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Integrating genomics into the taxonomy and systematics of the <i>Bacteria</i> and <i>Archaea</i>
Chun, Jongsik,Rainey, Fred A. International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.2
<P>The polyphasic approach used today in the taxonomy and systematics of the <I>Bacteria</I> and <I>Archaea</I> includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the <I>Bacteria</I> and <I>Archaea</I> coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of <I>International Journal of Systematic and Evolutionary Microbiology</I> contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.</P>
Chun, Jeesun,Bae, Jin-Woo,Cha, Chang-Jun,Cho, Jang-Cheon,Chun, Jongsik,Im, Wan-Taek,Jeon, Che Ok,Joh, Kiseong,Kim, Seung Bum,Seong, Chi Nam,Yoon, Jung-Hoon,Jahng, Kwang Yeop The National Institute of Biological Resources 2015 Journal of species research Vol.4 No.2
As a result of the research project 'Survey and excavation of Korean indigenous species' to secure unrecorded species in Korea, a total of 14 unreported bacterial strains assigned to the phyla Deinococcus-Thermus and Bacteroidetes were isolated from various environmental habitats all around Korea. On the basis of 16S rRNA gene sequence similarity and affiliation to the clade with the closest species, it was concluded that the isolates represent deep groups of the phyla Deinococcus-Thermus and Bacteroidetes. There have been no records about these 14 unreported species in Korea; therefore 2 species of 2 genera in the class Deinococci within the phylum Deinococcus-Thermus, and 11 species of 9 genera in the class Flavobacteriia and one species in one genus in the class Sphigobacteriia within the phylum Bacteroidetes are described as unreported species found in Korea. Gram staining reaction, morphological and other biochemical characteristics are described in the species description section.
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Chun, Jongsik,Oren, Aharon,Ventosa, Antonio,Christensen, Henrik,Arahal, David Ruiz,da Costa, Milton S.,Rooney, Alejandro P.,Yi, Hana,Xu, Xue-Wei,De Meyer, Sofie,Trujillo, Martha E. Microbiology Society 2018 International journal of systematic and evolutiona Vol.68 No.1
Technologies and concepts of human microbiome
천종식 ( Jongsik Chun ) 대한간학회 2016 간학회 싱글토픽 심포지움 Vol.2016 No.2
Human body is a habitat for a large number of microorganisms, called microbiome. Microbiome has been recognized as a key factor in understanding human health and diseases. Bacteria are a major component of most of human body including gut. The study of human microbiome has been accelerated by the invention of next generation sequencing and bioinformatics. Application of the concept and techniques used in microbial ecology to microbiome allows us to understand the role and effects of microbiome, especially gut microbiome to human health and diseases. In this presentation, the principles of human microbiome and related methodology will be explained.
Jeesun Chun,Jin-Woo Bae,CHANG-JUN CHA,조장천,JONGSIK CHUN,임완택,Che Ok Jeon,KISEONG JOH,김승범,성치남,Jung-Hoon Yoon,Kwang-Yeop Jahng 국립생물자원관 2015 Journal of species research Vol.4 No.2
As a result of the research project ‘Survey and excavation of Korean indigenous species’ to secure unrecorded species in Korea, a total of 14 unreported bacterial strains assigned to the phyla Deinococcus- Thermus and Bacteroidetes were isolated from various environmental habitats all around Korea. On the basis of 16S rRNA gene sequence similarity and affiliation to the clade with the closest species, it was concluded that the isolates represent deep groups of the phyla Deinococcus-Thermus and Bacteroidetes. There have been no records about these 14 unreported species in Korea; therefore 2 species of 2 genera in the class Deinococci within the phylum Deinococcus-Thermus, and 11 species of 9 genera in the class Flavobacteriia and one species in one genus in the class Sphigobacteriia within the phylum Bacteroidetes are described as unreported species found in Korea. Gram staining reaction, morphological and other biochemical characteristics are described in the species description section.
Lee, Jongsik,Chun, Jaeyoul Architectural Institute of Japan 2009 JOURNAL OF ASIAN ARCHITECTURE AND BUILDING ENGINEE Vol.8 No.1
<P>Although the selection of a construction method for each type of work is an important factor in determining the quality of a building, the construction duration, costs, and methods are currently being selected according to the subjective judgment of the person in charge, without sufficient consideration of the characteristics of the work type. As a response to this issue, this study proposes a process model to support decision making when selecting the most suitable construction method for major types of construction work. The study used the risk response level model, which connects the conditions of the order and the site, the constructability of the type of work within the site, a review of the economic efficiency of the work site, the forced-decision method, and binary weighting analysis in the construction planning phase. As a result of the application of this model to the construction method selection process for the construction of soil-retaining walls, the factors to be preferably considered in the field cases were analyzed in the order of the environmental, ground, design, construction, structural, and site conditions. Further, the risk response level of each construction method was calculated via risk response level analysis, subject to four applicable construction methods.</P>
Yi, Hana,Chun, Jongsik International Union of Microbiological Societies 2015 International journal of systematic and evolutiona Vol.65 No.2
<P>Two species of the genus <I>Neisseria</I>, namely <I>Neisseria weaveri</I> Andersen <I>et al.</I> 1993 and <I>Neisseria weaveri</I> Holmes <I>et al.</I> 1993, were simultaneously proposed and described in the same volume of <I>International Journal of Systematic Bacteriology</I>, and have been maintained as heterotypic homonyms. However, the identical 16S rRNA gene sequence and high (99.1 %) average nucleotide identity (ANI) between the genome sequences of the two type strains implied that these two taxa should be united as a single genomic species. To clarify their taxonomic status, phenotypic properties including enzymic activities and substrate-utilization profiles were investigated. The results demonstrated that the two taxa have no pronounced differences and should constitute a single species. Therefore, the reclassification of <I>N. weaveri</I> Andersen <I>et al.</I> 1993 as a later heterotypic synonym of <I>N. weaveri</I> Holmes <I>et al.</I> 1993 is proposed.</P>