Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects

McDowell Andrea,Kang Juwon,Yang Jinho,Jung Jihee,Oh Yeon-Mok,Kym Sung-Min,Shin Tae-Seop,Kim Tae-Bum,Jee Young-Koo,Kim Yoon-Keun 생화학분자생물학회 2022 Experimental and molecular medicine Vol.54 No.-

Although mounting evidence suggests that the microbiome has a tremendous influence on intractable disease, the relationship between circulating microbial extracellular vesicles (EVs) and respiratory disease remains unexplored. Here, we developed predictive diagnostic models for COPD, asthma, and lung cancer by applying machine learning to microbial EV metagenomes isolated from patient serum and coded by their accumulated taxonomic hierarchy. All models demonstrated high predictive strength with mean AUC values ranging from 0.93 to 0.99 with various important features at the genus and phylum levels. Application of the clinical models in mice showed that various foods reduced high-fat diet-associated asthma and lung cancer risk, while COPD was minimally affected. In conclusion, this study offers a novel methodology for respiratory disease prediction and highlights the utility of serum microbial EVs as data-rich features for noninvasive diagnosis.

Diagnostic Models for Atopic Dermatitis Based on Serum Microbial Extracellular Vesicle Metagenomic Analysis: A Pilot Study

양진호,Andrea McDowell,서호찬,김성원,민택기,지영구,최영우,박해심,편복양,김윤근 대한천식알레르기학회 2020 Allergy, Asthma & Immunology Research Vol.12 No.5

Purpose: Associations between a wide variety of diseases and the microbiome have been extensively verified. Recently, there has been a rising interest in the role the microbiome plays in atopic dermatitis (AD). Furthermore, metagenomic analysis of microbe-derived extracellular vesicles (EVs) has revealed the importance and relevance of microbial EVs in human health. Methods: We compared the diversity and proportion of microbial EVs in the sera of 24 AD patients and 49 healthy controls, and developed a diagnostic model. After separating microbial EVs from serum, we specifically targeted the V3–V4 hypervariable regions of the 16S rDNA gene for amplification and subsequent sequencing. Results: Alpha and beta diversity between controls and AD patients both differed, but only the difference in beta diversity was significant. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in healthy controls and AD patients, accounting for over 85% of the total serum bacterial EVs. Also, Proteobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, and Cyanobacteria relative abundances were significantly different between the AD and control groups. At the genus level, the proportions of Escherichia-Shigella, Acinetobacter, Pseudomonas, and Enterococcus were drastically altered between the AD and control groups. AD diagnostic models developed using biomarkers selected on the basis of linear discriminant analysis effect size from the class to genus levels all yielded area under the receiver operating characteristic curve, sensitivity, specificity, and accuracy of value 1.00. Conclusions: In summary, microbial EVs demonstrated the potential in their use as novel biomarkers for AD diagnosis. Therefore, future work should investigate larger case and control groups with cross-sectional or longitudinal clinical data to explore the utility and validity of serum microbiota EV-based AD diagnosis.

Bile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile

윤수빈,유준선,Andrea McDowell,김성호,유현주,고광표 한국미생물학회 2017 The journal of microbiology Vol.55 No.11

Clostridium difficile infection (CDI) is one of the most common nosocomial infections. Dysbiosis of the gut microbiota due to consumption of antibiotics is a major contributor to CDI. Recently, fecal microbiota transplantation (FMT) has been applied to treat CDI. However, FMT has important limitations including uncontrolled exposure to pathogens and standardization issues. Therefore, it is necessary to evaluate alternative treatment methods, such as bacteriotherapy, as well as the mechanism through which beneficial bacteria inhibit the growth of C. difficile. Here, we report bile acid-mediated inhibition of C. difficile by Bacteroides strains which can produce bile salt hydrolase (BSH). Bacteroides strains are not commonly used to treat CDI; however, as they comprise a large proportion of the intestinal microbiota, they can contribute to bile acid-mediated inhibition of C. difficile. The inhibitory effect on C. difficile growth increased with increasing bile acid concentration in the presence of Bacteroides ovatus SNUG 40239. Furthermore, this inhibitory effect on C. difficile growth was significantly attenuated when bile acid availability was reduced by cholestyramine, a bile acid sequestrant. The findings of this study are important due to the discovery of a new bacterial strain that in the presence of available bile acids inhibits growth of C. difficile. These results will facilitate development of novel bacteriotherapy strategies to control CDI.

