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Jae-Hak Lee 4 Articles
TBC: A Clustering Algorithm Based on Prokaryotic Taxonomy
Jae-Hak Lee , Hana Yi , Yoon-Seong Jeon , Sungho Won , Jongsik Chun
J. Microbiol. 2012;50(2):181-185.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1214-6
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  • 20 Crossref
AbstractAbstract PDF
High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRITTree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw. ezbiocloud.net/tbc.

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  • hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction
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  • Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing
    Jakub Kreisinger, Dagmar Čížková, Lucie Kropáčková, Tomáš Albrecht, Roberto Ambrosini
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  • Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities
    Su-Kyoung Shin, Jinman Kim, Sung-min Ha, Hyun-Seok Oh, Jongsik Chun, Jongryeul Sohn, Hana Yi, Vishnu Chaturvedi
    PLOS ONE.2015; 10(5): e0126960.     CrossRef
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    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
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    Jong‐Geol Kim, Soo‐Je Park, Zhe‐Xue Quan, Man‐Young Jung, In‐Tae Cha, So‐Jeong Kim, Kyoung‐Ho Kim, Eun‐Jin Yang, Young‐Nam Kim, Sang‐Hoon Lee, Sung‐Keun Rhee
    Environmental Microbiology.2014; 16(6): 1566.     CrossRef
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    Yung Mi Lee, Doshik Hahm, You-Jung Jung, Sung Hyun Park, Jongsik Chun, Soon Gyu Hong
    Polar Biology.2014; 37(4): 587.     CrossRef
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    Sokhee Philemon Jung, Youngwook Cheong, Giljae Yim, Sangwoo Ji, Hojeong Kang
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    Mira Park, Hyoungseok Lee, Soon Gyu Hong, Ok-Sun Kim
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  • A Unique Prokaryotic Assemblage of Wall Biofilm of a Volcanic Cave (Daesubee) in Jeju
    Jong-Geun Moon, Man-Young Jung, Jong-Geol Kim, Soo-Je Park, Dae-Shin Kim, Jong-Shik Kim, Sung-Keun Rhee
    The Korean Journal of Microbiology.2013; 49(2): 184.     CrossRef
  • Resolving Ambiguity of Species Limits and Concatenation in Multilocus Sequence Data for the Construction of Phylogenetic Supermatrices
    Douglas Chesters, Alfried P. Vogler
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  • CLUSTOM: A Novel Method for Clustering 16S rRNA Next Generation Sequences by Overlap Minimization
    Kyuin Hwang, Jeongsu Oh, Tae-Kyung Kim, Byung Kwon Kim, Dong Su Yu, Bo Kyeng Hou, Gustavo Caetano-Anollés, Soon Gyu Hong, Kyung Mo Kim, George E. Fox
    PLoS ONE.2013; 8(5): e62623.     CrossRef
  • Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era
    Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun, Hana Yi
    Genomics & Informatics.2013; 11(3): 102.     CrossRef
  • Bacterial Diversity in the Guts of Sea Cucumbers (Apostichopus japonicus) and Shrimps (Litopenaeus vannamei) Investigated with Tag-Encoded 454 Pyrosequencing of 16S rRNA Genes
    Eun Soo Noh, Young-Sam Kim, Dong-Hyun Kim, Kyoung-Ho Kim
    The Korean Journal of Microbiology.2013; 49(3): 237.     CrossRef
  • Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica
    Ok-Sun Kim, Namyi Chae, Hyun Soo Lim, Ahnna Cho, Jeong Hoon Kim, Soon Gyu Hong, Jeongsu Oh
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rRNASelector: A Computer Program for Selecting Ribosomal RNA Encoding Sequences from Metagenomic and Metatranscriptomic Shotgun Libraries
Jae-Hak Lee , Hana Yi , Jongsik Chun
J. Microbiol. 2011;49(4):689-691.   Published online September 2, 2011
DOI: https://doi.org/10.1007/s12275-011-1213-z
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  • 29 Crossref
AbstractAbstract PDF
Metagenomic and metatranscriptomic shotgun sequencing techniques are gaining popularity as more cost-effective next-generation sequencing technologies become commercially available. The initial stage of bioinformatic analysis generally involves the identification of phylogenetic markers such as ribosomal RNA genes. The sequencing reads that do not code for rRNA can then be used for protein-based analysis. Hidden Markov model is a well-known method for pattern recognition. Hidden Markov models that are trained on well-curated rRNA sequence databases have been successfully used to identify DNA sequence coding for rRNAs in prokaryotes. Here, we introduce rRNASelector, which is a computer program for selecting rRNA genes from massive metagenomic and metatranscriptomic sequences using hidden Markov models. The program successfully identified prokaryotic 5S, 26S, and 23S rRNA genes from Roche 454 FLX Titanium-based metagenomic and metatranscriptomic libraries. The rRNASelector program is available at http://sw.ezbiocloud.net/rrnaselector.

