• Subject : Microbial Systematics

  • 분자계통학은 염기서열 또는 아미노산서열 정보를 바탕으로 개체나 유전자의 진화적 연관관계를 밝히는 학 문이다. 진화 경로를 밝히는 것은 현존하는 진화의 결과를 바탕으로 과거를 추정하는 과정이다. 한 종의 유전체 에함께유전되는여러개의유전자들조차변이속도가각각다르고, 종마다서로다른변이및진화속도를가지 고있음을고려할때, 진화경로예측을위해서는다양한분석방법을동원하여복잡한계산을수행해야한다. 이 강의에서는 미생물 유전체 정보의 계통적 분석을 위해 최근 주로 사용하고 있는 진화 모델과 계통수 작성방법에 대해 살펴보고자 한다. 각 분석법의 원리와 장단점을 살펴봄으로써, 여러 가지의 가능한 진화경로 중 진실 값에 가까운 계통수를 찾아내는 길을 확인해본다.

Ha-na Yi,

School of Biosystem and Biomedical Science,
Korea University,
Republic of Korea

• Subject : Bacterial Genome Sequencing

  • Min-Gyu Park, Ji-Yeon Kim, and Dong-Woo Lee*

    
    

  • 지난 20년간 DNA염기서열 분석기술이 눈부시게 발전함에 따라 대량의 고급 유전체 정보가 획기적으로 증가 하고 있다. 특히, 원핵생물의 유전체 초안(draft) 및 완성본(completed genomes)정보가 약 125,000개(2017년 11월현재)에육박하고있다. 이로말미암아원핵생물의유전체구성및진화의원리를밝혀내고있으며, 유전체 분석은생물종다양성, 표현형특성검증, 미개척생물학적특성규명, 다른생명체유래의유전자기능예측등다 양한분야에서활용되고있다. 이에본강연에서는세균유전체분석에주로사용되는차세대염기서열분석기술 에대한고찰및해당장비의작동원리를살펴보고자한다. 또한, 원핵생물의유전체연구를위해직접활용할수 있는 유전체 정보처리, 기능 주석화 및 비교 유전체학 연구에 유용한 웹프로그램을 소개하고자 한다.

Dong-Woo Lee,

School of Applied Biosciences,
Kyungpook National University,
Republic of Korea

• Basic Tools for Analyzing Microbiome Data

  • 현대미생물학에서는정보, 통계및전산과관련된도구들이PCR, sequencing과같은전통적인기술로얻어진 데이터를통합, 관리하는유비쿼터스기술이되고있습니다. 2017년현재, 다양한환경에서얻어진microbiome 데이터를해석하는과정은유전체및생태계에공통적인도구를사용하는명령줄환경에서이루어지며, 고성능 의컴퓨팅클러스터에작업을제출하고, 입력및출력파일을관리하며, 이것들을시각화하는과정들로이루어지 고 있습니다. 처음으로 빅데이터를 처리해야하는 미생물학자들은 이것이 프로그래밍 언어를 배우고 습득하는 과정으로오해를하는경우가종종있습니다만, 대부분의경우에는초보적인수준의unix (혹은linus) 환경에대 한 이해와, 미리 준비되어있는 함수나 프로그램의 조합으로 원하는 분석을 실시할 수 있습니다. 대학원에서 공부를 시작한 학생들이 분석을 위한 각종 환경의 샘플을 준비하고 NGS를 실시하여 데이터를 얻 는 Wet-Lab. 과정과 얻어진 microbiome 데이터를 분석하여 기본적인 out-put 혹은 display를 하는 Dry-Lab. 과 정을 실습하고 이해하는 데는 대략 한 학기 정도의 시간이 필요합니다. 제 경험상, 학생들이 Dry-Lab. 과정에 훨 씬시간을소비하는주요한이유는, 다양한생물정보학적분석의도구들이(open source 프로그램, 공식, 제안등 등) 여러갈래의방향으로열려있거나제시되고있기때문에, 필수적으로시행착오를겪을수밖에없기때문입 니다. 본워크샵에서는, microbiome 분석에필요한여러가지도구들의기본개념과간략한결과물을소개하고, 2017는11월현재를기준으로, 일반적인microbiome 분석을위한가장합리적인갈래를제시하고자합니다. 덧 붙여, 기본분석을바탕으로, microbiome 데이터로시도할수있는여러가지확장된분석의개념과결과물도함 께 소개하고자 합니다.

