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Aljohani A, Clarke D, Byrne M, Fleming G. The bacterial microbiome and resistome of house dust mites in Irish homes. Sci Rep 2024; 14:19621. [PMID: 39179632 PMCID: PMC11343766 DOI: 10.1038/s41598-024-70686-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024] Open
Abstract
Dust samples were collected from Irish homes. House Dust Mite and storage mites were separated from the dust. The microbiome and resistome of mites and originating dust were assessed using a culture-independent approach. The bacterial microbiome of mites and dust were predominantly populated by Staphylococci. There was a highly significant (P = 0.005; Spearman's rank test) correlation between the bacterial microbiome of mites and the dust. One-hundred and eighteen antimicrobial resistance genes (ARGs) were associated with mites and 176 with dust. Both contained ARGs encoding resistance for multi drug resistances, macrolide-lincosamide-streptogramin B, mobile genetic elements, Beta-lactam, Tetracycline and Aminoglycosides. By contrast, 15 ARGs were found for a laboratory-grown strain of Dermatophagoides pteronyssinus. A significant difference (P = 0.03; t test) was found in means between the resistome of mites and the household dust from which they emanated. No significant correlations (P = 0.23 and P = 0.22; Mantel test) were observed between the microbiome and resistome of mite and dust samples. There was not a significant difference (P = 0.54; t-test) between the means of ARGs for homes with and without a history of antibiotic use.
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Affiliation(s)
- Amal Aljohani
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland.
| | | | - Miriam Byrne
- Physics, School of Natural Sciences, University of Galway, Galway, Ireland
| | - Gerard Fleming
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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Wierz JC, Dirksen P, Kirsch R, Krüsemer R, Weiss B, Pauchet Y, Engl T, Kaltenpoth M. Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders. THE ISME JOURNAL 2024; 18:wrae099. [PMID: 38874172 PMCID: PMC11322605 DOI: 10.1093/ismejo/wrae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/05/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Insects engage in manifold interactions with bacteria that can shift along the parasitism-mutualism continuum. However, only a small number of bacterial taxa managed to successfully colonize a wide diversity of insects, by evolving mechanisms for host-cell entry, immune evasion, germline tropism, reproductive manipulation, and/or by providing benefits to the host that stabilize the symbiotic association. Here, we report on the discovery of an Enterobacterales endosymbiont (Symbiodolus, type species Symbiodolus clandestinus) that is widespread across at least six insect orders and occurs at high prevalence within host populations. Fluorescence in situ hybridization in several Coleopteran and one Dipteran species revealed Symbiodolus' intracellular presence in all host life stages and across tissues, with a high abundance in female ovaries, indicating transovarial vertical transmission. Symbiont genome sequencing across 16 host taxa revealed a high degree of functional conservation in the eroding and transposon-rich genomes. All sequenced Symbiodolus genomes encode for multiple secretion systems, alongside effectors and toxin-antitoxin systems, which likely facilitate host-cell entry and interactions with the host. However, Symbiodolus-infected insects show no obvious signs of disease, and biosynthetic pathways for several amino acids and cofactors encoded by the bacterial genomes suggest that the symbionts may also be able to provide benefits to the hosts. A lack of host-symbiont cospeciation provides evidence for occasional horizontal transmission, so Symbiodolus' success is likely based on a mixed transmission mode. Our findings uncover a hitherto undescribed and widespread insect endosymbiont that may present valuable opportunities to unravel the molecular underpinnings of symbiosis establishment and maintenance.
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Affiliation(s)
- Jürgen C Wierz
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Philipp Dirksen
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Roy Kirsch
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Ronja Krüsemer
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Benjamin Weiss
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Tobias Engl
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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Liu HH, Chen L, Shao HB, Gao S, Hong XY, Bing XL. Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape. MICROBIAL ECOLOGY 2023; 87:1. [PMID: 37991578 DOI: 10.1007/s00248-023-02314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.
