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Xia H, Lin J, Wang Y, Yu J, Wang H, Cheng C, Yang Y, Bian T, Wu Y, Liu Q. Stenotrophomonas maltophilia contributes to smoking-related emphysema through IRF1-triggered PANoptosis of alveolar epithelial cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123913. [PMID: 38582189 DOI: 10.1016/j.envpol.2024.123913] [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: 02/06/2024] [Revised: 03/18/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Cigarette smoke (CS), the main source of indoor air pollution and the primary risk factor for respiratory diseases, contains chemicals that can perturb microbiota through antibiotic effects. Although smoking induces a disturbance of microbiota in the lower respiratory tract, whether and how it contributes to initiation or promotion of emphysema are not well clarified. Here, we demonstrated an aberrant microbiome in lung tissue of patients with smoking-related COPD. We found that Stenotrophomonas maltophilia (S. maltophilia) was expanded in lung tissue of patients with smoking-related COPD. We revealed that S. maltophilia drives PANoptosis in alveolar epithelial cells and represses formation of alveolar organoids through IRF1 (interferon regulatory factor 1). Mechanistically, IRF1 accelerated transcription of ZBP1 (Z-DNA Binding Protein 1) in S. maltophilia-infected alveolar epithelial cells. Elevated ZBP1 served as a component of the PANoptosome, which triggered PANoptosis in these cells. By using of alveolar organoids infected by S. maltophilia, we found that targeting of IRF1 mitigated S. maltophilia-induced injury of these organoids. Moreover, the expansion of S. maltophilia and the expression of IRF1 negatively correlated with the progression of emphysema. Thus, the present study provides insights into the mechanism of lung dysbiosis in smoking-related COPD, and presents a potential target for mitigation of COPD progression.
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Affiliation(s)
- Haibo Xia
- School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China; Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Jiaheng Lin
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Yue Wang
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Jinyan Yu
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, People's Republic of China
| | - Hailan Wang
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Cheng Cheng
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Yi Yang
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Tao Bian
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, People's Republic of China
| | - Yan Wu
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, People's Republic of China
| | - Qizhan Liu
- School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China; Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Suzhou Institute of Public Health, Gusu School, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.
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2
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Chotirmall SH, Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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 in chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline searches between Jan 2010 and March 2024 were retrieved and summarized. The review examines clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, anti-inflammatories and antimicrobial strategies are 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 'pathogen-centric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving cross-disciplinary 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)
- 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
| | - 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
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY
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Roth-Walter F, Adcock IM, Benito-Villalvilla C, Bianchini R, Bjermer L, Caramori G, Cari L, Chung KF, Diamant Z, Eguiluz-Gracia I, Knol EF, Jesenak M, Levi-Schaffer F, Nocentini G, O'Mahony L, Palomares O, Redegeld F, Sokolowska M, Van Esch BCAM, Stellato C. Metabolic pathways in immune senescence and inflammaging: Novel therapeutic strategy for chronic inflammatory lung diseases. An EAACI position paper from the Task Force for Immunopharmacology. Allergy 2024; 79:1089-1122. [PMID: 38108546 DOI: 10.1111/all.15977] [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: 09/13/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
The accumulation of senescent cells drives inflammaging and increases morbidity of chronic inflammatory lung diseases. Immune responses are built upon dynamic changes in cell metabolism that supply energy and substrates for cell proliferation, differentiation, and activation. Metabolic changes imposed by environmental stress and inflammation on immune cells and tissue microenvironment are thus chiefly involved in the pathophysiology of allergic and other immune-driven diseases. Altered cell metabolism is also a hallmark of cell senescence, a condition characterized by loss of proliferative activity in cells that remain metabolically active. Accelerated senescence can be triggered by acute or chronic stress and inflammatory responses. In contrast, replicative senescence occurs as part of the physiological aging process and has protective roles in cancer surveillance and wound healing. Importantly, cell senescence can also change or hamper response to diverse therapeutic treatments. Understanding the metabolic pathways of senescence in immune and structural cells is therefore critical to detect, prevent, or revert detrimental aspects of senescence-related immunopathology, by developing specific diagnostics and targeted therapies. In this paper, we review the main changes and metabolic alterations occurring in senescent immune cells (macrophages, B cells, T cells). Subsequently, we present the metabolic footprints described in translational studies in patients with chronic asthma and chronic obstructive pulmonary disease (COPD), and review the ongoing preclinical studies and clinical trials of therapeutic approaches aiming at targeting metabolic pathways to antagonize pathological senescence. Because this is a recently emerging field in allergy and clinical immunology, a better understanding of the metabolic profile of the complex landscape of cell senescence is needed. The progress achieved so far is already providing opportunities for new therapies, as well as for strategies aimed at disease prevention and supporting healthy aging.