Jae-Ho Shin,

School of Applied Biosciences,
Kyungpook National University,
Republic of Korea

• Subject: Analysis of the Whole Metagenome Shotgun Sequence Data

  • 대용량 염기서열 해독 기술의 발달은 미생물 유전체 연구 분야에 큰 영향과 변화를 가져왔다. 신속한 대용량 염기서열생산과이를지원하는생물정보학적기술개발에따라미생물유전체해독서열및정보량의증가, 분 석 범위와 수준의 확대되었다. 대용량 염기서열 해독은 미생물 유전체 연구를 단일 유전체 연구뿐 아니라, 환경 내 전체 DNA를 해독할 수 있는 수준으로 가능할 수 있게 이끌었고, 이는 배양이 어려운 미생물의 발굴에서부터 현재까지발견하지못하였던유전자들을발굴가능하게하였다. 또한메타유전체염기서열해독은자연계의생 물학적현상들을설명할수있도록하는중요한자료와기회를제공해주고있다. 특정환경내의전미생물유전 체의 해독과 분석은 메타유전체 데이터의 다양성과 복잡성으로 인해 여러가지 연구 접근 방법들이 시도되고 있 으며, 새로운분석기술및생물정보학적도구들이계속적으로개발되고있다. 따라서최근의메타유전체연구를 위한기술동향과함께전메타유전체연구관련분석단계의몇가지실험및결과들을소개하고자한다. 우선, 전 메타유전체염기서열해독을위해환경내미생물DNA의분리, 대용량염기서열생산, 환경또는기주DNA 서열 의처리를통해메타유전체결과에영향을줄수있는요소들을배제하도록한다. 이후, 전메타유전체염기서열 의 분석은 sequencing read 기반의 분석과 조립서열 contig 기반의 분석 방법으로 접근할 수 있다. Sequencing read들을 가지고 여러 가지 생물정보학적 기술에 의해 개발된 도구들을 가지고 군집 구조를 분석하여 환경 내의 미생물의종류를파악할수있으며, read 및contig 서열들을가지고유전자기능예측을수행한다. 이후, 특정유 전자 서열의 비율 분석 및 대사 유전자들을 중심으로 한 대사 경로 분석을 통해 수행 환경 내 미생물의 구성과 역 할들을 파악할 수 있다.

Ju Yeon Song,

Institute of Life Science and Biotechnology,
Yonsei University,
Republic of Korea

• Subject : Transcriptome Analysis Using RNA-Seq

  • Genome-wide analyses 및 high-throughput screening은 genetic model organisms 및 biomedical applications에서매우유용하게사용되어왔다. Bioinformatics tools의빠른개발은오믹스연구를매우활발하 게 성장시키고 있다. RNA-Seq은 전사체에 대한 absolute expression values을 제공해 주기 때문에, RNA-Seq에 의한전사체분석은유전자발현변화, 새로운유전자탐색, 특정조직에서발현된유전자들의splice variants 등 을정량화하는데있어매우유용하여뛰어난resolution 수준에서전사체전반에관한변화에대한이해를가능 케해준다. 본발표는sampling, RNA extraction, library preparation, data analysis에관련된practical guidance 를 제시해 주어 연구자들에게 RNA-Seq에 의한 전사체 분석에 대한 이해를 높여 주고자 한다.

Chang Pyo Hong,

Division of Bioinformatics,
TheragenEtex Bio Institute,
Republic of Korea

• Subject : Introduction of Proteomics Research Trends and Its State-of-the-Art Technology

  • 단백질체학(Proteomics)은 주어진 환경에서 유전체에 의해 발현되는 세포내 모든 단백질들을 총체적으로 연 구하는학문을말합니다. 인간게놈프로젝트가성공적으로마무리되면유전자의정보만으로는모든형질의표 현하기에는 한계가 존재한다는 새로운 화두를 던져주는 계기가 되었습니다. 대부분의 단백질들은 세포질에서 번역된 후 인산화 등의 번역 후 변형(post-translation modification) 과정을 거친 후에 단백질의 활성을 가지게 됩니다. 따라서단백질체학은단백질동정, 외부자극이나세포내상태에따른발현차이, 번역후변형상태및단 백질상호작용등을규명할수있습니다. 최근질량분석기의고도화된성능향상으로인해정확하면서대량으로 단백질체분석이가능하게되었습니다. 단백질체분석에대한이해를돕고다양한분야에서활용이가능하도록, 최신 단백질체 분석 방법 및 분석 사례를 중심으로 소개하고자 합니다.

