• 한국미생물·생명공학회지
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• 제44권2호
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• pp.171-179
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• 2016

최근 빙하의 융해로 인해 빙하 해안지역에 다양한 토양 미생물과 초목들이 드러나고있다. 본 연구에서는 북극 스발바르 군도 중앙로벤 빙하 해안 지역으로부터 Ion Torrent Personal Genome Machine(PGM)을 활용한 메타지놈 분석을 통해 세균(bacteria), 고균(archaea), 및 진핵생물(eukaryotes)를 포함하는 다양한 미생물 군집을 분석하였다. 연구에 사용된 토양시료는 빙하 후퇴에 따른 토양의 노출 시기에 따라 2개 지역(ML4 및 ML7)으로부터 수집하였다. ML4 및 ML7 시료의 메타지놈 염기서열을 기반으로 총 2,798,108 및 1,691,859 reads가 각각 미생물 군집 분석에 활용되었다. Domain (계) 수준에서 미생물 군집의 상대 빈도를 분석한 결과 2개 시료 모두 세균(86−87%)이 높은 반면 고균과 진핵생물은 1% 미만으로 존재하는 것으로 나타났다. 또한 약 12%의 염기서열은 기존에 분류되지 않은(unclassified) 서열로 분석되었다. 세균의 경우 Proteobacteria(40.3% for ML4 and 43.3% for ML7)와 Actinobacteria(22.9% and 24.9%)가 우점하는 것으로 분석되었다. 고균의 경우에는 Euryarchaeota(84.4% and 81.1%) 및 Crenarchaeota(10.6% and 13.1%), 그리고 진핵생물의 경우에는 Ascomycota(33.8% and 45.0%)가 우점하는 것으로 분석되었다. 본 연구를 통해 Ion Torrent PGM 플랫폼을 활용한 메타지놈 분석이 북극의 중앙로벤 빙하 해안 지역의 전체 미생물 군집 구조를 파악하는데 충분히 적용될 수 있을 것으로 사료된다.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.317-321
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• 2005

L- arabinose residues are widely distributed in plant cell walls, where they are present in polymers such as arabinans, arabinoxylans, arabinogalactans and arabinogalactan proteins. L-arabinose suppress intestinal sucrase and decrease the adsorption of sugar in the small intestine, consequently, weight loss and fatness prevent. Now, xylose be used replacement sugar and arabinose be utilized fatness prevent of our time. Various Agricultural surplus like com fiber, contain $20\;{\sim}\;40%$ of hemicellulose. Corn fiber from Agricultural Renewable Biomass was chosen the best suitable material for arabinose production. In this work, we searched about for L-arabinose gene in compost, metagenome pool and indonesian soil. So, the B1029 TS2-8 of L-arabinase gene in compost was selected by YNB media(5% yeast nitrogen base, 5% arabinogalactan). After enzyme reaction with corn fiver, B1029 TS2-8 produced 2.15 g/L of L-arabonose.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제16권2호
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• pp.71-79
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• 2013

The human-associated microbiota is diverse, varies between individuals and body sites, and is important in human health. Microbes in human body play an essential role in immunity, health, and disease. The human microbiome has been studies using the advances of next-generation sequencing and its metagenomic applications. This has allowed investigation of the microbial composition in the human body, and identification of the functional genes expressed by this microbial community. The gut microbes have been found to be the most diverse and constitute the densest cell number in the human microbiota; thus, it has been studied more than other sites. Early results have indicated that the imbalances in gut microbiota are related to numerous disorders, such as inflammatory bowel disease, colorectal cancer, diabetes, and atopy. Clinical therapy involving modulating of the microbiota, such as fecal transplantation, has been applied, and its effects investigated in some diseases. Human microbiome studies form part of human genome projects, and understanding gleaned from studies increase the possibility of various applications including personalized medicine.

• BMB Reports
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• 제45권1호
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• pp.14-19
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• 2012

A feruloyl esterase encoding gene (designated fae6), derived from a leachate metagenomic library, was cloned and the nucleotide sequence of the insert DNA determined. Translational analysis revealed that fae6 consists of a 515 amino acid poly-peptide, encoding a 55 kDa pre-protein. The Fae6 primary structure contained the G-E-S-A-G sequence, which corresponds well with a typical catalytic serine sequence motif (G-x-S-x-G). The fae6 gene was successfully over-expressed in E. coli and the recombinant protein was purified to 8.4 fold enrichment with 17% recovery. The $K_M$ data showed Fae6 has a high affinity to methyl sinapate while thermostability data indicated that fae6 was thermolabile with a half life ($T_{1/2}$) < 30 min at $50^{\circ}C$. High affinity for Fae6 against methyl sinapate, methyl ferulate and ethyl ferulate suggest that the enzyme can be useful in hydrolyzing ferulated polysaccharides in a biorefinery process.

