• 대한임상검사과학회지
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• 제52권3호
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• pp.202-213
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• 2020

미생물 연구에서 대량의 마이크로바이옴 데이터를 효율적으로 얻는 기술이 발전해왔지만, 마이크로바이옴 빅 데이터를 적절하게 분석하는 도구는 여전히 부족하다. 또한 빈약한 데이터베이스를 사용하여 미생물 군집을 분석하면 잘못된 결과를 초래할 수 있다. 따라서 본 연구는 대량의 미생물 데이터베이스 분석을 위한 적절한 방법을 설계하고자 하였다. 박테리아는 개인의 손끝과 개인 소지품(휴대 전화 및 랩탑 키보드)에서 수집되었다. 박테리아로부터 게놈 DNA를 추출하고 16S rRNA 유전자를 표적으로 하여 차세대 시퀀싱을 실시하였다. 손끝과 개인 소지품 간의 박테리아 매칭 비율의 정확성은 공식과 함께 환경 및 인간관련 데이터베이스를 사용하여 확인하였다. 적절한 분석을 설계하기 위해 다음 세가지 범주를 기준으로: 정성적 분석과 정량적 분석 비교, 성별에 관계없이 모든 참여자뿐만 아니라 동일 성별 참여자 내 비교, 환경(eDB) 및 인간 관련 데이터 베이스(hDB)를 이용하여 샘플간 비교하였다. 결과는 정성적 분석과 동일 성별 참가자 내에서의 비교 및 hDB의 사용이 비교적 정확한 결과를 제공하였다. 우리의 연구는 인간 유래 미생물을 사용하여 대량의 미생물학적 데이터를 포함하는 연구를 수행할 때 정확한 결과를 얻을 수 있는 분석 방법을 제공한다.

• Fisheries and Aquatic Sciences
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• 제25권3호
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• pp.117-139
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• 2022

Synucleinopathies such as Parkinson's disease (PD) are incurable neurodegenerative conditions characterised by the abnormal aggregation of α-synuclein protein in neuronal cells. In PD, fibrillary synuclein aggregation forms Lewy bodies and Lewy neurites in the substantia nigra and cortex on the brain. Dementia with Lewy bodies and multiple system atrophy are also associated with α-synuclein protein abnormalities. α-synuclein is one of three synuclein proteins, and while its precise function is still unknown, one hypothesis posits that α-synuclein propagates from the enteric nervous system through the vagus nerve and into the brain, resulting in synucleinopathy. Studies on synucleinopathies should thus encompass not only the central nervous system but must necessarily include the gut and microbiome. The zebrafish (Danio rerio) is a well-established model for human neuronal pathologies and have been used in studies ranging from genetic models of hereditary disorders to neurotoxin-induced neurodegeneration as well as gut-brain-axis studies. There is significant genetic homology between zebrafish and mammalian vertebrates which is what makes the zebrafish so amenable to modelling human conditions but in the case of synucleinopathies, the zebrafish notably does not possess an α-synuclein homolog. Synuclein orthologs are present in the zebrafish however, and transgenic zebrafish that carry human α-synuclein have been generated. In addition, the zebrafish is a highly advantageous model and ideal replacement for reducing the use of mammalian models. This review discusses the application of the zebrafish as a model for synucleinopathies in efforts to further understand synuclein function and explore therapeutic strategies.

• Journal of Microbiology and Biotechnology
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• 제33권10호
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• pp.1317-1328
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• 2023

Green tea (GT) polyphenols undergo extensive metabolism within gastrointestinal tract (GIT), where their derivatives compounds potentially modulate the gut microbiome. This biotransformation process involves a cascade of exclusive gut microbial enzymes which chemically modify the GT polyphenols influencing both their bioactivity and bioavailability in host. Herein, we examined the in vitro interactions between 37 different human gut microbiota and the GT polyphenols. UHPLC-LTQ-Orbitrap-MS/MS analysis of the culture broth extracts unravel that genera Adlercreutzia, Eggerthella and Lactiplantibacillus plantarum KACC11451 promoted C-ring opening reaction in GT catechins. In addition, L. plantarum also hydrolyzed catechin galloyl esters to produce gallic acid and pyrogallol, and also converted flavonoid glycosides to their aglycone derivatives. Biotransformation of GT polyphenols into derivative compounds enhanced their antioxidant bioactivities in culture broth extracts. Considering the effects of GT polyphenols on specific growth rates of gut bacteria, we noted that GT polyphenols and their derivate compounds inhibited most species in phylum Actinobacteria, Bacteroides, and Firmicutes except genus Lactobacillus. The present study delineates the likely mechanisms involved in the metabolism and bioavailability of GT polyphenols upon exposure to gut microbiota. Further, widening this workflow to understand the metabolism of various other dietary polyphenols can unravel their biotransformation mechanisms and associated functions in human GIT.

