• Korean Journal of Microbiology
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• v.45 no.1
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• pp.1-9
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• 2009

Microbes within complex communities show quite different physiology from pure cultured microbes. However, historically the study of microbes has focused on single species in pure culture and most of microbes are unculturable in our labs, so understanding of complex communities lags behind understanding of pure cultured cells. Methodologies including stable isotope probing (SIP), a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR), isotope micrarray, and metagenomics have given insights into the uncultivated majority to link phylogenetic and functional information. Here, we review some of the most recent literatures, with an emphasis on methodological improvements to the sensitivity and utilities of these methods to link phylogeny and function in complex microbial communities.

• Journal of Life Science
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• v.33 no.4
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• pp.325-333
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• 2023

This study compared and analyzed the microbial composition and physicochemical characteristics of kimchi (gimjang kimchi) and mukeunji (aged kimchi). Commercial kimchi and mukeunji products were purchased through an online market. After an analysis of physicochemical characteristics, the pH of the mukeunji samples was found to be lower and the acidity higher than in the kimchi samples. There was no significant difference in salinity between kimchi and mukeunji, but the sugar content was higher in the kimchi samples. The phylogenetic diversity index, which incorporates phylogenetic difference between species, was significantly higher in mukeunji than in the kimchi. The most dominant order in both groups was Lactobacillales, but several lactic acid bacteria, such as the Pediococcus and Lactobacillus species, which may be more acid tolerant or more competitive, are relatively predominant in mukeunji. Beta set-significance analysis based on two different distance metric results revealed that microbial distributions of population were different at the statistical confidence level (p<0.001). We investigated the effect of respective species on total microbial community using the LEfSe (linear discriminant analysis effect size) mechanism. According to the results of LEfSe testing, a relatively higher abundance of Weissella kandleri in kimchi and a higher abundance of Pediococcus inopinatus in mukeunji have the greatest influence on the differences in microbial structure between the two groups.

• Microbiology and Biotechnology Letters
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• v.39 no.4
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• pp.374-381
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• 2011

The beneficial effects of Eisenia fetida on soil properties have been attributed to their interaction with soil microorganisms. The bacterial diversity of the intestinal tract of E. fetida was investigated by culture-dependent and culture-independent methods including denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses. In a pure culture, Lysinibacillus fusiformis (51%), Bacillus cereus (30%), Enterobacter aerogenes (21%), and L. sphaericus (15%) were identified as the dominant microorganisms. In the DGGE analyses, B. cereus (15.1%), Enterobacter sp. (13.6%), an uncultured bacterium (13.1%), and B. stearothermophilus (7.8%) were identified as the dominant microorganisms. In the pyrosequencing analyses, Microbacterium soli (26%), B. cereus (10%), M. esteraromaticum (6%), and Frigoribacterium sp. (6%) were identified as the dominant microorganisms. The other strains identified were Aeromonas sp., Pseudomonas sp., Borrelia sp., Cellulosimicrobium sp., Klebsiella sp., and Leifsonia sp. The results illustrate that culture independent methods are better able to detect unculturable microorganisms and a wider range of species, as opposed to isolation by culture dependent methods.

• Proceedings of the Korea Water Resources Association Conference
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• 2023.05a
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• pp.487-487
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• 2023

농업 분야에서 미생물은 영양분 가용화, 유기물 분해 등 토양 영양분 공급에 중요한 역할을 하며, 토양 건강성 증진, 식량 안보 및 식품 건강 면에서 많은 활용 가능성을 지니고 있다. 최근 유역 환경 건강성, 생물 다양성 보존, 효율적인 고품질 농산물 생산에 대한 관심이 커져, 지속 가능한 농업 중 하나인 유기농업과 관행농업 토양의 이화학적 및 생물학적 특성에 관한 비교 연구가 진행되고 있다. 미생물은 지속 가능한 농업 발전의 중요한 요소 중 하나로써, 미생물 다양성이 풍부할수록 토양 비옥도, 작물 성장 면에서 긍정적인 영향을 미친다고 알려져 있다. 본 연구는 이에 대한 기초 데이터를 제공하기 위해 논 경작지를 대상으로 유기 및 관행농업 토양의 미생물 군집조성과 Alpha diversity analysis(Chao1, Shannon, Simpson index)을 통해 비교하였다. 경기도 양평군에서 유기 및 관행 논 지역을 각각 1지점씩 선정하였으며, 8월부터 11월까지 총 4회 현장 조사를 진행하였다. 미생물 분석은 차세대염기서열분석을 실시하였으며, bacteria는 16S rRNA V3-4 영역, fungi는 ITS 3-4 영역을 sequencing 하였다. 미생물 군집조성은 문수준에서는 큰 차이가 없었으나, 속수준에서는 fungi 군집조성에 차이를 보였다. 예로 Ustilaginoidea 속은 관행 논 토양에서만 발견되었으며, 벼 이삭누룩병을 일으키는 병원균으로 과도한 질소 비료 시비가 원인으로 추정된다. 종 다양성은 bacteria diversity의 경우 관행 논 토양에서 높게 측정되는 반면, fungi diversity의 경우 유기 논 토양에서 높게 측정되었다. 결론적으로 체계적인 시비 관리 통해 미생물 군집은 조절될 수 있으며, 관행농업은 적절한 시비를 통해 토양 건강성 및 식품 건강성 면에서 유기농업과 비슷한 효과를 보여줄 가능성이 있다고 판단된다.

