• Genomics & Informatics
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• 제11권3호
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• pp.102-113
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• 2013

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.

• 환경생물
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• 제30권2호
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• pp.77-89
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• 2012

With the advent of the genomics era powered by DNA sequencing technologies, life science is being transformed significantly and biological research and development have been accelerated. Environmental biology concerns the relationships among living organisms and their natural environment, which constitute the global biogeochemical cycle. As sustainability of the ecosystems depends on biodiversity, examining the structure and dynamics of the biotic constituents and fully grasping their genetic and metabolic capabilities are pivotal. The high-speed high-throughput next-generation sequencing can be applied to barcoding organisms either thriving or endangered and to decoding the whole genome information. Furthermore, diversity and the full gene complement of a microbial community can be elucidated and monitored through metagenomic approaches. With regard to human welfare, microbiomes of various human habitats such as gut, skin, mouth, stomach, and vagina, have been and are being scrutinized. To keep pace with the rapid increase of the sequencing capacity, various bioinformatic algorithms and software tools that even utilize supercomputers and cloud computing are being developed for processing and storage of massive data sets. Environmental genomics will be the major force in understanding the structure and function of ecosystems in nature as well as preserving, remediating, and bioprospecting them.

• 한국축산식품학회지
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• 제39권4호
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• pp.585-600
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• 2019

Gouda cheese, one of most popular cheeses in the Korea, has been produced from only pasteurized milk in Korean dairy farms. Recently, it has become legally possible to produce ripened cheese manufactured with raw milk in Korea. In the present study, we investigated the physico-chemical and microbiological characteristics of Gouda cheese manufactured with raw (R-GC) or pasteurized milk (P-GC) during manufacturing and ripening. Particularly, this study characterized the bacterial community structure of two cheese types, which are produced without pasteurization during ripening based on next generation sequencing of 16S rRNA gene amplicons. During ripening, protein and fat content increased slightly, whereas moisture content decreased in both P-GC and R-GC. At the 6 wk of ripening, R-GC became softer and smoother and hence, the values of hardness and gumminess, chewiness in R-GC was lower than that of P-GC. Metagenomic analysis revealed that the bacterial genera used a starter cultures, namely Lactococcus and Leuconostoc were predominant in both P-GC and R-GC. Moreover, in R-GC, the proportion of coliform bacteria such as Escherichia, Leclercia, Raoultella, and Pseudomonas were detected initially but not during ripening. Taken together, our finding indicates the potential of manufacturing with Gouda cheese from raw milk and the benefits of next generation sequencing for microbial community composition during cheese ripening.

• Journal of Microbiology and Biotechnology
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• 제24권6호
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• pp.812-822
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• 2014

Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.

• BMB Reports
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• 제49권12호
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• pp.662-670
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• 2016

The human oral cavity contains a highly personalized microbiome essential to maintaining health, but capable of causing oral and systemic diseases. Thus, an in-depth definition of "healthy oral microbiome" is critical to understanding variations in disease states from preclinical conditions, and disease onset through progressive states of disease. With rapid advances in DNA sequencing and analytical technologies, population-based studies have documented the range and diversity of both taxonomic compositions and functional potentials observed in the oral microbiome in healthy individuals. Besides factors specific to the host, such as age and race/ethnicity, environmental factors also appear to contribute to the variability of the healthy oral microbiome. Here, we review bioinformatic techniques for metagenomic datasets, including their strengths and limitations. In addition, we summarize the interpersonal and intrapersonal diversity of the oral microbiome, taking into consideration the recent large-scale and longitudinal studies, including the Human Microbiome Project.

• Journal of Microbiology and Biotechnology
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• 제34권8호
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• pp.1617-1626
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• 2024

Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제16권2호
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• pp.71-79
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• 2013

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.