• 식물병연구
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• 제26권4호
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• pp.202-209
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• 2020

유기농업은 지속가능한 농업을 위해서 필요하며, 생물 다양성 유지를 위해 필수적인 경작 방법으로 전 세계적으로 성장하고 있는 농업 분야 중 하나이다. 유기농업은 인류의 건강과 환경에 유해한 영향을 끼질 수 있는 화학적 제재의 사용을 줄이고, 친환경적 동·식물성 비료, 식물 추출물, 미생물 제재 등이 사용되기 때문에 소비자에게 안전한 농산물을 제공할 수 있다. 노지 고추를 대상으로 3년간 유기농업 환경과 관행농업 환경에서 주요 병해 발생과 토양 미생물상의 조사하였다. 토양 미생물상의 차이는 차세대 염기서열 분석 기법을 활용하여 조사하였으며, 유기농업에 사용되는 제제의 종류에 따라 토양 미생물상이 다르게 형성되었다. 바이러스, 탄저병에 대해서는 관행농업에서의 병 발생률이 낮았으나, 청고병은 미생물 제재 사용에 의해 병 발생률이 낮게 나타났다. 미생물 제재를 사용한 토양에서 투입된 미생물이 토양 미생물에서 검출되었으며, 이는 미생물이 실제 토양에 정착했음을 시사한다.

• IMMUNE NETWORK
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• 제12권4호
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• pp.129-138
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• 2012

Allergic disorders such as atopic dermatitis and asthma are common hyper-immune disorders in industrialized countries. Along with genetic association, environmental factors and gut microbiota have been suggested as major triggering factors for the development of atopic dermatitis. Numerous studies support the association of hygiene hypothesis in allergic immune disorders that a lack of early childhood exposure to diverse microorganism increases susceptibility to allergic diseases. Among the symbiotic microorganisms (e.g. gut flora or probiotics), probiotics confer health benefits through multiple action mechanisms including modification of immune response in gut associated lymphoid tissue (GALT). Although many human clinical trials and mouse studies demonstrated the beneficial effects of probiotics in diverse immune disorders, this effect is strain specific and needs to apply specific probiotics for specific allergic diseases. Herein, we briefly review the diverse functions and regulation mechanisms of probiotics in diverse disorders.

• Genomics & Informatics
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• 제18권4호
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• pp.35.1-35.7
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• 2020

Identifying the patterns of gene expression in breast cancers is essential to understanding their pathophysiology and developing anticancer drugs. Breast cancer is a heterogeneous disease with different subtypes determined by distinct biological features. Luminal breast cancer is characterized by a relatively high expression of estrogen receptor (ER) and progesterone receptor (PR) genes, which are expressed in breast luminal cells. In ~25% of invasive breast cancers, human epidermal growth factor receptor 2 (HER2) is overexpressed; these cancers are categorized as the HER2 type. Triple-negative breast cancer (TNBC), in which the cancer cells do not express ER/PR or HER2, shows highly aggressive clinical outcomes. TNBC can be further classified into specific subtypes according to genomic mutations and cancer immunogenicity. Herein, we discuss the brief history of TNBC classification and its implications for promising treatments.

• 한국미생물·생명공학회지
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• 제50권4호
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• pp.465-476
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• 2022

The importance of beneficial microorganisms, particularly probiotics, that coexist in the human body, is being increasingly recognized. Probiotics are representative health functional foods that provide health benefits to humans through the production of various metabolites, including short-chain fatty acids. However, the health benefits are strain-specific, and the use of each probiotic strain should follow guidelines that assure its safety. Accurate identification of the strain should be managed through genetic and phenotypic analyses of the strain. Besides, the functionality of probiotics should be disclosed in vitro and in vivo so that they can be used as legal functional ingredients (i.e., individual standards). In this review, we deal with the guidelines, including the technical factors related to probiotic strains. The common health effects of probiotic strains include proliferation of beneficial bacteria, control of harmful bacteria, and facilitation of bowel activities. Probiotics with various functionalities (e.g., body fat and cholesterol reduction, vaginal health, and improvement of skin's immune system) have been investigated as "individual standards of raw materials for health functional foods" provided by MFDS. In the future, various biotechnologies including synthetic biology can be applied to produce customized probiotics to improve human health.

