Identification of Essential Genes in Streptococcus pneumoniae by Allelic Replacement Mutagenesis

천종식,Jae-Hoon Song,Kwan Soo Ko,이지영,Jin Yang Baek,오원섭,Ha Sik Yoon,정진용 한국분자세포생물학회 2005 Molecules and cells Vol.19 No.3

To find potential targets of novel antimicrobial agents,we identified essential genes of Streptococcus pneumoniae using comparative genomics and allelic replacement mutagenesis. We compared the genome of S. pneumoniae R6 with those of Bacillus subtilis, Enterococcus faecalis, Escherichia coli, and Staphylococcus aureus, and selected 693 candidate target genes with > 40% amino acid sequence identity to the corresponding genes in at least two of the other species. The 693 genes were disrupted and 133 were found to be essential for growth. Of these, 32 encoded proteins of unknown function, and we were able to identify orthologues of 22 of these genes by genomic comparisons. The experimental method used in this study is easy to perform, rapid and efficient for identifying essential genes of bacterial pathogens.

미생물,그 복잡다단한 세계

천종식,Cheon, Jong-Sik 한국단미사료협회 2006 피드저널 Vol.4 No.4

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.

Thalassobius aestuarii sp. nov., Isolated from Tidal Flat Sediment

이하나,천종식 한국미생물학회 2006 The journal of microbiology Vol.44 No.2

A strictly aerobic, non-motile, ovoid-shaped Alphaproteobacteria, designated strain JC2049T, was isolated from a tidal flat sediment sample. The results of 16S rRNA gene sequence analysis indicated that this isolate belonged to the genus Thalassobius, with a sequence similarity of 96.9-97.3% to other valid Thalassobius spp. The cells required 1-7% NaCl for growth (optimum 2%) and accumulated poly-β-hydroxybutyrate. Nitrite was reduced to nitrogen, but nitrate was not reduced to nitrite. No genetic potential for aerobic anoxygenic photosynthesis was detected. The primary isoprenoid quinone (Ubiquinone-10), predominant cellular fatty acids (C18:1ω7c, 11 methyl C18:1ω7c and C16:0) and DNA G+C content (61 mol%) were all consistent with the assignment of this isolate to the genus Thalassobius. Several phenotypic characteristics clearly distinguished our isolate from other Thalassobius species. The degree of genomic relatedness between strain JC2049T and other Thalassobius species was in a range of 20-43%. The polyphasic data presented in this study indicates that our isolate should be classified as a novel species within the genus Thalassobius. The name Thalassobius aestuarii sp. nov. is therefore proposed for this isolate; the type strain is JC2049T (= IMSNU 14011T = KCTC 12049T = DSM 15283T).

Current Status and Future Promise of the Human Microbiome

김봉수,전윤성,천종식 대한소아소화기영양학회 2013 Pediatric gastroenterology, hepatology & nutrition Vol.16 No.2

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. (Pediatr Gastroenterol Hepatol Nutr 2013; 16: 71∼79)

A Method for Comparing Multiple Bacterial Community Structures from 16S rDNA Clone Library Sequences

Inae Hur,천종식 한국미생물학회 2004 The journal of microbiology Vol.42 No.1

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

rRNASelector: A Computer Program for Selecting Ribosomal RNA Encoding Sequences from Metagenomic and Metatranscriptomic Shotgun Libraries

이재학,이하나,천종식 한국미생물학회 2011 The journal of microbiology Vol.49 No.4

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.

Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era

김민철,이기현,윤석환,김봉수,천종식,이하나 한국유전체학회 2013 Genomics & informatics Vol.11 No.3

Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform

전윤성,박상철,임정민,천종식,김봉수 한국미생물학회 2015 The journal of microbiology Vol.53 No.1

The cost of DNA sequencing has decreased due to advancementsin Next Generation Sequencing. The number of sequencesobtained from the Illumina platform is large, use ofthis platform can reduce costs more than the 454 pyrosequencer. However, the Illumina platform has other challenges,including bioinformatics analysis of large numbersof sequences and the need to reduce erroneous nucleotidesgenerated at the 3 -ends of the sequences. These erroneoussequences can lead to errors in analysis of microbial communities. Therefore, correction of these erroneous sequencesis necessary for accurate taxonomic identification. Severalstudies that have used the Illumina platform to perform metagenomicanalyses proposed curating pipelines to increaseaccuracy. In this study, we evaluated the likelihood of obtainingan erroneous microbial composition using the MiSeq250 bp paired sequence platform and improved the pipelineto reduce erroneous identifications. We compared differentsequencing conditions by varying the percentage of controlphiX added, the concentration of the sequencing library, andthe 16S rRNA gene target region using a mock communitysample composed of known sequences. Our recommendedmethod corrected erroneous nucleotides and improved identificationaccuracy. Overall, 99.5% of the total reads shared95% similarity with the corresponding template sequencesand 93.6% of the total reads shared over 97% similarity. Thisindicated that the MiSeq platform can be used to analyze microbialcommunities at the genus level with high accuracy. The improved analysis method recommended in this studycan be applied to amplicon studies in various environmentsusing high-throughput reads generated on the MiSeq platform.

Draft Genome Sequence of Pseudomonas sp. Strain G5, Isolated from a Traditional Indigo Fermentation Dye Vat

박선화,허호길,이지훈,조용준,천종식 한국응용생명화학회 2013 Applied Biological Chemistry (Appl Biol Chem) Vol.56 No.3

In previous study, alkaliphilic and thermotolerant bacterium strain, Pseudomonas sp. strain G5, capable of reducing insoluble indigo was isolated from Korean traditional fermentation liquor. Here, we report the draft genome sequence and annotation of strain G5 to provide the genomic information involved in indigo reduction process.