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Affiliation(s)
- Huan-Huan Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hui-Biao Shao
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shuo Gao
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Yang T, Xu Z, Yu J, Liu J, Wang W, Hong S. Exosomes Derived from Dermatophagoides farinae Induce Allergic Airway Inflammation. Microbiol Spectr 2023; 11:e0505422. [PMID: 37314339 PMCID: PMC10434197 DOI: 10.1128/spectrum.05054-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/04/2023] [Indexed: 06/15/2023] Open
Abstract
House dust mites (HDMs) are a major source of indoor allergens that cause airway allergic disease. Dermatophagoides farinae, a predominant species of HDMs in China, has demonstrated pathogenic role in allergic disorders. Exosomes derived from human bronchoalveolar lavage fluid have been strongly associated with allergic respiratory diseases progression. However, the pathogenic role of D. farinae-derived exosomes in allergic airway inflammation has remained unclear until now. Here, D. farinae was stirred overnight in phosphate-buffered saline, and the supernatant was used to extract exosomes by ultracentrifugation. Then, shotgun liquid chromatography-tandem mass spectrometry and small RNA sequencing were performed to identify proteins and microRNAs contained in D. farinae exosomes. Immunoblotting, Western blotting, and enzyme-linked immunosorbent assay demonstrated the specific immunoreactivity of D. farinae-specific serum IgE antibody against D. farinae exosomes, and D. farinae exosomes were found to induce allergic airway inflammation in a mouse model. In addition, D. farinae exosomes invaded 16-HBE bronchial epithelial cells and NR8383 alveolar macrophages to release the inflammation-related cytokines interleukin-33 (IL-33), thymic stromal lymphopoietin, tumor necrosis factor alpha, and IL-6, and comparative transcriptomic analysis of 16-HBE and NR8383 cells revealed that immune pathways and immune cytokines/chemokines were involved in the sensitization of D. farinae exosomes. Taken together, our data demonstrate that D. farinae exosomes are immunogenic and may induce allergic airway inflammation via bronchial epithelial cells and alveolar macrophages. IMPORTANCE Dermatophagoides farinae, a predominant species of house dust mites in China, has displayed pathogenic role in allergic disorders, and exosomes derived from human bronchoalveolar lavage fluid have been strongly associated with allergic respiratory diseases progression. However, the pathogenic role of D. farinae-derived exosomes in allergic airway inflammation has remained unclear until now. This study, for the first time, extracted exosomes from D. farinae, and sequenced their protein cargo and microRNAs using shotgun liquid chromatography-tandem mass spectrometry and small RNA sequencing. D. farinae-derived exosomes trigger allergen-specific immune responses and present satisfactory immunogenicity, as revealed by immunoblotting, Western blotting, and enzyme-linked immunosorbent assay and may induce allergic airway inflammation via bronchial epithelial cells and alveolar macrophages. Our data provide insights into the mechanisms of allergic airway inflammation caused with D. farinae-derived exosomes and the treatment of house dust mite-induced allergic airway inflammation.
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Affiliation(s)
- Ting Yang
- Department of Dermatology, Affiliated Children’s Hospital of Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Zuyu Xu
- Graduate School of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Jinyan Yu
- Graduate School of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Jiaxi Liu
- Graduate School of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Wei Wang
- National Health Commission Key Laboratory on Parasitic Disease Prevention and Control, Jiangsu Provincial Key Laboratory on Parasites and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, People’s Republic of China
| | - Shanchao Hong
- Department of Clinical Laboratory, Jiangnan University Medical Center, Wuxi, Jiangsu, People’s Republic of China
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Yi MH, Kim M, Yong TS, Kim JY. Investigating the microbiome of house dust mites in South Korea. FRONTIERS IN ALLERGY 2023; 4:1240727. [PMID: 37655177 PMCID: PMC10466795 DOI: 10.3389/falgy.2023.1240727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
Understanding the house dust mites (HDMs) microbiome is crucial due to its potential effects on the development of allergic diseases. In 1998, our laboratory collected Dermatophagoides farinae and D. pteronyssinus from beds in a Korean household and began cultivating these HDMs. Our laboratory has been actively investigating several topics about HDMs in recent years, including the bacterial and fungal microbiome and their interactions, as well as the impact of the HDM microbiome on airway inflammation. To study the D. farinae microbiome, we employed high-throughput sequencing of the 16S rDNA amplicons. The results revealed that the two most abundant bacteria were Enterococcus faecalis and Bartonella spp. In contrast, we found almost no bacteria in D. pteronyssinus. By inoculating bacteria to HDMs, we found that D. farinae is more susceptible to bacteria than D. pteronyssinus. This susceptibility was associated with the presence of certain fungal species in D. pteronyssinus. Additionally, we have recently made efforts to produce HDMs with reduced levels of symbiotic bacteria. We believe that standardizing and controlling the microbiome in HDMs are crucial steps for the future development and improvement of allergic immunotherapies.
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Affiliation(s)
| | | | | | - Ju Yeong Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
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Kim JY, Yi MH, Kim M, Choi JH, Lee S, Yong TS. Production of Dermatophagoides farinae Having Low Bacterial Content Using Ampicillin. J Immunol Res 2023; 2023:9024595. [PMID: 37252681 PMCID: PMC10212681 DOI: 10.1155/2023/9024595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
Background Symbiotic bacteria in house dust mites pose a risk of immunological side effects in the clinical use of immunotherapeutic agents. In this study, we investigated the duration for which the bacterial concentration in Dermatophagoides farinae could be kept low with antibiotic treatment, and whether the allergenic properties of the mite changed under ampicillin treatment. Methods D. farinae was cultivated in the presence of ampicillin powder in an autoclaved medium for 6 weeks. After subsequent subcultures without ampicillin, the mites were harvested, and the extract was prepared. The amounts of bacteria, lipopolysaccharides (LPS), and two major allergens (Der f 1 and Der f 2) were measured. Human bronchial epithelial cells and mice were treated with the D. farinae extract to assess the allergic airway inflammation. Results The number of bacteria and level of LPS were reduced by 150-fold and 33-fold, respectively, at least 18 weeks after ampicillin treatment. The concentration of Der f 1 and Der f 2 remained unchanged by ampicillin treatment. The secretion of interleukin (IL)-6 and IL-8 from the human airway epithelial cells decreased when treated with the extract of ampicillin-treated D. farinae compared with that of ampicillin-untreated D. farinae. A mouse asthma model was developed using ampicillin-treated D. farinae. We observed that the level of lung function, airway inflammation, and serum-specific immunoglobulin were not different for the mouse asthma model developed using ampicillin-treated D. farinae than the model developed using ampicillin-untreated D. farinae. Conclusions We showed that bacterial content in D. farinae was reduced by ampicillin treatment, which was sufficient to induce allergic sensitization and an immune response. This method will be used to develop more controlled allergy immunotherapeutic agents.