Development of a colorectal cancer diagnostic model and dietary risk assessment through gut microbiome analysis

Jinho Yang,Andrea McDowell,Eun Kyoung Kim,Hochan Seo,Won Hee Lee,Chang-Mo Moon,Sung-Min Kym,Dongho Lee,Young Soo Park,Young-Koo Jee,Yoon-Keun Kim 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

Colorectal cancer (CRC) is the third most common form of cancer and poses a critical public health threat due to theglobal spread of westernized diets high in meat, cholesterol, and fat. Although the link between diet and colorectalcancer has been well established, the mediating role of the gut microbiota remains elusive. In this study, we sought toelucidate the connection between the gut microbiota, diet, and CRC through metagenomic analysis of bacteriaisolated from the stool of CRC (n = 89) and healthy (n = 161) subjects. This analysis yielded a dozen genera that weresignificantly altered in CRC patients, including increased Bacteroides, Fusobacterium, Dorea, and Porphyromonasprevalence and diminished Pseudomonas, Prevotella, Acinetobacter, and Catenibacterium carriage. Based on thesealtered genera, we developed two novel CRC diagnostic models through stepwise selection and a simplified modelusing two increased and two decreased genera. As both models yielded strong AUC values above 0.8, the simplifiedmodel was applied to assess diet-based CRC risk in mice. Mice fed a westernized high-fat diet (HFD) showed greaterCRC risk than mice fed a regular chow diet. Furthermore, we found that nonglutinous rice, glutinous rice, and sorghumconsumption reduced CRC risk in HFD-fed mice. Collectively, these findings support the critical mediating role of thegut microbiota in diet-induced CRC risk as well as the potential of dietary grain intake to reduce microbiota-associatedCRC risk. Further study is required to validate the diagnostic prediction models developed in this study as well as thepreventive potential of grain consumption to reduce CRC risk.

Consumption of a Leuconostoc holzapfeliienriched synbiotic beverage alters the composition of the microbiota and microbial extracellular vesicles

Jinho Yang,Andrea McDowell,Eun Kyoung Kim,Hochan Seo,Kyujin Yum,Won Hee Lee,Young-Koo Jee,김윤근 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

Synbiotics, the combination of probiotics and prebiotics, are known to confer health benefits via intestinal microbiota modulation. However, significant intestinal microbiota alterations can be difficult to determine in intervention studies based on solely bacterial stool metagenomic analysis. Intestinal microbiota constituents secrete 20–200-nm-sized extracellular vesicles (EVs) containing microbial DNA, proteins, and lipids that are distributed throughout the body, providing an alternative target for microbiota metagenomic analysis. Here, we determined the impact of a synbiotic beverage enriched with the kimchi-derived bacterium Leuconostoc holzapfelii (L. holzapfelii) on the intestinal microbiota and local and circulatory microbiota-derived EV composition of healthy Korean adults. We isolated microbial DNA from stool bacteria, stool EVs, and urinary EVs and conducted next-generation sequencing of the 16S rDNA V3–V4 regions before and after synbiotic consumption. The species diversity of circulating urinary EVs was significantly increased after synbiotic consumption, while stool bacterial and EV diversity remained unchanged. Furthermore, we found that while a single genus was decreased among the stool bacteria constituents, stool EVs and urinary EVs showed significant alterations in four and eight genera, respectively. Blood chemistry assays revealed that synbiotic consumption significantly lowered aspartate aminotransferase (AST) serum levels, particularly in subjects with starting levels above the normal range (>40 UI/L). In conclusion, the L. holzapfelii-enriched synbiotic beverage greatly altered serum AST levels and microbial EV composition in urine and stool, while only minor changes were observed in the gut microbiota composition. Based on these findings, we suggest the potential use of microbiota-derived EVs as surrogate markers in future predictive diagnosis studies.

