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Zhang G, Le Souëf P. The influence of modern living conditions on the human microbiome and potential therapeutic opportunities for allergy prevention. World Allergy Organ J 2024; 17:100857. [PMID: 38235259 PMCID: PMC10793171 DOI: 10.1016/j.waojou.2023.100857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/01/2023] [Accepted: 12/09/2023] [Indexed: 01/19/2024] Open
Abstract
Modern living conditions and the recent surge in global urbanization have transformed the human microbiome. This transformation is believed to be a significant factor in the recent spike of common chronic inflammatory diseases like asthma and allergies worldwide, evident in both developed and developing nations. Immigrants from less developed regions who settle in highly urbanized and affluent areas present an ideal demographic for research. Investigating immigrant populations can yield valuable insights, particularly when studying microbiome changes that occur as individuals transition from areas with low asthma prevalence to regions with a high prevalence of the condition. The application of prebiotics and probiotics as potential treatments for asthma and allergies faces challenges. This is due to the complex interplay of numerous factors that contribute to their aetiology. Exploring the interaction between the human microbiome and potential epigenetic changes in specific populations, such as immigrants adapting to new, urbanized environments, may offer crucial insights. Such research could underscore the role of prebiotics and probiotics in preventing allergic conditions. Recognizing the changes in the human microbiome in the context of a Western/modern environment might be essential in addressing the increasing prevalence of allergic diseases. Persistent research in this domain is pivotal for devising effective interventions such as dietary supplementation with prebiotics and probiotics.
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Affiliation(s)
- Guicheng Zhang
- School of Population Health, Curtin University, Perth, 6102, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Peter Le Souëf
- School of Population Health, Curtin University, Perth, 6102, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia 6008, Australia
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Schwager MJ, Song Y, Laing IA, Saiganesh A, Guo J, Le Souëf PN, Zhang G. Increased nasal Streptococcus pneumoniae presence in Western environment associated with allergic conditions in Chinese immigrants. Int J Hyg Environ Health 2021; 234:113735. [PMID: 33725492 DOI: 10.1016/j.ijheh.2021.113735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/15/2021] [Accepted: 03/04/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Chinese immigrants living in Australia experience increased allergic conditions: asthma, eczema, hay fever and wheeze. Recently we reported diminished innate cytokine responses in long-term immigrants, potentially increasing their pathogenic viral load and microbial carriage. We hypothesise that a Western environment changes the nasal microbiome profile, and this altered profile may be associated with the development of allergic conditions. In this cross-sectional study, we aimed to examine the loading of viral and microbial respiratory pathogens in the upper airway. METHODS Adult Chinese immigrants were grouped depending on time spent in Australia: short-term (<6 years) or long-term (≥6 years). First, age- and gender-matched immigrants were selected for an initial screen using quantitative polymerase chain reaction (qPCR) micro-array panels. Then based on initial results the viruses, human parainfluenza 3 and rhinovirus, and the bacteria, Burkholderia spp., Staphylococcus aureus and Streptococcus pneumoniae, were validated using qPCR in the population. Associations for bacterial prevalence with atopic phenotypes were investigated. RESULTS Pooling the initial screen and validation subjects, S. aureus and S. pneumoniae had higher prevalence in long-term compared with short-term subjects (25.0% vs 8.1%, P = 0.012; and 76.8% vs 48.4%, P = 0.002). Those immigrants with nasal S. pneumoniae presence resided longer (average time 90.4 months) in Australia than immigrants without S. pneumoniae (52.7 months; P = 0.001). After adjusting for confounders, Chinese immigrants with S. pneumoniae carriage have a five-fold increased risk of doctor-diagnosed eczema (odds ratio, OR 5.36, 95% CI: 1.10-26.14; P = 0.038) compared to immigrants without S. pneumoniae carriage. There was a trend of S. pneumoniae abundance correlating with reduced host Toll-like receptor gene expression. CONCLUSION Our findings suggest that nasal S. pneumoniae may play a role in the development of allergic conditions in Chinese immigrants in a Western environment.