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Affiliation(s)
- Ju Yeong Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Institute of Allergy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myung-hee Yi
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Institute of Allergy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myungjun Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jun Ho Choi
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seogwon Lee
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tai-Soon Yong
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Institute of Allergy, Yonsei University College of Medicine, Seoul, Republic of Korea
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Vackova T, Pekar S, Klimov PB, Hubert J. Population growth and respiration in the dust mite Dermatophagoides farinae under different temperature and humidity regimes. EXPERIMENTAL & APPLIED ACAROLOGY 2023; 89:157-169. [PMID: 36723778 DOI: 10.1007/s10493-022-00775-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Dermatophagoides farinae is an important house dust mite species that causes allergies in humans worldwide. In houses, these mites are commonly found in actively used mattresses and pillows, which provide food (i.e. sloughed skin and microorganisms), moisture, and increased temperature for faster mite development. In mattresses, feeding mites prefer the upper sector, as close as possible to the resting human (temperature 32-36 °C, humidity between 55 and 59%). However, mites that are not actively feeding prefer staying at deeper zones of the mattress. Here, we analyzed mite responses to different temperatures (15-35 °C) and relative humidity (62-94% RH) in terms of their population size growth and respiration (CO2 production) using lab mite cultures. The intrinsic rate of population increase had a single maximum at approximately 28 °C and 85% RH. At 30 °C, there were two respiration peaks at RH 90% (smaller peak) and 65% (larger peak). Therefore, there is a mismatch between the optimal temperature/humidity for the population size increase vs. respiration. We propose preliminary hypotheses explaining the two respiration peaks and suggest that future research should be done to elucidate the nature of these peaks.
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Affiliation(s)
- Tereza Vackova
- Crop Research Institute, Drnovska 507/73, 161 06, Prague 6 - Ruzyne, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 1594/7, 128 44, Prague 2 - New Town, Czechia
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 267/2, 611 37, Brno, Czechia
| | - Pavel B Klimov
- Lilly Hall of Life Sciences, Purdue University, G-225, 915 W State St, West Lafayette, IN, 47907, USA
- X-Bio Institute, Tyumen State University, 10 Semakova Str., 625003, Tyumen, Russia
| | - Jan Hubert
- Crop Research Institute, Drnovska 507/73, 161 06, Prague 6 - Ruzyne, Czechia.
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6 - Suchdol, Czechia.
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Woo C, Bhuiyan MIU, Kim D, Kumari P, Lee SK, Park JY, Dong K, Lee K, Yamamoto N. DNA metabarcoding-based study on bacteria and fungi associated with house dust mites (Dermatophagoides spp.) in settled house dust. EXPERIMENTAL & APPLIED ACAROLOGY 2022; 88:329-347. [PMID: 36301451 DOI: 10.1007/s10493-022-00755-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
House dust mites (HDMs) including Dermatophagoides spp. are an important cause of respiratory allergies. However, their relationship with microorganisms in house dust has not been fully elucidated. Here, we characterized bacteria and fungi associated with HDMs in house dust samples collected in 107 homes in Korea by using DNA barcode sequencing of bacterial 16S rRNA gene, fungal internal transcribed spacer 2 (ITS2) region, and arthropod cytochrome c oxidase I (COI) gene. Our inter-kingdom co-occurrence network analysis and/or indicator species analysis identified that HDMs were positively related with a xerophilic fungus Wallemia, mycoparasitic fungi such as Cystobasidium, and some human skin-related bacterial and fungal genera, and they were negatively related with the hygrophilous fungus Cephalotrichum. Overall, our study has succeeded in adding novel insights into HDM-related bacteria and fungi in the house dust ecosystem, and in confirming the historically recognized fact that HDMs are associated with xerophilic fungi such as Wallemia. Understanding the microbial ecology in house dust is thought to be important for elucidating the etiology of human diseases including allergies, and our study revealed baseline information of house dust ecology in relation to HDMs. The findings could be useful from a perspective of human health.
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Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mohammad Imtiaj Uddin Bhuiyan
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Donghyun Kim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Priyanka Kumari
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung-Kyung Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji Young Park
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ke Dong
- Major of Life Science, College of Natural Sciences, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Kiyoung Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.
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