Brain tumor diagnostic model and dietary effect based on extracellular vesicle microbiome data in serum

양진호,문효은,박형우,Andrea McDowell,Tae-Seop Shin,Young Koo Jee,금성민,백선하,김윤근 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-

The human microbiome has been recently associated with human health and disease. Brain tumors (BTs) are a particularly difficult condition to directly link to the microbiome, as microorganisms cannot generally cross the blood–brain barrier (BBB). However, some nanosized extracellular vesicles (EVs) released from microorganisms can cross the BBB and enter the brain. Therefore, we conducted metagenomic analysis of microbial EVs in both serum (152 BT patients and 198 healthy controls (HC)) and brain tissue (5 BT patients and 5 HC) samples based on the V3–V4 regions of 16S rDNA. We then developed diagnostic models through logistic regression and machine learning algorithms using serum EV metagenomic data to assess the ability of various dietary supplements to reduce BT risk in vivo. Models incorporating the stepwise method and the linear discriminant analysis effect size (LEfSe) method yielded 12 and 29 significant genera as potential biomarkers, respectively. Models using the selected biomarkers yielded areas under the curves (AUCs) >0.93, and the model using machine learning resulted in an AUC of 0.99. In addition, Dialister and [Eubacterium] rectale were significantly lower in both blood and tissue samples of BT patients than in those of HCs. In vivo tests showed that BT risk was decreased through the addition of sorghum, brown rice oil, and garlic but conversely increased by the addition of bellflower and pear. In conclusion, serum EV metagenomics shows promise as a rich data source for highly accurate detection of BT risk, and several foods have potential for mitigating BT risk.

The impact of bacteria-derived ultrafine dust particles on pulmonary diseases

양진호,김은경,박현주,Andrea McDowell,김윤근 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-

The relationship between ambient particulate matter exposure and health has been well established. Ultrafine particles (UFP) with a diameter of 100nm or less are known to increase pulmonary disease risk. Biological factors in dust containing UFP can cause severe inflammatory reactions. Pulmonary diseases develop primarily as a result of chronic inflammation caused by immune dysfunction. Thus, this review focuses on the adverse pulmonary effects of biological UFP, principally lipopolysaccharide (LPS), and bacterial extracellular vesicles (EVs), in indoor dust and the pathophysiological mechanisms involved in the development of chronic pulmonary diseases. The impact of LPSinduced pulmonary inflammation is based primarily on the amount of inhaled LPS. When relatively low levels of LPS are inhaled, a cascade of immune responses leads to Th2 cell induction, and IL-5 and IL-13 released by Th2 cells contributes to asthma development. Conversely, exposure to high levels of LPS induces a Th17 cell response, leading to increased production of IL-17, which is associated with asthma, COPD, and lung cancer incidence. Responses to bacterial EV exposure can similarly be broadly divided based on whether one of two mechanisms, either intracellular or extracellular, is activated, which depends on the type of the parent cell. Extracellular bacteria-derived EVs can cause neutrophilic inflammation via Th17 cell induction, which is associated with asthma, emphysema, COPD, and lung cancer. On the other hand, intracellular bacteria-derived EVs lead to mononuclear inflammation via Th1 cell induction, which increases the risk of emphysema. In conclusion, future measures should focus on the overall reduction of LPS sources in addition to the improvement of the balance of inhaled bacterial EVs in the indoor environment to minimize pulmonary disease risk.

Bile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile

Yoon, Soobin,Yu, Junsun,McDowell, Andrea,Kim, Sung Ho,You, Hyun Ju,Ko, GwangPyo MICROBIOLOGICAL SOCIETY OF KOREA 2017 JOURNAL OF MICROBIOLOGY -SEOUL- Vol. No.