• Journal of Life Science
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• v.31 no.12
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• pp.1079-1087
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• 2021

To analyze gut microbiota of livestock in Korea and compare taxonomic differences, we conducted 16S rRNA metagenomic analysis through next-generation sequencing. Fecal samples from broiler chickens, pigs, and cattle were collected from domestic feedlots randomly. α-diversity results showed that significant differences in estimated species richness estimates (Chao1 and ACE, Abundance-based coverage estimators) and species richness index (OUTs, Operational taxonomic units) were identified among the three groups. However, NPShannon, Shannon, and Simpson indices revealed that abundance and evenness of the species were statistically significant only for poultry (broiler chickens) and mammals (pigs and cattle). Firmicutes was the most predominant phylum in the three groups of fecal samples. Linear discriminant (LDA) effect size (LEfSe) analysis was conducted to reveal the ranking order of abundant taxa in each of the fecal samples. A size-effect over 2.0 on the logarithmic LDA score was used as a discriminative functional biomarker. As shown by the fecal analysis at the genus level, broiler chickens were characterized by the presence of Weissella and Lactobacillus, as well as pigs were characterized by the presence of provetella and cattele were characterized by the presence of Acinetobacter. A permutational multivariate analysis of variance (PERMANOVA) showed that differences of microbial clusters among three groups were significant at the confidence level. (p=0.001). This study provides basic data that could be useful in future research on microorganisms associated with performance growth, as well as in studies on the livestock gut microbiome to increase productivity in the domestic livestock industry.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.170-179
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• 2017

Tea is the most popular beverage in the world. In fact, there are mainly three different kinds of tea (Green tea, black tea, and post-fermented tea). Post-fermented tea is produced by the microbial fermentation process using sun-dried green tea leaves (Camellia sinensis) as the raw material. Chungtaejeon was a traditional tea introduced in the age of the ancient three states and is the only "Ddeok-cha or Don-cha" culture in the world that survived on the southwestern shore of Republic of Korea. In this study, the structures of the bacterial community involved in the production of oriental traditional post-fermented tea (Chungtaejeon) were investigated using 16S rRNA gene analysis. The 16S rRNA gene analysis of dominant microbial bacteria in post-fermented tea confirmed the presence of Pantoea sp., and Klebsiella oxytoca. Phylogenetic analysis suggested that the taxonomic affiliation of the dominant species in the post-fermented tea was ${\gamma}$-proteobacteria. As a result of the microbial community size analysis, it was confirmed that the size of the microbial communities of Chungtaejeon was the largest compared to other teas

• Journal of Environmental Impact Assessment
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• v.27 no.6
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• pp.595-603
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• 2018

This study was conducted to understand the growth of attached microbial community in small and medium streams of Gyeonggi-do and the removal efficiency of fluoride with changes in growth. The sites monitoring were carried out for 12 weeks at the P1 and P2(P1 is the point where the discharge water flows. P2 is the downstream point of about 2 km flow), and investigated the water quality and the biomass analysis of the attached microbial community. The growth of the attached microbial community increased up to the 7th investigation, and it was observed that detachment phenomenon occurred. Influencing factors about growth of the attached microbial community were flow rate, velocity, and organic material(T-N & T-P). Meanwhile, fluoride content of attached microbial community also tended to increase until the 7th investigation, and decrease from the 8th. It is assumed that fluoride content has also be reduced with the detachment phenomenon of the attached microbial community. It is expected that this will contribute to the evaluation and management of the use of attached microbial community as a means of stream management. The application of techniques using the attached microbial community should include basic investigation of factors that may affect the growth of the attached microbial community and replacement of the attachment plate according to the time of removal.

