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Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN, Chotirmall SH. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024; 18:111-125. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology, and treatment outcomes. AREAS COVERED We detail the dynamics of the airway microbiome, its influence on chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline (January 2010-March 2024) were retrieved and summarized. We examine clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, antiinflammatories and antimicrobial strategies is discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management. EXPERT OPINION Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogencentric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving crossdisciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials, and therapeutic development pipelines.
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Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Shivani Singh
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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Tiew PY, Meldrum OW, Chotirmall SH. Applying Next-Generation Sequencing and Multi-Omics in Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2023; 24:ijms24032955. [PMID: 36769278 PMCID: PMC9918109 DOI: 10.3390/ijms24032955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microbiomics have significantly advanced over the last decade, driven by the widespread availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allow for a holistic assessment of endophenotypes across a range of chronic respiratory disease states, including chronic obstructive pulmonary disease (COPD). Valuable insight has been attained into the nature, function, and significance of microbial communities in disease onset, progression, prognosis, and response to treatment in COPD. Moving beyond single-biome assessment, there now exists a growing literature on functional assessment and host-microbe interaction and, in particular, their contribution to disease progression, severity, and outcome. Identifying specific microbes and/or metabolic signatures associated with COPD can open novel avenues for therapeutic intervention and prognosis-related biomarkers. Despite the promise and potential of these approaches, the large amount of data generated by such technologies can be challenging to analyze and interpret, and currently, there remains a lack of standardized methods to address this. This review outlines the current use and proposes future avenues for the application of NGS and multi-omic technologies in the endophenotyping, prognostication, and treatment of COPD.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 169608, Singapore
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Oliver W. Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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Xu X, Ding F, Hu X, Yang F, Zhang T, Dong J, Xue Y, Liu T, Wang J, Jin Q. Upper respiratory tract mycobiome alterations in different kinds of pulmonary disease. Front Microbiol 2023; 14:1117779. [PMID: 37032908 PMCID: PMC10076636 DOI: 10.3389/fmicb.2023.1117779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The human respiratory tract is considered to be a polymicrobial niche, and an imbalance in the microorganism composition is normally associated with several respiratory diseases. In addition to the well-studied bacteriome, the existence of fungal species in the respiratory tract has drawn increasing attention and has been suggested to have a significant clinical impact. However, the understanding of the respiratory fungal microbiota (mycobiome) in pulmonary diseases is still insufficient. Methods In this study, we investigated the fungal community composition of oropharynx swab (OS) samples from patients with five kinds of pulmonary disease, including interstitial lung disease (ILD), bacterial pneumonia (BP), fungal pneumonia (FP), asthma (AS) and lung cancer (LC), and compared them with healthy controls (HCs), based on high-throughput sequencing of the amplified fungal internal transcribed spacer (ITS) region. Results The results showed significant differences in fungal composition and abundance between disease groups and HCs. Malassezia was the most significant genus, which was much more abundant in pulmonary diseases than in the control. In addition, many common taxa were shared among different disease groups, but differences in taxa abundance and specific species in distinct disease groups were also observed. Based on linear discriminant analysis effect size (LefSe), each group had its characteristic species. Furthermore, some species showed a significant correlation with the patient clinical characteristics. Discussion Our study deepened our understanding of the respiratory tract mycobiome in some diseases that are less studied and identified the commonalities and differences among different kinds of pulmonary disease. These results would provide the solid basis for further investigation of the association between the mycobiome and pathogenicity of pulmonary diseases.
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Affiliation(s)
- Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangping Ding
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiangqi Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Xue
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Tao Liu,
| | - Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Jing Wang,
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Qi Jin,
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Zhang Y, Shen F, Yang Y, Niu M, Chen D, Chen L, Wang S, Zheng Y, Sun Y, Zhou F, Qian H, Wu Y, Zhu T. Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6282-6293. [PMID: 35512288 PMCID: PMC9113006 DOI: 10.1021/acs.est.2c00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 05/04/2023]
Abstract
Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a part of environmental microbiotas. However, the expiratory microbiota community and its associations with environmental microbiotas remain poorly understood. Here, expiratory bacteria and fungi and the corresponding microbiotas from the living environments were characterized by DNA amplicon sequencing of residents' exhaled breath condensate (EBC) and environmental samples collected from 14 residences in Nanjing, China. The microbiotas of EBC samples, with a substantial heterogeneity, were found to be as diverse as those of skin, floor dust, and airborne microbiotas. Model fitting results demonstrated the role of stochastic processes in the assembly of the expiratory microbiota. Using a fast expectation-maximization algorithm, microbial community analysis revealed that expiratory microbiotas were differentially associated with other types of microbiotas in a type-dependent and residence-specific manner. Importantly, the expiratory bacteria showed a composition similarity with airborne bacteria in the bathroom and kitchen environments with an average of 12.60%, while the expiratory fungi showed a 53.99% composition similarity with the floor dust fungi. These differential patterns indicate different relationships between expiratory microbiotas and the airborne microbiotas and floor dust microbiotas. The results here illustrated for the first time the associations between expiratory microbiotas and indoor microbiotas, showing a potential microbial exchange between the respiratory tract and indoor environment. Thus, improved hygiene and ventilation practices can be implemented to optimize the indoor microbial exposome, especially in indoor bathrooms and kitchens.