Dong-Gi Lee,

College of Life Science and Biotechnology,
Yonsei University,
Republic of Korea

• Subject : Microbial Metabolomics

  • 대사체학이란 시스템생물학에 있어서 가장 최근에 주목을 받고 있는 연구분야이며, 1500 Da 이하의 분자량 을가지고있는화합물의통합적분석을일컫는다. 이는타겟물질의범위및분석의정확성에따라표적대사물질 분석, 대사체프로파일링, 메타볼로믹스로구분이된다. 본워크샵은질량분석기반메타볼로믹스의기본적원리 와최근연구동향을포함하고있으며, 다른오믹스분야와의연계를통한시스템생물학적접근방법을제시하고 있다. 이의 예로 미세조류의 대사체학 기반 멀티오믹스기반 기술 및 적용을 다룬다.

Do Yup Lee,

Department of Bio and Fermentation Convergence Technology,
Kookmin University,
Republic of Korea

• Subject : ChIP-seq

  • ChIP-seq (Chromatin ImmunoPrecipitation-sequencing)은 그 방법에 대해서만 설명하자면, 유전자의 발현 이나, 다른 목적으로 DNA와 결합하고 있는 단백질의 DNA상의 위치를 확인할 수 있는 방법이다. 이렇게 DNA와 결합하고 있는 단백질의 위치는 전사인자들이나 다른 크로마틴과 결합하고 있는 단백질들이 유전자 발현에 미 치는영향을설명해줄수있다. 이것은후성유전적조절에매우중요한정보를제공할수있지만, ChIP-seq 데이 터만으로는설명할수없는경우가많다. 더욱자세한정보를얻기위해서RNA-seq 데이터와비교하면서해석을 하며, 전사가 일어나고 있을 때 만들어지는 RNA를 분석하기 위해서 Gro-seq과 Net-seq 데이터가 필요하다. 또 한, 크로마틴과결합하고있는단백질의정확한위치를알기위해서는exo-ChIP-seq 데이터를얻어야하며, 3차 원적인 결합을 알기 위해서는 Hi-C 등이 필요하다. 본 워크샵은 원핵생물과 진핵생물에서 ChIP-seq을 수행하는 방법과 진핵생물의 RNA-seq, Gro-seq, Net-seq, exo-ChIP-seq, Hi-C의 방법 및 이러한 실험방법이 필요한 구체 적인연구내용, 그리고ChIP-seq 데이터와함께이러한데이터에서얻을수있는정보에대한내용으로진행할예 정이다.

Jung-Shin Lee,

Department of Molecular Bioscience,
Kangwon National University,
Republic of Korea

• Subject : nanoString nCounter Analysis System

  • nanoString nCounter Analysis System은 다양한 샘플에서 추출된 genomic DNA, total RNA, Protein을 이용 하여 다양한 유전자는 돌연변이 및 Copy Number Variation, Gene expression 정도를 정량하는 시스템이다. 본시스템은기존의다른실험기법과달리enzyme을이용한증폭과정없이실험이진행되므로enzyme-bias 없는 결과 도출이 가능하며 추출된 핵산의 Quality 및 Purity에 상관 없이 실험 진행이 가능하다. 또한, 나노스트링의 특화 기술은 Barcode Probe를 이용하여 Single tube에서 최대 800개 유전자까지 multiplex가 가능하여 다양한 유전자에 대한 동시 분석이 가능하다는 장점을 갖고 있으며, 매우 Simple 한 실험 과정을통해실험이진행되므로실험자간편차없이재현성이높은결과를도출할수있다. 또한, 기존의아날로 그방식의검출방식을이용하지않고Digital Counting 방식을이용하여정량이되므로정확도및dynamic range 가 넓은 결과 도출이 가능하며 nSolver software를 이용한 매우 간단한 분석 방법을 통해 다양한 데이터 도출이 가능하다 nanoString nCounter Analysis System은 Simple한 실험 방법을 통해 정확한 데이터 구현이 가능하므로 다양 한 샘플 및 Species를 대상으로 다양한 연구가 가능한 시스템이라 할 수 있다.

