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Byung Kwon Kim 4 Articles
PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences
Jeongsu Oh , Byung Kwon Kim , Wan-Sup Cho , Soon Gyu Hong , Kyung Mo Kim
J. Microbiol. 2012;50(5):766-769.   Published online November 4, 2012
DOI: https://doi.org/10.1007/s12275-012-2494-6
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  • 22 Crossref
AbstractAbstract PDF
The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct lowquality sequences. We have developed a program called Pyro-Trimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.

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  • Linking biogeochemical signatures to archaeal community structure at active methane seeps in the Tatar trough, far eastern Russia
    Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Helge Niemann, Carme Huguet, Young-Keun Jin, Hirotsugu Minami, Akihiro Hachikubo, Kyung-Hoon Shin
    Marine Chemistry.2026; : 104677.     CrossRef
  • Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
    Bilal Wajid, Faria Anwar, Imran Wajid, Haseeb Nisar, Sharoze Meraj, Ali Zafar, Mustafa Kamal Al-Shawaqfeh, Ali Riza Ekti, Asia Khatoon, Jan S. Suchodolski
    Functional & Integrative Genomics.2022; 22(1): 3.     CrossRef
  • Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions
    Hyun-Ju Noh, Yung Mi Lee, Chae Haeng Park, Hong Kum Lee, Jang-Cheon Cho, Soon Gyu Hong
    Frontiers in Microbiology.2020;[Epub]     CrossRef
  • DNA Sequencing Technologies
    Ka-Chun Wong, Jiao Zhang, Shankai Yan, Xiangtao Li, Qiuzhen Lin, Sam Kwong, Cheng Liang
    ACM Computing Surveys.2020; 52(5): 1.     CrossRef
  • Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
    Yung Mi Lee, Kyuin Hwang, Jae Il Lee, Mincheol Kim, Chung Yeon Hwang, Hyun-Ju Noh, Hakkyum Choi, Hong Kum Lee, Jongsik Chun, Soon Gyu Hong, Seung Chul Shin
    Frontiers in Microbiology.2018;[Epub]     CrossRef
  • Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea
    Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, Kyung-Hoon Shin
    Biogeosciences.2018; 15(24): 7419.     CrossRef
  • Niche specialization of bacteria in permanently ice‐covered lakes of the McMurdo Dry Valleys, Antarctica
    Miye Kwon, Mincheol Kim, Cristina Takacs‐Vesbach, Jaejin Lee, Soon Gyu Hong, Sang Jong Kim, John C Priscu, Ok‐Sun Kim
    Environmental Microbiology.2017; 19(6): 2258.     CrossRef
  • Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents
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    BMC Evolutionary Biology.2017;[Epub]     CrossRef
  • Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment
    Yung Mi Lee, Kyung Hee Cho, Kyuin Hwang, Eun Hye Kim, Mincheol Kim, Soon Gyu Hong, Hong Kum Lee
    The Korean Journal of Microbiology.2016; 52(1): 49.     CrossRef
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    Hyun G. Kong, Byung K. Kim, Geun C. Song, Soohyun Lee, Choong-Min Ryu
    Frontiers in Microbiology.2016;[Epub]     CrossRef
  • CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment
    Jeongsu Oh, Chi-Hwan Choi, Min-Kyu Park, Byung Kwon Kim, Kyuin Hwang, Sang-Heon Lee, Soon Gyu Hong, Arshan Nasir, Wan-Sup Cho, Kyung Mo Kim, Christophe Antoniewski
    PLOS ONE.2016; 11(3): e0151064.     CrossRef
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    Hye Young Kwon, Ji Young Jung, Ok-Sun Kim, Dominique Laffly, Hyoun Soo Lim, Yoo Kyung Lee
    Journal of Ecology and Environment.2015; 38(4): 461.     CrossRef
  • Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform
    Yoon-Seong Jeon, Sang-Cheol Park, Jeongmin Lim, Jongsik Chun, Bong-Soo Kim
    Journal of Microbiology.2015; 53(1): 60.     CrossRef
  • Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica
    Mincheol Kim, Ahnna Cho, Hyoun Soo Lim, Soon Gyu Hong, Ji Hee Kim, Joohan Lee, Taejin Choi, Tae Seok Ahn, Ok-Sun Kim, Jack Anthony Gilbert
    PLOS ONE.2015; 10(3): e0119966.     CrossRef
  • Algal and Fungal Diversity in Antarctic Lichens
    Chae Haeng Park, Kyung Mo Kim, Arve Elvebakk, Ok‐Sun Kim, Gajin Jeong, Soon Gyu Hong
    Journal of Eukaryotic Microbiology.2015; 62(2): 196.     CrossRef
  • Bacterial community of sediments from the Australian-Antarctic ridge
    Yung Mi Lee, Doshik Hahm, You-Jung Jung, Sung Hyun Park, Jongsik Chun, Soon Gyu Hong
    Polar Biology.2014; 37(4): 587.     CrossRef
  • Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis
    Ok-Hwa Hwang, Sebastian Raveendar, Young-Ju Kim, Ji-Hun Kim, Tae-Hun Kim, Dong-Yoon Choi, Che Ok Jeon, Sung-Back Cho, Kyung-Tai Lee
    Journal of Microbiology.2014; 52(11): 918.     CrossRef
  • Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash
    Jae Ho Joa, Hang Yeon Weon, Hae Nam Hyun, Young Chull Jeun, Sang Wook Koh
    Journal of Microbiology.2014; 52(12): 995.     CrossRef
  • A metagenomics‐based approach to the top‐down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest
    Donald M. Walker, Brandy R. Lawrence, Dakota Esterline, Sean P. Graham, Michael A. Edelbrock, Jessica A. Wooten
    Ecology and Evolution.2014; 4(21): 4106.     CrossRef
  • Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods
    Chang Soo Eun, Byung Kwon Kim, Dong Soo Han, Seon Young Kim, Kyung Mo Kim, Bo Youl Choi, Kyu Sang Song, Yong Sung Kim, Jihyun F. Kim
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  • Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica
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    Journal of Microbiology.2012; 50(6): 1081.     CrossRef
Assessment of Soil Fungal Communities Using Pyrosequencing
Young Woon Lim , Byung Kwon Kim , Changmu Kim , Hack Sung Jung , Bong-Soo Kim , Jae-Hak Lee , Jongsik Chun
J. Microbiol. 2010;48(3):284-289.   Published online June 23, 2010
DOI: https://doi.org/10.1007/s12275-010-9369-5
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  • 1 Download
  • 89 Crossref
AbstractAbstract PDF
Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived from the 5′ region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and 95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporic Ascomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales, Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities in soils.

