it is difficult to obtain the information of nucleotide sequences because the T-RFs are fragmented and lack a priming site of 3'-end for efficient cloning and sequence analysis. Here, we improved on the T-RFLP method in order to analyze the nucleotide sequences of the distinct T-RFs. The first method is to selectively amplify the portion of T-RF ligated with specific oligonucleotide adapters. In the second method, the termini of T-RFs were tailed with deoxynucleotides using terminal deoxynucleotidyl transferase (TdT) and amplified by a second round of PCR. The major T-RFs generated from reference strains and from T-RFLP profiles of activated sludge samples were efficiently isolated and identified by using two modified T-RFLP methods. These methods are less time consuming and labor-intensive when compared with other methods. The T-RFLP method using TdT has the advantages of being a simple process and having no limit of restriction enzymes. Our results suggest that these methods could be useful tools for the taxonomic interpretation of T-RFs.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.704-715
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• 2006

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.870-879
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• 2006

The present study describes the formation of succinic acid by a nonvirulent, highly osmotolerant Klebsiella pneumoniae strain SAP (succinic acid producer), its profile of metabolites, and enzymes of the succinate production pathway. The strain produced succinate along with other metabolites such as lactate, acetate, and ethanol under aerobic as well as anaerobic growth conditions. The yield of succinate was higher in the presence of $MgCO_3$ under $N_2$ atmosphere as compared with that under $CO_2$ atmosphere. Analysis of intracellular metabolites showed the presence of a smaller PEP pool than that of pyruvate. Oxaloacetate, citrate, and $\alpha$-ketoglutarate pools were considerably larger than those of isocitrate and fumarate. In order to understand the synthesis of succinate, the enzymes involved in end-product formation were studied. Levels of phosphoenolpyruvate carboxykinase, fumarate reductase, pyruvate kinase, and acetate kinase were higher under anaerobic growth conditions. Based on the profiles of the metabolites and enzymes, it was concluded that the synthesis of succinate took place via oxaloacetate, malate, and fumarate in the strain under anaerobic growth conditions. The strain SAP showed potential for the bioconversion of fumarate to succinate under $N_2$ atmosphere in the presence of $MgCO_3$. At an initial fumarate concentration of 10 g/l, 7.1 g/l fumarate was converted to 7 g/l succinate with a molar conversion efficiency of 97.3%. The conversion efficiency and succinate yield were increased in the presence of glucose. Cells grown on fumarate contained an 18-fold higher fumarate reductase activity as compared with the activity obtained when grown on glucose.

• Journal of The Korean Society of Grassland and Forage Science
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• v.34 no.3
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• pp.169-173
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• 2014

The aim of present study was to improve the quality of silage using lactic acid bacteria (LAB) and chlorella as a supplement. Italian ryegrass (IRG) mediated silage was prepared with lactic acid bacteria (L. plantarum) and different concentration of chlorella. We analyzed the nutritional profiles such as crude protein (CP), acid detergent fiber (ADF) neutral detergent fiber (NDF), total digestible nutrient (TDN) and in-vitro dry matter digestibility (IVDMD), microbial counts and fermentative acids such as lactic acid, acetic acid and butyric acid in the control and experimental silage after three months. It shows increased crude protein content and also maintains the rest of nutritional values as compared with control silage. LAB inoculation with chlorella as supplementation slightly reduced the pH of the silage. In addition, it increased the fermentative acids production as compared with control silage and inhibits the undesired microbial growth especially fungi in the silage. Therefore, we suggest that LAB inoculation and chlorella supplementation to the IRG mediated silage could be improved the nutritional quality of the silage which is an intrinsic feature for the application in the preparation of animal feeds and functional foods.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.205-210
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• 2004

The change of bacterial communities during cyanobacterial bloom was analyzed by DGGE in Daechung Reservoir from July to October in 2003. The traditional morphological analysis showed that the genera of Microcystis, Chroococcus, Oscillatoria, and Phormidium were dominated. The most frequent band in the DGGE profile by 16S rDNA sequence analysis was identified as Microcystis flos-aquae and the cyanobacterial bloom was peaked on September 2. Oscillatoria spp. were also identified and Aphanizomenon flos-aquae dominated in the middle of August. Judging from the analysis of the digitalized DGGE profiles using the cluster analysis technique, the microbial community on September 2 was considerably different from others. Consequently, it seems that the gene fingerprinting method can give not only the similar results to the traditional morphological method but also additional information on the bacterial species and similarity among the examined microbial communities.