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Affiliation(s)
- Michelle J Schwager
- School of Public Health, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia; Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia (M409), Perth, Western Australia, 6009, Australia; Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia; Telethon Kids Institute, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia.
| | - Yong Song
- School of Public Health, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia; Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia (M409), Perth, Western Australia, 6009, Australia.
| | - Ingrid A Laing
- Telethon Kids Institute, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia; Division of Cardiovascular and Respiratory Sciences, The University of Western Australia (M560), 35 Stirling Highway, Perth, Western Australia, 6009, Australia.
| | - Aarti Saiganesh
- Telethon Kids Institute, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia.
| | - Jing Guo
- School of Public Health, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia; Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia (M409), Perth, Western Australia, 6009, Australia.
| | - Peter N Le Souëf
- Telethon Kids Institute, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia; Division of Paediatrics, School of Medicine, The University of Western Australia (M561), 35 Stirling Highway, Perth, Western Australia, 6009, Australia.
| | - Guicheng Zhang
- School of Public Health, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia; Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia (M409), Perth, Western Australia, 6009, Australia; Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia; Telethon Kids Institute, The University of Western Australia, PO Box 855, West Perth, Western Australia, 6872, Australia.
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Guo J, Zhang X, Saiganesh A, Peacock C, Chen S, Dykes GA, Hales BJ, Le Souëf PN, Zhang G. Linking the westernised oropharyngeal microbiome to the immune response in Chinese immigrants. Allergy Asthma Clin Immunol 2020; 16:67. [PMID: 32944027 PMCID: PMC7491349 DOI: 10.1186/s13223-020-00465-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background Human microbiota plays a fundamental role in modulating the immune response. Western environment and lifestyle are envisaged to alter the human microbiota with a new microbiome profile established in Chinese immigrants, which fails to prime the immune system. Here, we investigated how differences in composition of oropharyngeal microbiome may contribute to patterns of interaction between the microbiome and immune system in Chinese immigrants living in Australia. Methods We recruited 44 adult Chinese immigrants: newly-arrived (n = 22, living in Australia < 6 months) and long-term Chinese immigrants (n = 22, living in Australia > 5 years), with age and gender matched. Oropharyngeal swabs, serum and whole blood were collected. The 16 s ribosomal RNA gene from the swabs was sequenced on the Illumina MiSeq platform. Innate immune responses were determined by 23 Toll-like receptors (TLR) pathway cytokines, while adaptive immune responses were determined by IgG-associated response to specific microbial/viral pathogens. Results The relative abundance of the genus Leptotrichia was higher in long-term immigrants as compared to that in newly-arrived Chinese immigrants, while the genus Deinococcus was significantly lower in long-term Chinese immigrants. The genera uncultured Lachnospiraceae, Erysipelotrichaceae UCG-007, Veillonella, and Actinomycetales_ambiguous taxa were negatively correlated with cytokine IL-6 in long-term Chinese immigrants (rho range: − 0.46 ~ − 0.73). With respect to adaptive immunity, several microbial taxa were significantly associated with IgG1 responsiveness to microbial antigens in long-term immigrants, while a significant correlation with IgG1 responsiveness to viral antigens was detected in newly-arrived immigrants. Conclusions The composition of the oropharyngeal microbiome varies between newly-arrived and long-term Chinese immigrants. Specific microbial taxa are significantly associated with immunological parameters but with different association patterns between newly-arrived and long-term Chinese immigrants.