• Journal of Applied Biological Chemistry
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• 제65권1호
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• pp.63-74
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• 2022

Microbial dysbiosis in the gut is associated with human diseases, and variations in mucus alter gut microbiota. Therefore, we explored the effects of mucin on the gut microbiota using a community of 19 synthetic gut microbial species. Cultivation of these species in modified Gifu anaerobic medium (GAM) supplemented with mucin before synthetic community assembly facilitated substantial growth of the Bacteroides, Akkermansia, and Clostridium genera. The results of 16S rRNA microbial relative abundance profiling revealed more of the beneficial microbes Collinsella, Bifidobacterium, Ruminococcus, and Lactobacillus. This increased acetate levels in the community cultivated with, rather than without (control), mucin. We identified differences in predicted cell function and metabolism between microbes cultivated in GAM with and without mucin. Mucin not only changed the composition of the gut microbial community, but also modulated metabolic functions, indicating that it could help to modulate microbial changes associated with human diseases.

• Clinical and Experimental Pediatrics
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• 제63권8호
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• pp.301-309
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• 2020

Human breast milk (HBM) is essential for the infant's growth and development right after birth and is an irreplaceable source of nutrition for early human survival. Various infant formulas have many similarities to HBM in many components, but there is no perfect substitute for HBM. Recently, various breast milk components and their roles have been studied according to the development of various analysis techniques. As is already well known, HBM contains about 87%-88% water, and 124-g/L solid components as macronutrients, including about 7% (60-70 g/L) carbohydrates, 1% (8-10 g/L) protein, and 3.8% (35-40 g/L) fat. The composition may vary depending on the environmental factors, including maternal diet. Colostrum is low in fat but high in protein and relatively rich in immuneprotective components. Although HBM contains enough vitamins to ensure normal growth of the infant, vitamins D and K may be insufficient, and the infant may require their supplementation. Growth factors in HBM also serve as various bioactive proteins and peptides on the intestinal tract, vasculature, nervous system, and endocrine system. In the past, HBM of a healthy mother was thought to be sterile. However, several subsequent studies have confirmed the presence of rich and diverse microbial communities in HBM. Some studies suggested that the genera Staphylococcus and Streptococcus may be universally predominant in HBM, but the origin of microbiota still remains controversial. Lastly, milk is the one of most abundant body fluid of microRNAs, which are known to play a role in various functions, such as immunoprotection and developmental programming, through delivering from HBM and absorption by intestinal epithelial cells. In conclusion, HBM is the most important source of nutrition for infants and includes microbiomes and miRNAs for growth, development, and immunity.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제25권3호
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• pp.194-210
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• 2022

Human milk contains a number of nutritional and bioactive molecules including microorganisms that constitute the so-called "Human Milk Microbiota (HMM)". Recent studies have shown that not only bacterial but also viral, fungal, and archaeal components are present in the HMM. Previous research has established, a "core" microbiome, consisting of Firmicutes (i.e., Streptococcus, Staphylococcus), Proteobacteria (i.e., Serratia, Pseudomonas, Ralstonia, Sphingomonas, Bradyrhizobium), and Actinobacteria (i.e., Propionibacterium, Corynebacterium). This review aims to summarize the main characteristics of HMM and the role it plays in shaping a child's health. We reviewed the most recent literature on the topic (2019-2021), using the PubMed database. The main sources of HMM origin were identified as the retrograde flow and the entero-mammary pathway. Several factors can influence its composition, such as maternal body mass index and diet, use of antibiotics, time and type of delivery, and mode of breastfeeding. The COVID-19 pandemic, by altering the mother-infant dyad and modifying many of our previous habits, has emerged as a new risk factor for the modification of HMM. HMM is an important contributor to gastrointestinal colonization in children and therefore, it is fundamental to avoid any form of perturbation in the HMM that can alter the microbial equilibrium, especially in the first 100 days of life. Microbial dysbiosis can be a trigger point for the development of necrotizing enterocolitis, especially in preterm infants, and for onset of chronic diseases, such as asthma and obesity, later in life.