• Journal of Microbiology and Biotechnology
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• 제17권4호
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• pp.668-672
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• 2007

A microcosmal experiment using a metagenomic technique was designed to assess the effect of BTEX (benzene, toluene, ethylbenzene, and xylenes) on an indigenous bacterial community in a Daejeon forest soil. A compositional shift of bacterial groups in an artificial BTEX-contaminated soil was examined by the 16S rDNA PCR-DGGE method. Phylogenetic analysis of 16S rDNAs in the dominant DGGE bands showed that the number of Actinobacteria and Bacillus populations increased. To confirm these observations, we performed PCR to amplify the 23S rDNA and 16S rDNA against the sample metagenome using Actinobacteria-targeting and Bacilli-specific primer sets, respectively. The result further confirmed that a bacterial community containing Actinobacteria and Bacillus was affected by BTEX.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2007년도 추계학술발표대회
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• pp.262-263
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• 2007

유전체학 (genomics)의 가장 기초적인 기반이 되는 것은 염기서열을 정확하게 결정해 내는 것이다. 많은 진핵생물들 (eukaryotes)은 두개의 상동염색체를 가지며 두개의 염색체의 염기서열에는 차이가 존재한다. 현재의 유전체 염기서열 결정방법으로는 염기변이가 많이 존재할 경우 유전체의 염기서열을 결정하기 어렵다. 특정한 장소에 서식하는 무수히 많은 미생물들의 유전체의 염기서열을 동시에 결정하는 문제도 미생물학에서 중요성을 인정받는 문제이지만, 미생물들간의 염기변이의 정도는 단일개체의 경우보다 복잡하며 염기서열을 효과적으로 결정하기 힘들다. 따라서 염기변이가 많은 생물들과 미생물들 집합의 염기서열을 결정할 수 있는 방법론의 개발이 시급한 실정이다. 본 논문에서는 조립된 다염기변이 유전체및 메타유전체의 염기서열의 정확성을 평가하기 위한 유전체 서열과 시뮬레이션에 기반한 read 들을 생성하는 도구를 개발하는 것을 목표로 한다.

• Genomics & Informatics
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• 제17권1호
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• pp.6.1-6.9
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• 2019

Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial genomes and allowing a more precise quantification of microbiome abundances and function. Microbiome data analysis is challenging because it involves high-dimensional structured multivariate sparse data and because of its compositional nature. In this review we outline some of the procedures that are most commonly used for microbiome analysis and that are implemented in R packages. We place particular emphasis on the compositional structure of microbiome data. We describe the principles of compositional data analysis and distinguish between standard methods and those that fit into compositional data analysis.

• Animal Bioscience
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• 제37권2_spc호
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• pp.346-359
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• 2024

Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.

• 한국미생물·생명공학회지
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• 제46권3호
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• pp.234-243
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• 2018

남극해에는 산업적으로 유용한 신규 효소촉매를 생산하는 미생물들이 들어 있다. 우리는 로스해(Ross Sea)로부터 분리한 여러 저온성 박테리아를 조사하였으며, 그 중에서 지방분해 능력이 뛰어난 Croceibacter atlanticus (No. 40-F12)를 찾았다. Shotgun 클로닝 방법으로 리파아제 유전자(lipCA)를 찾았으며 Escherichia coli 균에서 LipCA 효소를 발현하였다. Spain Arreo metagenome alpha/beta hydrolase를 기준으로 LipCA 상동구조모델을 만들어서 분석한 결과, ${\alpha}/{\beta}$ hydrolase fold, Gly-X-Ser-X-Gly motif, 그리고 lid 구조를 갖고 있기 때문에 전형적인 리파아제 효소임이 밝혀졌다. Ammonium sulfate 침전법과 겔여과 크로마토그래피를 통해서 세포추출액으로부터 LipCA 효소를 순수하게 분리한 후, 최적 온도, pH, 안정성, 기질특이성, 유기용매 안정성 등의 효소특성을 규명하였다. LipCA를 cross-linked enzyme aggregate (CLEA) 방법으로 고정화하고 효소특성을 조사, 비교하였다. 고정화를 통해 온도, pH, 유기용매에 대한 안정성이 증가하였고 기질특이성의 변화는 관찰되지 않았다. $LipCA^{CLEA}$는 원심분리 방법으로 쉽게 회수되었고 4번의 재사용 후에 40% 이상의 활성이 잔재하였다. 이 논문은 C. atlanticus 리파아제의 발현, 특성규명, Cross-linked Enzyme Aggregated 고정화를 바탕으로 안정성을 높여 산업적 활용 가능성을 제시한 최초의 보고이다.

• Journal of Microbiology and Biotechnology
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• 제22권12호
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• pp.1636-1643
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• 2012

Enzymatic pre-bleaching by modification of pulp fibers with xylanases is an attractive approach to reduce the consumption of toxic bleaching chemicals in the paper industry. In this study, an alkaliphilic endoxylanase gene was isolated from metagenomic DNA of a structurally stable thermophilic lignocellulose-degrading microbial consortium using amplification with conserved glycosyl hydrolase family 10 primers and subsequent genome walking. The full-length xylanase showed 78% sequence identity to an endo-${\beta}$-1,4-xylanase of Clostridium phytofermentans and was expressed in a mature form with an N-terminal His6 tag fusion in Escherichia coli. The recombinant xylanase Xyn3F was thermotolerant and alkaliphilic, working optimally at $65-70^{\circ}C$ with an optimal pH at 9-10 and retaining >80% activity at pH 9, $60^{\circ}C$ for 1 h. Xyn3F showed a $V_{max}$ of 2,327 IU/mg and $K_m$ of 3.5 mg/ml on birchwood xylan. Pre-bleaching of industrial eucalyptus pulp with no prior pH adjustment (pH 9) using Xyn3F at 50 IU/g dried pulp led to 4.5-5.1% increase in final pulp brightness and 90.4-102.4% increase in whiteness after a single-step hypochlorite bleaching over the untreated pulp, which allowed at least 20% decrease in hypochlorite consumption to achieve the same final bleaching indices. The alkaliphilic xylanase is promising for application in an environmentally friendly bleaching step of kraft and soda pulps with no requirement for pH adjustment, leading to improved economic feasibility of the process.