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Affiliation(s)
- Jing Guo
- School of Public Health, Curtin University, Perth, WA Australia.,Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, WA Australia
| | - Xiaoping Zhang
- School of Public Health, Curtin University, Perth, WA Australia.,China National Bamboo Research Centre, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou, Zhejiang China
| | - Aarti Saiganesh
- Telethon Kids Institute, The University of Western Australia, Perth, WA Australia
| | - Christopher Peacock
- Telethon Kids Institute, The University of Western Australia, Perth, WA Australia.,Marshall Centre for Infectious Disease, School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA Australia
| | - Shu Chen
- School of Public Health, Curtin University, Perth, WA Australia
| | - Gary A Dykes
- School of Public Health, Curtin University, Perth, WA Australia
| | - Belinda J Hales
- Telethon Kids Institute, The University of Western Australia, Perth, WA Australia
| | - Peter N Le Souëf
- Telethon Kids Institute, The University of Western Australia, Perth, WA Australia.,Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA Australia
| | - Guicheng Zhang
- School of Public Health, Curtin University, Perth, WA Australia.,Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, WA Australia.,Telethon Kids Institute, The University of Western Australia, Perth, WA Australia.,Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA Australia
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Shi TT, Hua L, Xin Z, Li Y, Liu W, Yang YL. Identifying and Validating Genes with DNA Methylation Data in the Context of Biological Network for Chinese Patients with Graves' Orbitopathy. Int J Endocrinol 2019; 2019:6212681. [PMID: 31001336 PMCID: PMC6437746 DOI: 10.1155/2019/6212681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/07/2019] [Accepted: 01/22/2019] [Indexed: 11/27/2022] Open
Abstract
AIM This study investigated the association of DNA methylation with Graves' orbitopathy (GO) incidence through a combined analysis in the context of biological network to identify and validate potential genes for Chinese patients with GO. METHODS A genome-scale screening of DNA methylation was performed on the peripheral blood sample of six patients with GO and six controls. After extracting differentially methylated regions (DMRs), the study focused on two classes of genes with obviously different methylation levels: low methylated genes (LMGs) and high methylated genes (HMGs). Mutual information was applied to construct LMG- and HMG-regulated networks, and the top 10 LMGs and HMGs were extracted based on the topological properties. Then, 9 candidate genes were extracted to validate their association with GO in an expanded population (48 patients with GO vs. 24 normal controls) using single-cell methylation sequencing. RESULTS In the LMG-regulated network, some LMGs displayed a higher degree, such as HIST1H2AL, EFCAB1, and BOLL. Similarly, in the HMG-regulated network, some HMGs, such as MBP, ANGEL1, and LYAR, also showed a higher degree. For validation using an enlarged population, BOLL still displayed the lower methylation level whereas CDK5 and MBP still displayed the higher methylation level in patients with GO in the multivariable logistic regression analysis adjusted by age and gender (P < 0.01). CONCLUSIONS BOLL, CDK5, and MBP are potential genes associated with GO. This study was novel in clinically investigating the relation of these genomic loci with GO. The findings might provide new insights into understanding this disease.
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Affiliation(s)
- Ting-Ting Shi
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lin Hua
- Department of Mathematics, School of Biomedical Engineering, Capital Medical University, Beijing, China
| | - Zhong Xin
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yu Li
- Physical Examination Department, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei Liu
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yi-Lin Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Tham EH, Loo EXL, Zhu Y, Shek LPC. Effects of Migration on Allergic Diseases. Int Arch Allergy Immunol 2018; 178:128-140. [PMID: 30466080 DOI: 10.1159/000494129] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022] Open
Abstract
Studies in migrant populations provide vital opportunities to investigate the role of environmental factors in the pathogenesis of allergic disorders. Differences in allergy prevalence have been observed between migrants and native-born subjects living in the same geographical location. Immigrants who migrate from less affluent countries with lower allergy prevalence tend to have a lower prevalence of allergic disorders compared to native-born residents of the more affluent host country. The patterns of allergic disease prevalence also differ between first- and second-generation migrants. The timing of migration in relation to birth, age at migration, and duration of residence in the host country also influence one's atopic risk. A complex interplay of multiple environmental, socioeconomic, and cultural factors is likely responsible for these observed differences. Further research into the roles of various risk factors in modulating differences in allergic disease prevalence between migrant and native populations will enhance our understanding of the complex gene-environment interactions involved in the pathogenesis of allergic disorders.
