Analysis of 16S rRNA gene sequencing data for the taxonomic characterization of the vaginal and the fecal microbial communities in Hanwoo

Choi Soyoung,Cha Jihye,Song Minji,Son JuHwan,Park Mi-Rim,Lim Yeong-jo,Kim Tae-Hun,Lee Kyung-Tai,Park Woncheoul 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.11

Objective: The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome. Methods: A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples. Results: The results revealed that the phylum-level microorganisms with the largest relative distribution were Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria in the vagina, and Firmicutes, Bacteroidetes, and Spirochaetes in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome. Conclusion: There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship. Objective: The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome.Methods: A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples.Results: The results revealed that the phylum-level microorganisms with the largest relative distribution were <i>Firmicutes</i>, <i>Actinobacteria</i>, <i>Bacteroidetes</i>, and <i>Proteobacteria</i> in the vagina, and <i>Firmicutes</i>, <i>Bacteroidetes</i>, and <i>Spirochaetes</i> in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome.Conclusion: There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship.

친환경적 생물 복원을 위한 Indigenous Microbiome Transplantation 기술

한송이 한국미생물학회 2020 미생물학회지 Vol.56 No.1

The whole world is suffering from climate change and accumulation of harmful compounds, pesticide, and antibiotics, caused by the highly advanced chemical industry and agricultural environment. As the measures for restoring the ecosystem environment-friendlily and then continuously maintaining it, the diversity and functions of indigenous microbiome are grabbing attention. So far, many researches on the functions of indigenous microbiome cultured through in vitro researches have been introduce, such an indigenous microbiome has been participating in many processes such as decomposition and production of organic matters within environment. This review discussed the importance of diversity of indigenous microbiome focusing on the environmental remediation technology, and introduced the core microbiome. This review also introduced some cases of applying the Indigenous Microbiome Transplantation (IMT) technology for the effective use of this core indigenous microbiome. Suggesting the new research results and the possibility of IMT technology using the indigenous microbiome in the future, this review expects to see the expansion of the base of researches on technologies that could apply the indigenous microbiome to the restoration of contaminate ecosystem and the continuous environmental management. 전세계적으로 고도화된 화학산업과 농업환경으로 인한 기후변화 및 유해화합물, 살충제, 항생제 등의 축적으로 인한 문제가 발생하고 있다. 이들 오염을 친환경적으로 회복시키고지속적으로 생태계를 유지하기 위한 방안으로 토착미생물의다양성과 기능이 주목받고 있다. 현재까지 많은 기내 연구(in vitro)를 통해 토착미생물이 환경 내에서 물질 분해와 유기물생산 등의 많은 과정에 참여하고 있음이 밝혀졌다. 본 리뷰에서는 환경복원기술을 중심으로 토착미생물 다양성의 중요성을 논하고 핵심미생물군집에 대하여 소개하였다. 이들 핵심토착미생물 군집을 효과적으로 이용하기 위해 토착미생물 군집이식 기술을 적용한 사례들을 소개하였다. 본 리뷰를 통하여토착미생물을 이용한 IMT 기술에 대한 새로운 연구결과와 가능성을 제안하고 오염된 생태계의 복원과 지속적인 환경관리에 토착미생물을 적용시키는 기술 연구에 대한 저변 확대를기대한다.

Exercise, the Gut Microbiome, and Frailty

신형은,곽성은,Ji-Hyun Lee,Didi Zhang,배준현,송욱 대한노인병학회 2019 Annals of geriatric medicine and research Vol.23 No.3

The gut microbiome is deeply associated with both skeletal muscle and brain function. In particular, gut microbiome dysbiosis may accelerate age-related diseases by affecting these systems. Although there is increasing evidence of the correlations between the gut microbiome and skeletal muscle and brain, it remains unclear whether changes in the gut microbiome due to exercise training can lead to healthy aging. This review discusses the current status of gut microbiome-related research and future directions related to aging (e.g., physical frailty and cognitive dysfunction) as well as the effect of exercise training on both. We reviewed relevant literature including original articles and reviews identified from searches of the PubMed, Google Scholar, SCOPUS, EBSCOHost, ScienceDirect, Cochrane Library, and EMBASE databases using the following terms: ‘gut microbiome’, ‘exercise’, ‘physical frailty’, and ‘cognitive dysfunction’. This review identified a strong positive correlation between cognitive dysfunction or physical frailty and the gut microbiome. Furthermore, exercise had a significant effect on the composition of the gut microbiome. These results suggest that exercise training can prevent physical frailty or cognitive dysfunction by altering the gut microbiome. However, the exact mechanism by which these effects occur is not yet clear. Further studies are needed to determine whether exercise training can prevent age-related diseases by balancing the gut microbiome.

