• The Plant Pathology Journal
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• 제21권2호
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• pp.93-98
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• 2005

Molecular ecological studies of microbial communities revealed that only tiny fraction of total microorganisms in nature have been identified and characterized, because the majority of them have not been cultivated. A concept, metagenome, represents the total microbial genome in natural ecosystem consisting of genomes from both culturable microorganisms and viable but non-culturable bacteria. The construction and screening of metagenomic libraries in culturable bacteria constitute a valuable resource for obtaining novel microbial genes and products. Several novel enzymes and antibiotics have been identified from the metagenomic approaches in many different microbial communities. Phenotypic analysis of the introduced unknown genes in culturable bacteria could be an important way for functional genomics of unculturable bacteria. However, estimation of the number of clones required to uncover the microbial diversity from various environments has been almost impossible due to the enormous microbial diversity and various microbial population structure. Massive construction of metagenomic libraries and development of high throughput screening technology should be necessary to obtain valuable microbial resources. This paper presents the recent progress in metagenomic studies including our results and potential of metagenomics in plant pathology and agriculture.

• Journal of Microbiology and Biotechnology
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• 제20권11호
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• pp.1592-1596
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• 2010

To verify the dominance of microorganisms in wastewater biological treatment, PCR-DGGE (denaturing gradient gel electrophoresis) was performed as a supplementary support method for screening of the dominant microorganisms from activated sludge. Results suggest that the dominant microorganisms in activated sludge are primarily responsible for strengthening its effectiveness as a biological treatment system, followed by the non-main dominant microorganisms, whereas the non-dominant microorganisms showed no effects. The degree of microbial abundance present on the profile of PCR-DGGE was in line with the treatment efficiency of augmented activated sludge with isolated cultures, suggesting that PCR-DGGE can be used as an effective supplementary method for verifying culturable dominant microorganisms in activated sludge of coking wastewater.

• 식품과학과 산업
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• 제50권1호
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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.

• 한국산학기술학회논문지
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• 제16권1호
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• pp.868-876
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• 2015

실내 공기 중 부유세균은 실내공기오염을 유발하고 재실자의 건강상 위해를 초래할 수 있다. 본 연구는 다중이용시설을 대상으로 주요목적으로 사용되는 실내에서 부유세균의 농도와 세균의 종류를 동정하고 실내공기오염물질 중 부유세균에 대한 기초정보 제공을 목적으로 한다. 노인시설 7개소 (노인요양시설, 노인전문병원, 복지관 포함), 대규모점포 4개소, 대학병원 4개소, 어린이집 7개소 (유치원, 어린이집, 보육원 포함), 지하역사 4개소 및 버스터미널 4개소 등 총 30개소 120개 지점에서 총부유세균의 농도를 측정 분석하고 세균의 종류를 동정하였다. 모든 시설군에서 측정된 실내 부유세균의 농도는 유지기준 $800CFU/m^3$이하 이었으나, I/O비가 1.09-2.36으로 실내의 총부유세균의 농도가 실외에 비해 높았고, 어린이집, 대학병원, 노인시설에서 동정된 세균의 종류별 높은 검출빈도 보였다. 국내 다중이용시설의 주요목적에 따른 실내 부유세균에 대한 지속적 관찰이 필요하며, 특히 어린이집, 대학병원, 노인시설 등에 대한 관심이 요구되고, 추후 배양 가능한 세균 뿐 아니라 알레르겐 등을 포함한 미생물학적 실내오염물질에 대한 추가 연구가 필요할 것으로 사료된다.

• 한국미생물·생명공학회지
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• 제43권2호
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• pp.142-149
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• 2015

바이오에어로졸은 0.02-100 μm 입자로, 자연 및 인위적 환경 또는 사람의 활동에 의해 발생된다. 바이오에어로졸은 바이러스, 세균, 곰팡이, 원생생물, 곰팡이 포자, 미생물 독소, 꽃가루, 동식물 기원의 물질, 타액 또는 글루칸 등으로 구성되며, 인간과 동물에게 호흡기 등의 질환을 유발한다. 본 연구에서는 농업, 축산, 하수처리장, 해변 및 청청지역의 바이오에어로졸 시료에서 분리한 배양성 미생물을 동정 및 계통분석을 수행한 결과, 우점 및 종의 구성 등 환경 유형 별 차이가 분석되었다. 한편 모든 시료에서 31 분리주가 Bacillus cereus로 동정되었고, 실내 양계장에서 Acinetobacter baumannii가 분리되었다. 또한 농업, 축산 및 해변에서 분리한 미생물 중 Domibacillus속, Chryceobacterium속, Nocardioides속 및 Comamonadaceae과에 속하는 새로운 종 또는 속이 분리되었다.

