Omics in gut microbiome analysis

원태웅,Shin Na-Ri,Kim Joon Yong,Roh Seong Woon 한국미생물학회 2021 The journal of microbiology Vol.59 No.3

Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.

Oceanobacillus kimchii sp. nov. Isolated from a Traditional Korean Fermented Food

원태웅,Mi-Ja Jung,노성운,Young-Do Nam,박은진,신기선,배진우 한국미생물학회 2010 The journal of microbiology Vol.48 No.6

A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0(optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).

자외선에 조사된 CHO-kl세포의 자매염색분체교환 빈도와 성장률에 미치는 DNA Hypomethylation의 영향

원태웅,이석우,김우갑 한국통합생물학회 1995 한국동물학회 뉴스레터 Vol.12 No.2

Comparative Viral Metagenomics of Environmental Samples from Korea

김민수,원태웅,배진우 한국유전체학회 2013 Genomics & informatics Vol.11 No.3

The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se,but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples. This review considers the current state of viral metagenomics, based on examples from Korean viral metagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere. Viral metagenomics has become widespread due to various methodological developments, and much attention has been focused on studies that consider the intrinsic role of viruses that interact with their hosts.

배양 인체 백혈구의 Sister Chromatid Exchange 빈도에 미치는 DNA hypomethylation 의 영향

김우갑,이석우,원태웅 한국유전학회 1995 Genes & Genomics Vol.17 No.2

To investigate the degree of sister chromatid exchange(SCE) induced by saccharin and benzo(a)pyrene, cultured human lymphocytes were treated with different concentrations of saccharin and benzo(a)pyrene. The frequency of SCEs was increased with increasing concentrations of saccharin or benzo(a)pyrene. In order to analyze the effect of DNA hypomethylation which induces SCEs, we treated 5-azacytidine (5-aza-C), an hypomethylating agent and saccharin or benzo(a)pyrene in human lymphocytes. As a result, the frequency of SCEs in the lymphocytes treated with 5-aza-C and saccharin was greater than that treated with saccharin only. Similar result was observed in the lymphocytes treated with 5-aza-C and benzo(a)pyrene at the same time. Our results suggest that DNA hypomethylation is responsible for instability of the DNA structure which means that DNA methylation is important for chromosome stability.

사람의 염색체에 제한효소 처리후 나타난 band pattern 과 그 작용 기작

이석우,이승길,남재환,원태웅 한국유전학회 1994 Genes & Genomics Vol.16 No.3

In situ digestion experiment using restriction enzyme applied to fixed human chromosome brought the following results ; First, Asn I and Dra I that recognized AT-rich sequence produced C-like band patterns and telomere bands which are the distintive feature of R-like band patterns. Therefore the existence of recognition base sequence greatly influenced for the action of restriction enzyme on fixed chromosome. Second, DNA loss had decisive influence upon C-like band pattern produced by restriction enzyme. But chromatin comformational change seems to have acted upon G-like band pattern. Third, analysis of the result of electrophoresis showed that among DNA fragments separated from a chromosome, by restriction enzyme, some DNA fragments that had large size and were not extracted under the influence of non-histone protein were remained on fixed chromosome. Fourth, human constitutive heterochromatin turned out to be heterogeneous by satellite DNA of highly repeated sequence. In conclusion, there's no doubt that DNA loss plays the most important role in the formation of bands by restriction enzyme and that DNA loss depends on the frequency of recognition sequence of restriction enzyme.

Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment

이해원,노성운,Kyung June Yim,신나리,이지나,원태웅,Joon-Yong Kim,현동욱,김대경,배진우 한국미생물학회 2013 The journal of microbiology Vol.51 No.3

A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35T was most closely related to Paenibacillus taiwanensis G-soil-2-3T (97.2% similarity). The optimal growth conditions for strain LHW35T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C15:0 and C16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminohospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35T (=KACC 16317T =JCM 17886T).

LHR 조건하에서 배양 인체 백혈구가 나타내는 SCE 와 excision DNA repair 능력

이광호,이석우,이승길,지성길,정계준,원태웅,박현숙 한국유전학회 1987 Genes & Genomics Vol.9 No.3

Go human lymphocytes were treated prior to culture initiation with 7 cytostatics (MMC, CLM, MTX, Ara-C, Act-D, HU, 5-FU) in order to determine whether cytostatics having different mode of action on DNA are equally effective in inducing DNA lesions in Go human lymphocytes. Go lymphocytes damaged with cytostatics showing positive results (MMC, CLM) were allowed to repair DNA damages under LHR conditions for 12-36 hr to compare excision DNA repair capacity in exposed lymphocytes. Additionally, we carried out a series of experiments to investigate the relevance of Go exposure duration (1-4 hr), SCE induction and excision repair capacity during limited LHR period (12 hr), the effect of BUdR on excision DNA repair activity in Go lymphocytes under LHR conditions and the characteristics of the unexcision repaired lesions remained in the DNA of Go lymphocytes after LHR that can lead to SCE formation, MMC and CLM induced exposure duration-related increase in SCEs, while MTX, Ara-C, Act-D, HU and 5-FU showed only minor variations in SCE indutions during Go exposure of 1-4 hr. There was a significant difference between SCEs after 2 hr of MMC/CLM treatment. and those after 12-36 hr LHR conditions. The effect of limited LHR period (12 hr) on SCE value was not dependent on the exposure duration or induced SCE frequencies. In cultures exposed to CLM, BUdR induced LHR period-dependent increase of SCEs during LHR period. LHR-allowed lymphocytes showed more rapid decrease of SCE as compare to those of cultures without LHR conditions. MMC-induced SCEs were more slowly decreased than CLM-induced SCEs with or without LHR conditions.

Rhodopirellula rosea sp. nov., a Novel Bacterium Isolated from an Ark Clam Scapharca broughtonii

노성운,이해원,Kyung June Yim,신나리,이지나,원태웅,Na-Lae Lim,김대경,배진우 한국미생물학회 2013 The journal of microbiology Vol.51 No.3

A novel Gram-negative, motile, and ovoid-shaped strain, LHWP3T, which belonged to the family Planctomycetaceae in the phylum Planctomycetes, was isolated from a dead ark clam Scapharca broughtonii collected during a mass mortality event on the south coast of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the isolate was most closely related to the type strain of Rhodopirellula baltica, with a shared 16S rRNA gene sequence similarity of 94.8%. The isolate grew optimally at 30°C in 4–6% (w/v) NaCl, and at pH 7. The major isoprenoid quinone was menaquinone-6 (MK-6). The dominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified polar lipids. The predominant cellular fatty acids were C16:0, C18:1 ω9c, and C18:0. The genomic DNA G+C content of strain LHWP3T was 53.0 mol%. Based on polyphasic taxonomic analyses, strain LHWP3T should be classified as a novel species in the genus Rhodopirellula in the family Planctomycetaceae, for which the name Rhodopirellula rosea sp. nov. is proposed. The type strain is LHWP3T (=KACC 15560T =JCM 17759T).

제 10 회 국제학술대회 발표 논문 : 일본국헌법하에 있어서 공무원의 노동기본권과 형벌권 ( 日本國憲法下における 公務員の勞動基本權と刑罰權 )

삼원태웅(Skihara) 한일법학회 1990 한일법학 Vol.9 No.-