Sook Lee,

PhileKorea Technology,
Republic of Korea

• Subject : CRISPR-Cas9 Tools for Your Research Application

  • 3세대 유전자가위인 CRISPR/Cas9의 개발로 다양한 생명체의 유전체교정이 전 세계적으로 폭발적으로 연구 되고있다. 크리스퍼유전자가위기술의이해를바탕으로연구자는목표유전자에만상보적인결합이가능하도 록guide RNA를선별적으로디자인할수있다. 따라서연구자가원하는유전자교정을손쉽고빠르게유도할수 있다. 본워크샵을통해연구자는크리스퍼유전자가위기술의핵심원리를이해하고활용법을익혀원하는유전 자교정을 할 수 있을 것이다.

Hyeran Kim,

Department of Biology,
Kangwon National University,
Republic of Korea

• Subject : Microbiome Research: from Products to Data

  • Microbiome research is rapidly transitioning into Data Science. The unprecedented volume of microbiome data being generated pose significant challenges with respect to standards and management strategies, but also bear great new opportunities that can fuel discovery. Computational analysis of microbiome samples involving previously uncultured organisms, is currently advancing our understanding of the structure and function of entire microbial communities and expanding our knowledge of genetic and functional diversity of individual micro-organisms. I will describe some of our computational approaches and will emphasize the value of data processing integration in enabling the exploration of large metagenomic datasets and the discovery of novelty. I will discuss current approaches and success stories for the discovery of novel phylogenetic lineages as well as the exploration of the viral dark matter.

Nikos C. Kyrpides,

Prokaryotic Super Program, DOE Joint Genome Institute,
2800 Mitchell Drive, Walnut Creek, CA 94598, USA

• Subject : Microbiome, Host Genetics, and Chronic Diseases

  • Recently, there were dramatically increased interests on human microbiome research related to metabolic diseases including obesity worldwide. Hence, we have determined the effects of microbiome and determined the genes and pathways of human subjects including twins and animal models. The specific aims of this presentation are 1) to determine and characterize the composition of human microbiome as related to clinical biomarkers, 2) to investigate the effects of host genetics and gut microbiota on metabolic syndrome, 3) to investigate the heritability of vagina microbiota and the effect on obesity in women. Our data suggest that specific OTUs and microbial functional genes in the gut and vagina may contain metabolic genes the characteristics of which differ according to host genetic background and/or diet. Our research will help us to understand the association between human microbiome and diseases and to improve human health.

GwangPyo Ko,

Center for Human and Environmental Microbiome,
Graduate School of Public Health,
Seoul National University,
Republic of Korea

• Subject : Functional Genomics Analysis of Fungal Pathogenic Signaling Pathways

  • Human fungal pathogens, including Cryptococcus neoformans, Aspergillus fumigatus, and Candida albicans, cause life-threatening systemic mycoses in humans and yet the signaling networks governing the fungal pathogenicity still remains elusive. Among these pathogens, the basidiomycete human fungal pathogen C. neoformans causes life-threatening meningoencephalitis, which are responsible for more than million infections and 600,000 deaths every year globally. Nevertheless, its treatment option is highly limited mainly due to a lack of complete understanding how the pathogen interacts with the host during infection and disease progression. Although a number of signalling components and pathways involved in the pathogenicity of C. neoformans have been characterized past years, it remains elusive how complex signalling pathways are coordinated and regulated during the whole infection process. Here we tackled this question by performing signature tagged mutagenesis (STM)-based infectivity assay and NanoString-based in vivo transcription profiling of 183 kinases, 178 transcription factors, and 139 phosphatases during the whole infection process of C. neoformans. The comparative STM and in vivo transcription profiling analysis of the infected lungs and brains revealed that C. neoformans employs not only core signalling pathways that are required for both initial and late stage of infections, but also utilizes infection stage specific signalling pathways.