• Korean Journal of Environmental Biology
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• v.22
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• pp.38-46
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• 2004

Effect of polycyclic aromatic hydrocarbons (PAHs) on the community structure of indigenous microorganisms in Gwangyang Bay sediments was investigated in Mar. & Aug.,2000. Microbial community structure was analyzed using 5'-terminal restriction fragment length polymorphism (T-RFLP) method. Microbial community structure based on T-RFLP method revealed that community differentiated by sampling period except station 1 located near the stream discharge site from Yeosu Industrial Complex. Even, microbial diversity was higher at stations showed relatively high concentrations of PAHs. The microbial community structure was severely changed during the enrichment culture with 1,000 ppm of PAHs mixture. It was also different between cultivated at 8$^{\circ}C$ and 30$^{\circ}C$. The results implied that temperature, poyosity, organic content and etc were more responsible than PAHs on the microbial community structure.

• Journal of Life Science
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• v.33 no.6
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• pp.481-489
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• 2023

The taste and quality of soy sauce, a fermented liquid condiment, is greatly influenced by microbial metabolism during fermentation. To investigate the microbiological characteristics of ganjang during the initial fermentation process, we prepared meju (fermented soybean) blocks fermented with starter cultures and solar salts and analyzed the microbial community quantitively using 16S rRNA gene profiling from ganjang that had been fermented over a five-week period. The ganjang samples were collected and analyzed after soaking for week one (1W), three (3W), and five (5W) weeks. We found that Halomonadaceae was significantly higher in the 1W group (89.83%) than the 3W and 5W groups (14.46%, and 13.78%, respectively). At a species level, Chromohalobacter beijerinckii and Chromohalobacter canadensis were the dominant species in the 1W group but several taxa such as Bacillus subtilis, Pediococcus acidilactici, and Enterococcus faecalis were more abundant in the 3W and 5W groups. Pearson correlation analysis of the relative abundance of the bacteria showed a negative correlation between Chromohalobacter and two bacterial genera Bacillus and Enterococcus. Beta-diversity showed a statistical distinction between the 1W and the 3W and 5W groups, while no significance was evident between the 3W and 5W groups. Linear discriminant effect size analysis was used to identify biomarkers and significant differences in the relative abundance of several halophilic bacteria, Bacillus sp. and lactic acid bacteria at 1W, 3W, and 5W, recpectively, which indicates the important role of the bacterial community at these time points.

• Proceedings of the Korea Water Resources Association Conference
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• 2009.05a
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• pp.2132-2137
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• 2009

갈대(Phragmites communis Trin.)란 염분이 있는 곳에서 자라는 염생식물로서 우리나라 전역에 분포하고 있다. 지난 50년 동안 우리나라의 여러 습지에 걸쳐서 갈대는 우점종으로 자라왔고, 육지와 수중서식지에서 갈대의 확산범위는 증가하고 있다. 갈대의 확산은 다른 습지 식물의 서식지를 파괴하고, 갈대가 번식하면 동 식물들의 번식 자체가 어려울 뿐 아니라 갈대숲에 포식자가 늘어나 살아가기 어려운 환경으로 변하기때문에 갈대를 체계적으로 관리할 수 있는 방안이 마련되어야 한다. 본 연구는 우점종이 다른 두 습지에서 갈대군집의 성장률을 관찰하고, 토양의 화학적 분석과 식물의 생리적 분석을 통해 갈대군집 성장에 미치는 영양염류의 영향을 규명하였다. 연구 대상지는 한강하구에 위치한 장항습지와 성동습지로서 동일하게 갈대가 분포하며, 장항습지에는 줄 군락이 성동습지에는 새섬매자기 군락이 우점하고 있다. 분석 항목은 이화학적 항목을 비롯하여 용존유기탄소(DOC, dissolved organic carbon), 체외미생물효소활성도(Extracellular enzyme activities), 암모니아성 질소($NH_4^+$), 질산성 질소($NO_3^-$)을 분석하였다. 실험결과, 두 습지 갈대의 성장은 7월부터 9월에 증가하였고 성동습지의 토양성분이 점토질로 형성되어 높은 수분함량과 유기물함량을 유지하고 있기 때문에 갈대의 밀도가 높고 성장률이 활발한 것으로 나타났다. 또한 미생물활성과 환경인자간 양의 상관관계를 보아 환경인자들이 미생물 활성을 자극하고 미생물들은 식물의 성장을 촉진하여 영향을 주며, 반면 식물 뿌리는 enzyme을 생성하는 미생물에게 C 삼출물을 공급해 enzyme 활성에 영향을 미칠 것으로 사료된다.