<P>Clostridium difficile infection (CDI) is one of the most common nosocomial infections. Dysbiosis of the gut microbiota due to consumption of antibiotics is a major contributor to CDI. Recently, fecal microbiota transplantation (FMT) has been applied to treat CDI. However, FMT has important limitations including uncontrolled exposure to pathogens and standardization issues. Therefore, it is necessary to evaluate alternative treatment methods, such as bacteriotherapy, as well as the mechanism through which beneficial bacteria inhibit the growth of C. difficile. Here, we report bile acid-mediated inhibition of C. difficile by Bacteroides strains which can produce bile salt hydrolase (BSH). Bacteroides strains are not commonly used to treat CDI; however, as they comprise a large proportion of the intestinal microbiota, they can contribute to bile acid-mediated inhibition of C. difficile. The inhibitory effect on C. difficile growth increased with increasing bile acid concentration in the presence of Bacteroides ovatus SNUG 40239. Furthermore, this inhibitory effect on C. difficile growth was significantly attenuated when bile acid availability was reduced by cholestyramine, a bile acid sequestrant. The findings of this study are important due to the discovery of a new bacterial strain that in the presence of available bile acids inhibits growth of C. difficile. These results will facilitate development of novel bacteriotherapy strategies to control CDI.</P>

Microbe-derived extracellular vesicles as a smart drug delivery system

Jinho Yang,Eun Kyoung Kim,Andrea McDowell,Yoon-Keun Kim 대한임상약리학회 2018 Translational and Clinical Pharmacology Vol.26 No.3

The human microbiome is known to play an essential role in influencing host health. Extracellularvesicles (EVs) have also been reported to act on a variety of signaling pathways, distally transportcellular components such as proteins, lipids, and nucleic acid, and have immunomodulatory effects. Here we shall review the current understanding of the intersectionality of the human microbiomeand EVs in the emerging field of microbiota-derived EVs and their pharmacological potential. Microbessecrete several classes of EVs: outer membrane vesicles (OMVs), membrane vesicles (MVs),and apoptotic bodies. EV biogenesis is unique to each cell and regulated by sophisticated signalingpathways. EVs are primarily composed of lipids, proteins, nucleic acids, and recent evidence suggeststhey may also carry metabolites. These components interact with host cells and control variouscellular processes by transferring their constituents. The pharmacological potential of microbiomederivedEVs as vaccine candidates, biomarkers, and a smart drug delivery system is a promisingarea of future research. Therefore, it is necessary to elucidate in detail the mechanisms of microbiome-derived EV action in host health in a multi-disciplinary manner.

Lactobacillus paracasei-derived extracellular vesicles attenuate the intestinal inflammatory response by augmenting the endoplasmic reticulum stress pathway

Ji Hyun Choi,문창모,Tae-Seop Shin,Eun Kyoung Kim,Andrea McDowell,Min-Kyung Jo,주양희,김성은,Hye-KyungJung,심기남,정성애,김윤근 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-

Lactobacillus paracasei is a major probiotic and is well known for its anti-inflammatory properties. Thus, we investigated the effects of L. paracasei-derived extracellular vesicles (LpEVs) on LPS-induced inflammation in HT29 human colorectal cancer cells and dextran sulfate sodium (DSS)-induced colitis in C57BL/6 mice. ER stress inhibitors (salubrinal or 4-PBA) or CHOP siRNA were utilized to investigate the relationship between LpEV-induced endoplasmic reticulum (ER) stress and the inhibitory effect of LpEVs against LPS-induced inflammation. DSS (2%) was administered to male C57BL/6 mice to induce inflammatory bowel disease, and disease activity was measured by determining colon length, disease activity index, and survival ratio. In in vitro experiments, LpEVs reduced the expression of the LPSinduced pro-inflammatory cytokines IL-1α, IL-1β, IL-2, and TNFα and increased the expression of the anti-inflammatory cytokines IL-10 and TGFβ. LpEVs reduced LPS-induced inflammation in HT29 cells and decreased the activation of inflammation-associated proteins, such as COX-2, iNOS and NFκB, as well as nitric oxide. In in vivo mouse experiments, the oral administration of LpEVs also protected against DSS-induced colitis by reducing weight loss, maintaining colon length, and decreasing the disease activity index (DAI). In addition, LpEVs induced the expression of endoplasmic reticulum (ER) stress-associated proteins, while the inhibition of these proteins blocked the anti-inflammatory effects of LpEVs in LPS-treated HT29 cells, restoring the pro-inflammatory effects of LPS. This study found that LpEVs attenuate LPS-induced inflammation in the intestine through ER stress activation. Our results suggest that LpEVs have a significant effect in maintaining colorectal homeostasis in inflammation-mediated pathogenesis.