Yong-Sun Bahno,

Department of Biotechnology,
Yonsei University,
Republic of Korea

• Subject : Reprogramming Biological Functionalities for Autonomous Therapeutic Cells

  • Synthetic biology aims to engineer genetically modified biological systems that perform novel functions that do not exist in nature, with reusable, standard interchangeable biological parts. The use of these standard biological parts enables the exploitation of common engineering principles such as standardization, decoupling, and abstraction for synthetic biology. With this engineering framework in place, synthetic biology has the potential to make the construction of novel biological systems a predictable, reliable, systematic process. While the development of most synthetic biological systems remains largely ad hoc, recent efforts to implement an engineering framework in synthetic biology have provided long-awaited evidences that engineering principles can facilitate the construction of novel biological systems. Synthetic biology has so far demonstrated that its framework can be applied to a wide range of areas such as energy, environment, and health care. In this talk, our recent efforts to develop microbes with programmable behaviors will be presented. In particular, an emphasis will be placed on our recent development of auto-regulatory genetic circuits for autonomous therapeutic cells. http://synCTI.org/

Matthew W. Chang,

NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), and Department of Biochemistry, Yong Loo Lin,
School of Medicine, National University of Singapore,
Singapore

• Subject : Bovine Gut Microbiome

  • In beef cattle, male castration in young period results in later onset of obese phenotype and increased meat tenderness of the carcass. However, the knowledge of the effect(s) of male castration, followed by hypogonadism, on host metabolism is scarce. In the current study, metagenomics and metabolomics approaches were used to evaluate the intestinal microbiota and host metabolism of male, castrated male (CtM), and female Korean brown cattle (n = 30), the Hanwoo, and Holstein Friesian cattle (n = 15). In postpubescent CtM cattle, the serum testosterone level was low, and the animals possessed distinct rectal microbial and serum metabolic profiles, with significantly higher levels of serum branched-chain amino acids (BCAAs) than age-matched male controls. Microbial and metabolic profiling of the different intestinal compartments of adult CtM Hanwoo (n = 10) revealed a strong positive correlation of the serum BCAA levels and the presence of bacteria representing two unclassified genera from the family Peptostreptococcaceae, and the genera Butyrivibrio, Acetitomaculum, and Atopobium, in the small intestine. Fresh striploin meat from CtM carcasses (n = 5 for each) was characterized by higher intramuscular fat accumulation, with significantly higher levels of several amino acids (including BCAAs) and ketone body (i.e., β-hydroxybutyrate) than male carcasses. Thus, the data suggest a link between male castration, alterations of the intestinal microbiota, and systemic amino acid metabolism in ruminants.

Jin-Woo Bae,

Department of Biology,
Kyung Hee University,
Republic of Korea

• Subject : Resource Allocation during Bacterial Adaptive Laboratory Evolution

  • We constructed a genome-reduced strain harboring 3,457 genes in total. It showed impaired growth in minimal media that is hard to decipher based on the genes removed. We thus deployed adaptive laboratory evolution (ALE) to re-optimize growth performance of the genome-reduced strain. Here, we showed cellular resources are reallocated during the ALE using multi-omic approaches. Importantly, the genome-reduced strain served as a better host for the production of proteins of interest encoded by highly transcribing genes. Re-optimization using ALE reveals that failure of prediction may not be associated with understanding individual gene products but rather result from insufficient understanding of the genome-reduced strain’s systems biology.

Byung-Kwan Cho,

Department of Biological Sciences,
Korea Advanced Institute of Science and Technology (KAIST),
Republic of Korea

• Subject : Plant Root Microbiome from Sequencing to Functional Research

  • Plants harbor abundant and diverse bacterial microbiota. Culture-independent 16S rRNA gene profiling revealed distinctive bacterial communities associated with Arabidopsis roots and leaves. The availability of comprehensive pure cultures of root- and leaf-derived bacteria is critical to deeply understand the colonization ability and organ specificity of Arabidopsis-associated bacteria in a bacterial community context. We established Arabidopsis root- and leaf-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detected by previous culture-independent community sequencing. We found an extensive species intersection between the leaf and root microbiotas. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we illustrated that the isolates form bacterial communities resembling natural microbiotas on their cognate host organs, and root- and leaf-derived bacteria have specific roles in the microbiota establishment of their original niches. The comprehensive bacteria culture collections and high quality genomes together with the remarkable reproducibility of the gnotobiotic reconstitution system enable future studies on bacterial community establishment and functions under laboratory conditions.