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Affiliation(s)
- Elizabeth Huiwen Tham
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System (NUHS), Singapore, Singapore, .,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore,
| | - Evelyn Xiu Ling Loo
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yanan Zhu
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lynette Pei-Chi Shek
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System (NUHS), Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
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Saiganesh A, Hales BJ, Li Y, Holt PG, Le Souëf PN, Zhang G. A marked shift in innate and adaptive immune response in chinese immigrants living in a western environment. Allergy 2018; 73:2092-2094. [PMID: 29935021 DOI: 10.1111/all.13531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Aarti Saiganesh
- School of Paediatrics and Child Health University of Western Australia Perth WA Australia
- Telethon Kids Institute University of Western Australia Perth WA Australia
| | - Belinda J. Hales
- Telethon Kids Institute University of Western Australia Perth WA Australia
| | - Yuchun Li
- Xinxiang Medical University Henan China
| | - Patrick G. Holt
- Telethon Kids Institute University of Western Australia Perth WA Australia
| | - Peter N. Le Souëf
- School of Paediatrics and Child Health University of Western Australia Perth WA Australia
| | - Guicheng Zhang
- School of Paediatrics and Child Health University of Western Australia Perth WA Australia
- Telethon Kids Institute University of Western Australia Perth WA Australia
- Xinxiang Medical University Henan China
- School of Public Health Curtin University Perth WA Australia
- Centre for Genetic Origins of Health and Disease Faculty of Health and Medical Sciences Faculty of Health and Medical Sciences Curtin University he University of Western Australia and Royal Perth Hospital Research Foundation Perth WA Australia
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Epigenetic modifications of gene expression by lifestyle and environment. Arch Pharm Res 2017; 40:1219-1237. [PMID: 29043603 DOI: 10.1007/s12272-017-0973-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
Epigenetics oftenly described as the heritable changes in gene expression independent of changes in DNA sequence. Various environmental factors such as nutrition-dietary components, lifestyle, exercise, physical activity, toxins, and other contributing factors remodel the genome either in a constructive or detrimental way. Since epigenetic changes are reversible and nutrition is one of the many epigenetic regulators that modify gene expression without changing the DNA sequence, dietary nutrients and bioactive food components contribute to epigenetic phenomena either by directly suppressing DNA methylation or histone catalyzing enzymes or by changing the availability of substrates required for enzymatic reactions. Diets that contain catechol-dominant polyphenols are reported to suppress enzyme activity and activate epigenetically silenced genes. Furthermore, several dietary nutrients play a crucial role in one-carbon metabolism including folate, cobalamin, riboflavin, pyridoxine, and methionine by directly affecting S-adenosyl-L-methionine. Soy polyphenols block DNA methyltransferases and histone deacetylases to reverse aberrant CpG island methylation. Organosulfur rich compounds such as the sulforaphane found in broccoli appear to normalize DNA methylation and activate miR-140 expression, which represses SOX9 and ALDH1 and decreases tumor growth. The purpose of this short communication is to overview the epigenetic regulatory mechanisms of diet and other environmental factors. We discuss the epigenetic contributions of dietary components with a particular focus on nutritional polyphenols and flavonoids as epigenetic mediators that modify epigenetic tags and control gene expression. These mechanisms provide new insights to better understand the influence of dietary nutrients on epigenetic modifications and gene expression.
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Lee KH, Song Y, O'Sullivan M, Pereira G, Loh R, Zhang GB. The Implications of DNA Methylation on Food Allergy. Int Arch Allergy Immunol 2017; 173:183-192. [PMID: 28848217 DOI: 10.1159/000479513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Food allergy is a major clinical and public health concern worldwide. The risk factors are well defined, however, the mechanisms by which they affect immune development remain largely unknown, and unfortunately the effective treatment or prevention of food allergy is still being researched. Recent studies show that the genes that are critical for the development of food allergy are regulated through DNA methylation. Environmental factors can affect host DNA methylation status and subsequently predispose people to food allergy. DNA methylation is therefore an important mediator of gene-environment interactions in food allergy and key to understanding the mechanisms underlying the allergic development. Indeed, the modification and identification of the methylation levels of specific genetic loci have gained increasing attention for therapeutic and diagnostic application in combating food allergy. In this review, we summarize and discuss the recent developments of DNA methylation in food allergy, including the pathogenesis, therapy, and diagnosis. This review will also summarize and discuss the environmental factors that affect DNA methylation levels in food allergy.
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Affiliation(s)
- Khui Hung Lee
- School of Public Health, Curtin University of Technology, Bentley WA, Australia
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