국내외 호흡기 및 인체 마이크로바이옴 연구

최성미 ( Sungmi Choi ),조상헌 ( Sang-heon Cho ),이하나 ( Hana Yi ) 대한천식알레르기학회(구 대한알레르기학회) 2016 Allergy Asthma & Respiratory Disease Vol.4 No.5

During the second half of the 2000s, the significant impact of human microbiome on human diseases and health conditions was found. Since the Human Microbiome Project, many microbiome studies have been reported in domestic and international references. Gastrointestinal tract microbiome has been most investigated so far, and the association with illness has been demonstrated in many diseases. Recently, the range of study was extended to multiple human organs, such as the respiratory tract, skin, and urogenital tract. Given the scale and speed of research and development in recent years, the role of microbiome in many diseases would be established before long. In this review, we aimed to summarize the current status of microbiome studies in Korea and foreign countries with an emphasis on respiratory tract microbiome. The main concept and analytical methods for microbiome research, associations of microbiome and diseases, and research projects on Korean microbiome are reviewed. (Allergy Asthma Respir Dis 2016:4:311-320)

Application of Microbiome-Based Therapies in Chronic Respiratory Diseases

Lee Se Hee,Lee Jang Ho,Lee Sei Won 한국미생물학회 2024 The journal of microbiology Vol.62 No.3

The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and affected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably different, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome influences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fiber diets, for example, present beneficial effects through the production of short-chain fatty acids. Additionally, genetically modified probiotics to secrete some beneficial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

Role of microbiome and its metabolite, short chain fatty acid in prostate cancer

양희조,김재헌 대한비뇨의학회 2023 Investigative and Clinical Urology Vol.64 No.1

The microbiome which is an assembly of all microbes living inside our bodies performs a major role in maintaining human health and wellness. It has been found that the imbalance of the microbiome can cause various diseases in humans. Similarly, there is growing evidence that the microbiome largely affects a person’s chance of contracting certain cancers and how the disease develops and progresses. Studies have shown that about 15% to 20% of all cancers are caused by microbial pathogens. The prevalence of prostate cancer, which is increasing rapidly in Korea, is related to lifestyle including diet. These diets can alter the gut microbial composition, and the effect of the microbiome on prostate cancer development can be estimated. However, the microbiome associated with prostate cancer has been reported differently according to race. This means that the metabolite rather than the specific microbiome will be important. Short chain fatty acids, metabolites of the microbiome, plays an important role in the action mechanism of the microbiome. Short chain fatty acids play roles such as immunomodulation and inhibition of histone deacetylase. Here, we examined the most up-to-date literature featuring the effects of the microbiome on the risk and pathogenesis of prostate cancer.

Gut microbiome-produced metabolites in pigs: a review on their biological functions and the influence of probiotics

Robie Vasquez,오주경,송지훈,Dae-Kyung Kang 한국축산학회 2022 한국축산학회지 Vol.64 No.4

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.

Effect of Consumption of Animal Products on the Gut Microbiome Composition and Gut Health

이채원,이준범,어주영,곽민진,허철성,김영훈 한국축산식품학회 2023 한국축산식품학회지 Vol.43 No.5

The gut microbiome is critical in human health, and various dietary factors influence its composition and function. Among these factors, animal products, such as meat, dairy, and eggs, represent crucial sources of essential nutrients for the gut microbiome. However, the correlation and characteristics of livestock consumption with the gut microbiome remain poorly understood. This review aimed to delineate the distinct effects of meat, dairy, and egg products on gut microbiome composition and function. Based on the previous reports, the impact of red meat, white meat, and processed meat consumption on the gut microbiome differs from that of milk, yogurt, cheese, or egg products. In particular, we have focused on animal-originated proteins, a significant nutrient in each livestock product, and revealed that the major proteins in each food elicit diverse effects on the gut microbiome. Collectively, this review highlights the need for further insights into the interactions and mechanisms underlying the impact of animal products on the gut microbiome. A deeper understanding of these interactions would be beneficial in elucidating the development of dietary interventions to prevent and treat diseases linked to the gut microbiome.

Correlations Between the Adenotonsillar Microbiome and Clinical Characteristics of Pediatric Patients With Snoring

김경수,민현진 대한이비인후과학회 2021 Clinical and Experimental Otorhinolaryngology Vol.14 No.3

Objectives. Few studies have reported combined analyses of the microbiome of the adenoids and tonsils in pediatric patients with snoring, and correlations of the adenotonsillar microbiome with clinical characteristics have not been evaluated to date. The aim of this study was to characterize the adenotonsillar microbiome and to determine its correlations with the subjective symptoms of pediatric patients with snoring and with levels of regional mucosal immune molecules. Methods. Twenty-four children who underwent tonsillectomy with adenoidectomy owing to snoring were enrolled in this cross-sectional study conducted between August 2017 and December 2018. The microbiome of the adenoids and tonsils was characterized, and its alpha- and beta-diversity was determined. Clinical characteristics, including subjective discomfort during sleep (assessed using the obstructive sleep apnea-18 questionnaire), the presence of allergic rhinitis, concentrations of heat shock protein (Hsp)27, Hsp70, and interleukin-8 (IL-8) in lavage fluids, and white blood cell (WBC) counts, were measured. Results. At the phylum level, the microbiome was not significantly different between the adenoids and tonsils; the alpha and beta indices were likewise not significantly different between these two regions. The alpha-diversity of the entire adenotonsillar microbiome was associated with sex, emotional stress, and IL-8 levels in the tonsil lavage fluids. Beta-diversity was associated with Hsp27 levels in the tonsil lavage fluids and WBC counts. Multiple allergen simultaneous test results were not significant, although total serum immunoglobulin E levels were significantly associated with the beta-diversity of the adenotonsillar microbiome. Conclusion. The data reported herein suggest, for the first time, that the adenotonsillar microbiome interacts with the regional mucosal immune system. The observed association of the microbiome with subjective discomfort is a novel finding that warrants further investigation.

Probing the diversity of healthy oral microbiome with bioinformatics approaches

( Ji-hoi Moon ),( Jae-hyung Lee ) 생화학분자생물학회(구 한국생화학분자생물학회) 2016 BMB Reports Vol.49 No.12

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. [BMB Reports 2016; 49(12): 662-670]