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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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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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    Geomicrobiology Journal.2013; 30(7): 593.     CrossRef
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    In-Hye Jeong, Kyoung-Ho Kim, Jin-Sook Park
    Journal of Microbiology.2013; 51(5): 570.     CrossRef
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    International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_11): 4309.     CrossRef
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    PLoS ONE.2013; 8(4): e59977.     CrossRef
  • Identification of a new subfamily of salt-tolerant esterases from a metagenomic library of tidal flat sediment
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    Applied Microbiology and Biotechnology.2012; 93(2): 623.     CrossRef
  • Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags
    Yu Wang, Hua-Fang Sheng, Yan He, Jin-Ya Wu, Yun-Xia Jiang, Nora Fung-Yee Tam, Hong-Wei Zhou
    Applied and Environmental Microbiology.2012; 78(23): 8264.     CrossRef
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    International Journal of Hydrogen Energy.2012; 37(10): 8330.     CrossRef
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    Food Microbiology.2012; 30(1): 197.     CrossRef
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    Indian Journal of Microbiology.2012; 52(4): 544.     CrossRef
  • Marinitalea sucinacia gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment
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    FEMS Microbiology Letters.2011; 314(1): 89.     CrossRef
  • Comparative approach to capture bacterial diversity of coastal waters
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    The Journal of Microbiology.2011; 49(5): 729.     CrossRef
  • Novel Biphenyl-Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat
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    Applied and Environmental Microbiology.2011; 77(11): 3888.     CrossRef
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    Journal of Microbiological Methods.2011; 86(1): 1.     CrossRef
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    Yi-Seul Kim, Min-Cheol Kim, Soon-Wo Kwon, Soo-Jin Kim, In-Cheol Park, Jong-Ok Ka, Hang-Yeon Weon
    The Journal of Microbiology.2011; 49(3): 340.     CrossRef
  • Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation
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    Applied and Environmental Microbiology.2011; 77(13): 4527.     CrossRef
  • The Intestinal Bacterial Community in the Food Waste-Reducing Larvae of Hermetia illucens
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    Current Microbiology.2011; 62(5): 1390.     CrossRef
  • Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of  the Severn Estuary, UK, revealed by stable-isotope probing
    Gordon Webster, Joachim Rinna, Erwan G. Roussel, John C. Fry, Andrew J. Weightman, R. John Parkes
    FEMS Microbiology Ecology.2010; 72(2): 179.     CrossRef
  • Discovery of commonly existing anode biofilm microbes in two different wastewater treatment MFCs using FLX Titanium pyrosequencing
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    Applied Microbiology and Biotechnology.2010; 87(6): 2335.     CrossRef
  • Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
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    The ISME Journal.2010; 4(1): 1.     CrossRef
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    The Journal of Microbiology.2010; 48(3): 284.     CrossRef
  • Identification and characterization of metagenomic fragments from tidal flat sediment
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    The Journal of Microbiology.2009; 47(4): 402.     CrossRef
  • The seasonal structure of microbial communities in the Western English Channel
    Jack A. Gilbert, Dawn Field, Paul Swift, Lindsay Newbold, Anna Oliver, Tim Smyth, Paul J. Somerfield, Sue Huse, Ian Joint
    Environmental Microbiology.2009; 11(12): 3132.     CrossRef

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