• Journal of dental hygiene science
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• v.19 no.2
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• pp.77-85
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• 2019

In the past gut microbiome has been the main focus of microbiome research. Studies about the microbiome inside oral cavities and other organs are underway. Studies about the relationship between noninfectious diseases and periodontal diseases, and the negative effects of harmful oral microbes on systemic health have been published in the recent past. A lot of attention is being paid towards fostering a healthy oral microbial ecosystem. This study aimed to understand the roles and effects of the microbiome inside the human body can potentially help cure various diseases including inflammatory bowel diseases with no known cure such as Crohn's disease, atopic dermatitis, obesity, cancer, diabetes, brain diseases and oral diseases. The present study examined technological trends in the correlation between the human microbiome and diseases in the human body, interactions between the human body's immunity, the metabolic system, and the microbiome, and research trends in other countries. While it has been proven that human microbiome is closely correlated with human diseases, most studies are still in the early stage of trying to compare the composition of microbiomes between health and patient groups. Since the oral environment is a dynamic environment that changes due to not only food intake but also other external factors such as lifestyle, hygiene, and drug intake, it is necessary to continue in-depth research on the microbiome composition characteristics to understand the complex functions of oral microorganisms. Analyzing the oral microbiome using computational technology may aid in disease diagnosis and prevention.

• BMB Reports
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• v.49 no.12
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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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• v.31 no.11
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• pp.1490-1500
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• 2021

Various microorganisms reside in the human vagina; the vaginal microbiome is closely linked to both vaginal and general health, and for this reason, microbiome studies of the vagina are an area of research. In this study, we analyzed the vaginal microbiome of women before and after menopause to further increase our understanding of the vaginal microbiome and its contribution to general health. We did a 16s rRNA gene-based metagenomic analysis on the vaginal fluids of 11 premenopausal and 19 postmenopausal women in Korea. We confirmed that the taxonomic composition was significantly different between the two groups. In postmenopausal women, species richness was significantly decreased, but species diversity was significantly increased. In particular, among the taxonomic components corresponding to all taxon ranks of the vaginal microbiome, a reduction in Lactobacillus taxa after menopause contributed the most to the difference between the two groups. In addition, we confirmed through metabolic analysis that the lactic-acid concentration was also decreased in the vaginal fluid of women after menopause. Our findings on the correlation between menopause and the microbiome could help diagnose menopause and enhance the prevention and treatment diseases related to menopause.

• Journal of Animal Science and Technology
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• v.64 no.4
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• pp.671-695
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• 2022

The gastrointestinal tract is a complex ecosystem that contains a large number of microorganisms with different metabolic capacities. Modulation of the gut microbiome can improve the growth and promote health in pigs. Crosstalk between the host, diet, and the gut microbiome can influence the health of the host, potentially through the production of several metabolites with various functions. Short-chain and branched-chain fatty acids, secondary bile acids, polyamines, indoles, and phenolic compounds are metabolites produced by the gut microbiome. The gut microbiome can also produce neurotransmitters (such as γ-aminobutyric acid, catecholamines, and serotonin), their precursors, and vitamins. Several studies in pigs have demonstrated the importance of the gut microbiome and its metabolites in improving growth performance and feed efficiency, alleviating stress, and providing protection from pathogens. The use of probiotics is one of the strategies employed to target the gut microbiome of pigs. Promising results have been published on the use of probiotics in optimizing pig production. This review focuses on the role of gut microbiome-derived metabolites in the performance of pigs and the effects of probiotics on altering the levels of these metabolites.

• BMB Reports
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• v.56 no.9
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• pp.469-481
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• 2023

The gut microbiome is widely recognized as a dynamic organ with a profound influence on human physiology and pathology. Extensive epidemiological and longitudinal cohort studies have provided compelling evidence that disruptions in the early-life microbiome can have long-lasting health implications. Various factors before, during, and after birth contribute to shaping the composition and function of the neonatal and infant microbiome. While these alterations can be partially restored over time, metabolic phenotypes may persist, necessitating research to identify the critical period for early intervention to achieve phenotypic recovery beyond microbiome composition. In this review, we provide current understanding of changes in the gut microbiota throughout life and the various factors affecting these changes. Specifically, we highlight the profound impact of early-life gut microbiota disruption on the development of diseases later in life and discuss perspectives on efforts to recover from such disruptions.