• Journal of Microbiology and Biotechnology
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• v.27 no.2
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• pp.226-233
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• 2017

Jeung-pyun, a fermented rice cake, is prepared by fermenting rice sourdough using makgeolli, a traditional Korean rice wine, in the presence of yeast and lactic acid bacteria (LAB). The goal of this study was to conduct biochemical and microbial analyses of five different rice sourdoughs, each fermented with a different commercial makgeolli, using culture-dependent and culture-independent approaches. All sourdough samples fermented with different makgeolli for 6.5 h showed different profiles in pH, total titratable acidity, organic acid concentration, and microbial growth. LAB belonging to different genera were identified based on colony morphology on modified MRS and sourdough bacteria agar medium. PCR-denaturing gradient gel electrophoresis analyses of the five sourdoughs showed different bands corresponding to LAB and yeast. 16S/26S rRNA gene sequence analyses of the samples confirmed that the predominant LAB in the five fermented rice doughs was Lactobacillus plantarum, Lb. pentosus, and Lb. brevis. Various other Lactobacillus spp. and Saccharomyces cerevisiae were common in all five fermented samples. This study provides comprehensive and comparative information on the microflora involved in fermentation of rice sourdough and signifies the need to develop effective starters to enrich the quality of jeung-pyun.

• The Korean Journal of Physiology and Pharmacology
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• v.25 no.6
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• pp.575-583
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• 2021

Composition of the gut microbiota changes with aging and plays an important role in age-associated disease such as metabolic syndrome, cancer, and neurodegeneration. The gut microbiota composition oscillates through the day, and the disruption of their diurnal rhythm results in gut dysbiosis leading to metabolic and immune dysfunctions. It is well documented that circadian rhythm changes with age in several biological functions such as sleep, body temperature, and hormone secretion. However, it is not defined whether the diurnal pattern of gut microbial composition is affected by aging. To evaluate aging effects on the diurnal pattern of the gut microbiome, we evaluated the taxa profiles of cecal contents obtained from young and aged mice of both sexes at daytime and nighttime points by 16S rRNA gene sequencing. At the phylum level, the ratio of Firmicutes to Bacteroidetes and the relative abundances of Verrucomicrobia and Cyanobacteria were increased in aged male mice at night compared with that of young male mice. Meanwhile, the relative abundances of Sutterellaceae, Alloprevotella, Lachnospiraceae UCG-001, and Parasutterella increased in aged female mice at night compared with that of young female mice. The Lachnospiraceae NK4A136 group relative abundance increased in aged mice of both sexes but at opposite time points. These results showed the changes in diurnal patterns of gut microbial composition with aging, which varied depending on the sex of the host. We suggest that disturbed diurnal patterns of the gut microbiome can be a factor for the underlying mechanism of age-associated gut dysbiosis.

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.354-358
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• 2019

In order to evaluate the migration of fungi into doenjang from its materials, meju and solar salt, microbial communities were analyzed using pyrosequencing. Dominant fungi of meju were Botrytis spp. (57.94%) and Dothiorella samentorum (24.08%). Unidentified fungal species (37.53%), unassigned species (32.60%) and several fungal species of small portion were identified in solar salt. In doenjang, Candida versatilis were predominantly detected (92.62%). Non-halophilic mold were dominantly identified from meju (low-salt fermented soybean), while halophilic bacteria and archaea for solar salt and salt-tolerance fungi such as C. versatilis for doenjang (high-salt fermented soybean) were frequently detected. These results implied that most predominant fungal species might not be migrated from meju and/or solar salt into doenjang.