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Identification and Characterization of Metagenomic Fragments from Tidal Flat Sediment
Byung Kwon Kim , Yoon-Dong Park , Hyun-Myung Oh , Jongsik Chun
J. Microbiol. 2009;47(4):402-410.   Published online September 9, 2009
DOI: https://doi.org/10.1007/s12275-009-0099-5
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AbstractAbstract PDF
Phylogenetic surveys based on cultivation-independent methods have revealed that tidal flat sediments are environments with extensive microbial diversity. Since most of prokaryotes in nature cannot be easily cultivated under general laboratory conditions, our knowledge on prokaryotic dwellers in tidal flat sediment is mainly based on the analysis of metagenomes. Microbial community analysis based on the 16S rRNA gene and other phylogenetic markers has been widely used to provide important information on the role of microorganisms, but it is basically an indirect means, compared with direct sequencing of metagenomic DNAs. In this study, we applied a sequence-based metagenomic approach to characterize uncultivated prokaryotes from tidal flat sediment. Two large-insert genomic libraries based on fosmid were constructed from tidal flat metagenomic DNA. A survey based on end-sequencing of selected fosmid clones resulted in the identification of clones containing 274 bacterial and 16 archaeal homologs in which majority were of proteobacterial origins. Two fosmid clones containing large metagenomic DNAs were completely sequenced using the shot- gun method. Both DNA inserts contained more than 20 genes encoding putative proteins which implied their ecological roles in tidal flat sediment. Phylogenetic analyses of evolutionary conserved proteins indicate that these clones are not closely related to known prokaryotes whose genome sequence is known, and genes in tidal flat may be subjected to extensive lateral gene transfer, notably between domains Bacteria and Archaea. This is the first report demonstrating that direct sequencing of metagenomic gene library is useful in underpinning the genetic makeup and functional roles of prokaryotes in tidal flat sediments.

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Rapid Phylogenetic Dissection of Prokaryotic Community Structure in Tidal Flat Using Pyrosequencing
Bong-Soo Kim , Byung Kwon Kim , Jae-Hak Lee , Myungjin Kim , Young Woon Lim , Jongsik Chun
J. Microbiol. 2008;46(4):357-363.   Published online August 31, 2008
DOI: https://doi.org/10.1007/s12275-008-0071-9
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AbstractAbstract PDF
Dissection of prokaryotic community structure is prerequisite to understand their ecological roles. Various methods are available for such a purpose which amplification and sequencing of 16S rRNA genes gained its popularity. However, conventional methods based on Sanger sequencing technique require cloning process prior to sequencing, and are expensive and labor-intensive. We investigated prokaryotic community structure in tidal flat sediments, Korea, using pyrosequencing and a subsequent automated bioinformatic pipeline for the rapid and accurate taxonomic assignment of each amplicon. The combination of pyrosequencing and bioinformatic analysis showed that bacterial and archaeal communities were more diverse than previously reported in clone library studies. Pyrosequencing analysis revealed 21 bacterial divisions and 37 candidate divisions. Proteobacteria was the most abundant division in the bacterial community, of which Gammaand Delta-Proteobacteria were the most abundant. Similarly, 4 archaeal divisions were found in tidal flat sediments. Euryarchaeota was the most abundant division in the archaeal sequences, which was further divided into 8 classes and 11 unclassified euryarchaeota groups. The system developed here provides a simple, in-depth and automated way of dissecting a prokaryotic community structure without extensive pretreatment such as cloning.

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