• Journal of Microbiology and Biotechnology
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• v.27 no.12
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• pp.2228-2236
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• 2017

During menopausal transition, the imbalance of estrogen causes body weight gain. Although gut microbiome dysbiosis has been reported in postmenopausal obesity, it is not clear whether there is any difference in the microbiome profile between dietary-induced obesity and postmenopausal obesity. Therefore, in this study, we analyzed intestinal samples from ovariectomized mice and compared them with those of mice with high-fat diet-induced obesity. To further evaluate the presence of menopause-specific bacteria-gene interactions, we also analyzed the liver transcriptome. Investigation of the 16S rRNA V3-V4 region amplicon sequence profile revealed that menopausal obesity and dietary obesity resulted in similar gut microbiome structures. However, Bifidobacterium animalis was exclusively observed in the ovariectomized mice, which indicated that menopausal obesity resulted in a different intestinal microbiome than dietary obesity. Additionally, several bacterial taxa (Dorea species, Akkermansia muciniphila, and Desulfovibrio species) were found when the ovariectomized mice were treated with a high-fat diet. A significant correlation between the above-mentioned menopause-specific bacteria and the genes for female hormone metabolism was also observed, suggesting the possibility of bacteria-gene interactions in menopausal obesity. Our findings revealed the characteristics of the intestinal microbiome in menopausal obesity in the mouse model, which is very similar to the dietary obesity microbiome but having its own diagnostic bacteria.

• Journal of Animal Environmental Science
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• v.21 no.3
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• pp.93-98
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• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• Biomedical Science Letters
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• v.24 no.4
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• pp.292-304
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• 2018

Microbes is becoming increasingly forensic possibility as a consequence of advances in massive parallel sequencing (MPS) and bioinformatics. Human DNA typing is the best identifier, but it is not always possible to extract a full DNA profile namely its degradation and low copy number, and it may have limitations for identical twins. To overcome these unsatisfactory limitations, forensic potential for bacteria found in evidence could be used to differentiate individuals. Prokaryotic cells have a cell wall that better protects the bacterial nucleoid compared to the cell membrane of eukaryotic cells. Humans have an extremely diverse microbiome that may prove useful in determining human identity and may even be possible to link the microbes to the person responsible for them. Microbial composition within the human microbiome varies across individuals. Therefore, MPS of human microbiome could be used to identify biological samples from the different individuals, specifically for twins and other cases where standard DNA typing doses not provide satisfactory results due to degradation of human DNA. Microbial forensics is a new discipline combining forensic science and microbiology, which can not to replace current STR analysis methods used for human identification but to be complementary. Among the fields of microbial forensics, this paper will briefly describe information on the current status of microbiome research such as metagenomic code, salivary microbiome, pubic hair microbiome, microbes as indicators of body fluids, soils microbes as forensic indicator, and review microbial forensics as the feasibility of microbiome-based human identification.

• Food Science and Industry
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• v.50 no.1
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• pp.2-10
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• 2017

Human have eaten various traditional fermented foods for a numbers of million years for health benefit as well as survival. The beneficial effects of fermented foods have been resulted from complex microbial communications within the fermented foods. Therefore, the holistic approaches for individual identification and complete microbial profiling involved in their communications have been of interest to food microbiology fields. Microbiome is the ecological community of microorganisms that literally share our environments including foods as well as human body. However, due to the limitation of culture-dependent methods such as simple isolations of just culturable microorganisms, the culture-independent methods have been consistently developed, resulting in new light on the diverse non-culturable and hitherto unknown microorganisms, and even microbial communities in the fermented foods. For the culture-independent approaches, the food microbiome has been deciphered by employing various molecular analysis tools such as fluorescence in situ hybridization, quantitative PCR, and denaturing gradient gel-electrophoresis. More recently, next-generation-sequencing (NGS) platform-based microbiome analysis has been of interest, because NGS is a powerful analytical tool capable of resolving the microbiome in respect to community structures, dynamics, and activities. In this overview, the development status of analysis tools for the fermented food microbiome is covered and research trend for NGS-based food microbiome analysis is also discussed.

• Journal of Microbiology and Biotechnology
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• v.32 no.9
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• pp.1086-1097
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• 2022

During the last decades, research and therapeutic methods in cancer treatment have been evolving. As the results, nowadays, cancer patients are receiving several types of treatments, ranging from chemotherapy and radiation therapy to surgery and immunotherapy. In fact, most cancer patients take a combination of current anti-cancer therapies to improve the efficacy of treatment. However, current strategies still cause some side effects to patients, such as pain and depression. Therefore, there is the need to discover better ways to eradicate cancer whilst minimizing side effects. Recently, immunotherapy, particularly immune checkpoint blockade, is rising as an effective anti-cancer treatment. Unlike chemotherapy or radiation therapy, immunotherapy has few side effects and a higher tumor cell removal efficacy depend on cellular immunological mechanisms. Moreover, recent studies suggest that tissue immune responses are regulated by their microbiome composition. Each tissue has their specific microenvironment, which makes their microbiome composition different, particularly in the context of different types of cancer, such as breast, colorectal, kidney, lung, and skin. Herein, we review the current understanding of the relationship of immune responses and tissue microbiome in cancer in both animal and human studies. Moreover, we discuss the cancer-microbiome-immune axis in the context of cancer development and treatment. Finally, we speculate on strategies to control tissue microbiome alterations that may synergistically affect the immune system and impact cancer treatment outcomes.