Byung-Kwan Cho,

State Key Laboratory of Plant Genomics, Centre of Excellence for Plant and Microbial Sciences (CEPAMS),
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing 100101,
P. R. China

• Subject : Reference Genome Analysis of Yeast Species in the Microbiome of Fermented Foods

  • Genomic studies of the microbial species involved in traditional food fermentation worldwide have gained increased attention due to their great biotechnological potential and implication on human health. From Nuruk samples for brewing a traditional Korean rice wine, collected at various provinces in Korea, four yeast isolates were selected for reference genome analysis based on their abundance, saccharification ability, and aromatic flavor. Whole genome sequencing of four amylolytic yeast isolates, including Saccharomycopsis fibuligera, KPH12 (haploid) and KJJ81 (diploid), Hyphopichia burtonii KJS14, and Hyphopichia pseudoburtonii KJJ43, were carried out using multiple sequencing technologies, such as long-read Illumina TruSeq, PacBio, and BioNano optical maps. Belonging to ascomycete fungus, all of them are dimorphic yeast found in indigenous food fermentation using rice in Asia and also reported as chalk molds on dark bread in Europe. Notably, all of them showed higher osmotolerance compared to the traditional yeast Saccharomyces cerevisiae. Our comparative genomics analysis, based on the completely assembled S. fibuligera genomes from telomere to telomere, revealed the unique genome structure and evolution of S. fibuligera and its interspecies hybrid. The S. fibuligera genome with high-quality annotation establishes an important foundation for functional inference of S. fibuligera, and it will serve as a reference genome to elucidate biological peculiarities specific to this yeast and its relative lineage. The gene inventory facilitates the discovery of new genes, such as cellulose degradation and aroma biosynthesis, applicable to the production of novel valuable enzymes and chemicals. Moreover, the ABC transporter domain was shown to be noticeably abundant in the proteomes of H. burtonii with the extreme halotolerence. Identification of yeast diversity with reference genome information will be useful for understanding the microbiota that participate in fermentation with defined function of a specific yeast species. This information will be applicable to the development of the improved starter strains tailored for the production of fermented foods with enhanced function and to the implementation of improved industrial processes, such as simultaneous saccharification/fermentation processes.

Hyun Ah Kang,

Dept. of Life Science,
Chung-Ang University,
Republic of Korea

• Subject : Comparative Genomics of Worldwide Fusarium fujikuroi Isolates
  • Sung-Hwan Yun1* and Bettina Tudzynski
  • Fusarium fujikuroi causes bakanae disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for production of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Here, we provide genome sequences of eight F. fujikuroi isolates from distant geographic regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the number and expression of secondary metabolite gene clusters. Whilst most of the isolates caused the typical bakanae symptoms, one isolate, B14 from Korea, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amounts of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three additional polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Analysis of additional field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.

Sung-Hwan Yun,

Department of Medical Biotechnology, , Republic of Korea,
Soonchunhyang University,
Republic of Korea

• Subject : Genomic and Metabolic Features of Leuconostoc mesenteroides and Weissella koreensis during Kimchi Fermentation

  • Byung Hee Chun, Kyung Hyun Kim, Hye Hee Jeon, Sang Eun Jung, and Che Ok Jeon*

  • Heterofermentative lactic acid bacteria (LAB) such as Leuconostoc mesenteroides and Weissella koreensis have been used as kimchi starters to produce kimchi with uniform quality and good organoleptic properties. To investigate genomic Insights into heterofermentative LAB and their comprehensive characteristics, we performed the pan-genome analysis using whole genome sequences of sixteen Leuconostoc (Leu.) mesenteroides strains available in GenBank database–– average nucleotide identity values also supported that all they belong to Leu. mesenteroides. The pan-genome of the sixteen Leu. mesenteroides strains was found to contain 3170 genes and 867 core genes. A phylogenetic tree was constructed using all core genes to investigate their phylogenetic relationships, which were a little different from the phylogenetic relationships based on 16S rRNA gene or house-keeping gene sequences and they could be grouped into four subspecies. For the analysis of functional capabilities of Leu. mesenteroides, all protein sequences were assigned into respective COG categories. The COG analysis showed that Leu. mesenteroides species have high fraction for transport and metabolism of carbohydrates and amino acids, which is similar with other Leuconostoc species. To investigate metabolic capability of Leu. mesenteroides, all functional genes of sixteen genomes were mapped onto the KEGG pathways. As the results, genes associated with carbohydrate and amino acid metabolism and PTS systems related to sugar transports were abundant, suggesting that Leu. mesenteroides was evolved to adapt to environments with various carbon sources like kimchi fermentation conditions. In addition, we will discuss the genomic and metabolic features of W. koreensis during kimchi fermentation.

Che Ok Jeon,

Department of Life Science,
Chung-Ang University,
Republic of Korea