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Affiliation(s)
- Yin Zhang
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Fangxia Shen
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Yi Yang
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Mutong Niu
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Da Chen
- School
of Environment and Guangdong Key Laboratory of Environmental Pollution
and Health, Jinan University, Guangzhou 510632, China
| | - Longfei Chen
- School
of Energy and Power Engineering, Beihang
University, Beijing 100191, China
| | - Shengqi Wang
- School
of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yunhao Zheng
- Institute
of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ye Sun
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Feng Zhou
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Hua Qian
- School
of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yan Wu
- School of
Environmental Science and Engineering, Shandong
University, Jinan 250100, China
| | - Tianle Zhu
- School
of Space and Environment, Beihang University, Beijing 100191, China
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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Tiew PY, Mac Aogáin M, Chotirmall SH. The current understanding and future directions for sputum microbiome profiling in chronic obstructive pulmonary disease. Curr Opin Pulm Med 2022; 28:121-133. [PMID: 34839338 DOI: 10.1097/mcp.0000000000000850] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Next-generation sequencing (NGS) has deepened our understanding of the respiratory microbiome in health and disease. The number of microbiome studies employing sputum as an airway surrogate has continued to increase over the past decade to include multiple large multicentre and longitudinal studies of the microbiome in chronic obstructive pulmonary disease (COPD). In this review, we summarize the recent advances to our understanding of the bacteriome, virome and mycobiome in COPD. RECENT FINDINGS Diverse microbiome profiles are reported in COPD. The neutrophilic Haemophilus-predominant bacteriome remains a prominent COPD phenotype, relatively stable over time and during exacerbations. Studies of the virome remain limited but reveal a potential involvement of viruses and bacteriophages particularly during COPD exacerbations and advancing disease severity. Mycobiome signatures, even in stable COPD are associated with poorer clinical outcomes including mortality. SUMMARY The sputum microbiome in COPD is being increasingly recognized for its clinical relevance, even in the stable state. Future studies integrating microbial kingdoms holistically (i.e. bacterial, viral and fungal) will provide deeper insight into its functionality including the relevance of microbial interactions and effect of treatment on microbiome-associated clinical outcomes.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Ireland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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Respiratory Mycoses: A Call to Action to Recognize, Educate and Invest. Mycopathologia 2021; 186:569-573. [PMID: 34490550 PMCID: PMC8421193 DOI: 10.1007/s11046-021-00589-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/21/2021] [Indexed: 02/08/2023]
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Mucus, Microbiomes and Pulmonary Disease. Biomedicines 2021; 9:biomedicines9060675. [PMID: 34199312 PMCID: PMC8232003 DOI: 10.3390/biomedicines9060675] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022] Open
Abstract
The respiratory tract harbors a stable and diverse microbial population within an extracellular mucus layer. Mucus provides a formidable defense against infection and maintaining healthy mucus is essential to normal pulmonary physiology, promoting immune tolerance and facilitating a healthy, commensal lung microbiome that can be altered in association with chronic respiratory disease. How one maintains a specialized (healthy) microbiome that resists significant fluctuation remains unknown, although smoking, diet, antimicrobial therapy, and infection have all been observed to influence microbial lung homeostasis. In this review, we outline the specific role of polymerizing mucin, a key functional component of the mucus layer that changes during pulmonary disease. We discuss strategies by which mucin feed and spatial orientation directly influence microbial behavior and highlight how a compromised mucus layer gives rise to inflammation and microbial dysbiosis. This emerging field of respiratory research provides fresh opportunities to examine mucus, and its function as predictors of infection risk or disease progression and severity across a range of chronic pulmonary disease states and consider new perspectives in the development of mucolytic treatments.
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Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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