• Asian Journal of Atmospheric Environment
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• 제5권3호
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• pp.172-180
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• 2011

The transfer of microorganisms is important process for ecosystems. Microorganisms in dryland can transport itself to wetland through atmospheric diffusion, but only few papers reported about the atmospheric bioaerosol present over dryland. We carried out the direct sampling using a tethered balloon over Dunhuang City, China's northwestern dryland. Bioaerosols were collected using a tethered balloon with a bioaerosol collector at 820 m above the ground (1,960 m above the sea level) around noon on August 17, 2007. The bioaerosols were cultured after the collection at Dunhuang Meteorological observatory. Two strains of molds were isolated using the Nutrient agar medium. About 400-bp 18S rRNA partial sequences were amplified by PCR and determined afterwards. The results of a homology search by 18S rRNA sequences of isolates in DNA databases (GenBank, DDBJ, and EMBL) and an observation of the form revealed that two bioaerosols in the convective mixed layer over Dunhuang City were Cladosporium sp. and Aspergillus sp.

• Genomics & Informatics
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• 제11권3호
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• pp.114-120
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• 2013

The microbial diversity in soil ecosystems is higher than in any other microbial ecosystem. The majority of soil microorganisms has not been characterized, because the dominant members have not been readily culturable on standard cultivation media; therefore, the soil ecosystem is a great reservoir for the discovery of novel microbial enzymes and bioactivities. The soil metagenome, the collective microbial genome, could be cloned and sequenced directly from soils to search for novel microbial resources. This review summarizes the microbial diversity in soils and the efforts to search for microbial resources from the soil metagenome, with more emphasis on the potential of bioprospecting metagenomics and recent discoveries.

• Asian-Australasian Journal of Animal Sciences
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• 제12권1호
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• pp.77-83
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• 1999

Molecular biological techniques that recently developed, have made it possible to realize some of new attempts in the research field of rumen microbiology. Those are 1) cloning of genes from rumen microorganisms mainly in E. coli, 2) transformation of rumen bacteria and 3) ecological analysis with nonculturing methods. Most of the cloned genes are for polysaccharidase enzymes such as endoglucanase, xylanase, amylase, chitinase and others, and the cloning rendered gene structural analyses by sequencing and also characterization of the translated products through easier purification. Electrotransformation of Butyrivibrio fibrisolvens and Prevotella ruminicola have been made toward the direction for obtaining more fibrolytic, acid-tolerant, depoisoning or essential amino acids-producing rumen bacterium. These primarily required stable and efficient gene transfer systems. Some vectors, constructed from native plasmids of rumen bacteria, are now available for successful gene introduction and expression in those rumen bacterial species. Probing and PCR-based methodologies have also been developed for detecting specific bacterial species and even strains. These are much due to accumulation of rRNA gene sequences of rumen microbes in databases. Although optimized analytical conditions are essential to reliable and reproducible estimation of the targeted microbes, the methods permit long term storage of frozen samples, providing us ease in analytical work as compared with a traditional method based on culturing. Moreover, the methods seem to be promissing for obtaining taxonomic and evolutionary information on all the rumen microbes, whether they are culturable or not.

• Tuberculosis and Respiratory Diseases
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• 제84권1호
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• pp.1-12
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• 2021

Mycobacterium tuberculosis has infected more than two billion individuals worldwide, of whom 5%-10% have clinically active disease and 90%-95% remain in the latent stage with a reservoir of viable bacteria in the macrophages for extended periods of time. The tubercle bacilli at this stage are usually called dormant, non-viable, and/or non-culturable microorganisms. The patients with latent bacilli will not have clinical pictures and are not infectious. The infections in about 2%-23% of the patients with latent status become reactivated for various reasons such as cancer, human immunodeficiency virus infection, diabetes, and/or aging. Many studies have examined the mechanisms involved in the latent state of Mycobacterium and showed that latency modified the expression of many genes. Therefore, several mechanisms will change in this bacterium. Hence, this study aimed to briefly examine the genes involved in the latent state as well as the changes that are caused by Mycobacterium tuberculosis. The study also evaluated the relationship between the functions of these genes.

• Ocean and Polar Research
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• 제27권2호
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.