• 환경생물
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• 제37권3호
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• pp.351-361
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• 2019

이매패류의 부유유생은 성패(양식자원)에 직접적인 영향을 미치고 있어, 부유유생의 출현시기 및 출현량에 관한 연구는 자연 채묘량의 증대와 인공종묘의 생산을 위해서 매우 중요하다. 이에 본 연구에서는 유전자 분석기법을 이용하여 보성 연안에서 총 21종의 이매패류 부유유생을 확인하였으며, 이 중 구마모토굴(M. sikamea), 왜홍합(X. atratus), 종밋(M. senhousia), 참굴(M. gigas), 가리맛 조개(S. constricta), 새꼬막(A. kagoshimensis), Kurtiella aff. bidentata 그리고 꼬막(T. granosa)이 중요 부유유생으로 관찰되었다. 특히, 보성 연안해역의 주요 수산자원인 새꼬막(A. kagoshimensis)과 꼬막(T. granosa)은 각각 이매패류의 0.51~12.50% (평균 4.00%), 0.01~12.50% (평균 1.92%)의 구성비율을 차지하며 다른 이매패류보다 낮은 출현량을 보였다. 꼬막(T. granosa)과 새꼬막(A. kagoshimensis)의 부유유생은 6월부터 9월까지 관찰되었으나, 각각 8월 초와 8월말에 가장 높은 출현율을 보였다.

• Genomics & Informatics
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• 제16권4호
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• pp.22.1-22.5
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• 2018

In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed "International Committee on Taxonomy of Viruses (ICTV)," by which it is still known today. The primary virus classification provided by ICTV in 1971 was for viruses infecting vertebrates, which includes 19 genera, 2 families, and 24 unclassified groups. Presently, the 10th virus taxonomy has been published. However, the early classification of viruses was based on clinical results "in vivo" and "in vitro," as well as on the shape of the Phenotype virus. Due to the development of next-generation sequencing and the accompanying bioinformatics analysis pipelines, a reconstruction of the classification system has been proposed. At a meeting held in Boston, USA between June 9-11, 2016, there was even an in-depth discussion regarding the classification of viruses using metagenomic data. One suggested activity that arose from the meeting was that viral taxonomy should be reconstructed, based on genotype and bioinformatics analysis "in silico." This article describes our efforts to achieve this goal by construction of a web-based system and the extension of an associated database, based on ICTV taxonomy. This virus taxonomy web system was designed specifically to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searches for specific viral genes; there are also links to journals provided by the EMBL RESTful API that improves accessibility for academic groups.

• 생명과학회지
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• 제28권10호
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• pp.1244-1253
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• 2018

반추위 속에는 박테리아, 고세균, 프로토조아, 곰팡이 및 바이러스와 같은 다양한 미생물들이 편성의 혐기조건에서 공생하고 있다. 사료의 발효에 중요한 역할을 하고 있는 반추위 미생물은 위내 발효과정에서 에너지 손실에 영향을 주는 메탄의 발생을 제외하면 에너지와 단백질 대사에 필수적인 다양한 휘발성 지방산을 생산한다. 반추위내 미생물의 이용효율을 개선시키기 위해 사료배합비조절, 천연사료첨가제, 생균제첨가 등의 다양한 접근방법들이 사용되고 있다. 최근에 반추위 군집에 대한 메타유전체 또는 메타전사체와 같은 차세대 유전체 해독기술 또는 차세대 시퀀싱 기술의 적용으로 반추위 미생물의 다양성 및 기능에 대한 이해가 크게 증가하였다. 특히 메타단백질체와 메타대사체는 반추위 생태계의 복잡한 미생물네트워크에 대한 더 깊은 통찰력을 제공할 뿐만 아니라, 다양한 반추가축용 사료에 대한 반응을 제공함으로서 생산효율을 개선시키는데 기여하였다. 본 논문에서는 반추위내 사료의 발효와 이용을 향상시키기 위한 메타오믹스 기술, 즉, 메타유전체, 메타전사체, 메타단백질체 및 메타대사체의 최신 응용기술을 요약하고자 한다.