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Affiliation(s)
- F Roth-Walter
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - I M Adcock
- Molecular Cell Biology Group, National Heart & Lung Institute, Imperial College London, London, UK
| | - C Benito-Villalvilla
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - R Bianchini
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
| | - L Bjermer
- Department of Respiratory Medicine and Allergology, Lung and Allergy research, Allergy, Asthma and COPD Competence Center, Lund University, Lund, Sweden
| | - G Caramori
- Department of Medicine and Surgery, University of Parma, Pneumologia, Italy
| | - L Cari
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - K F Chung
- Experimental Studies Medicine at National Heart & Lung Institute, Imperial College London & Royal Brompton & Harefield Hospital, London, UK
| | - Z Diamant
- Department of Respiratory Medicine and Allergology, Institute for Clinical Science, Skane University Hospital, Lund, Sweden
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Department of Clinical Pharmacy & Pharmacology, University Groningen, University Medical Center Groningen and QPS-NL, Groningen, The Netherlands
| | - I Eguiluz-Gracia
- Allergy Unit, Hospital Regional Universitario de Málaga-Instituto de Investigación Biomédica de Málaga (IBIMA)-ARADyAL, Málaga, Spain
| | - E F Knol
- Departments of Center of Translational Immunology and Dermatology/Allergology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M Jesenak
- Department of Paediatrics, Department of Pulmonology and Phthisiology, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, University Teaching Hospital, Martin, Slovakia
| | - F Levi-Schaffer
- Institute for Drug Research, Pharmacology Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - G Nocentini
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - L O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - O Palomares
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - F Redegeld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - M Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - B C A M Van Esch
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - C Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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Gao J, Yang Y, Xiang X, Zheng H, Yi X, Wang F, Liang Z, Chen D, Shi W, Wang L, Wu D, Feng S, Huang Q, Li X, Shu W, Chen R, Zhong N, Wang Z. Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease. Respir Res 2024; 25:165. [PMID: 38622589 DOI: 10.1186/s12931-024-02805-2] [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: 09/20/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10-5), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10-8). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yuqiong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaopeng Xiang
- The Hong Kong Polytechnic University, Hong Kong, Hung Hom Kowloon, China
| | - Huimin Zheng
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Fengyan Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhenyu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Dandan Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Weijuan Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Lingwei Wang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Di Wu
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengchuan Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qiaoyun Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xueping Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China.
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
| | - Zhang Wang
- Institute of Ecological Sciences, Biomedical Research Center, School of Life Sciences, State Key Laboratory of Respiratory Disease, South China Normal University, Guangzhou, Guangdong Province, China.
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Lipinksi JH, Ranjan P, Dickson RP, O’Dwyer DN. The Lung Microbiome. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1269-1275. [PMID: 38560811 PMCID: PMC11073614 DOI: 10.4049/jimmunol.2300716] [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: 10/25/2023] [Accepted: 01/01/2024] [Indexed: 04/04/2024]
Abstract
Although the lungs were once considered a sterile environment, advances in sequencing technology have revealed dynamic, low-biomass communities in the respiratory tract, even in health. Key features of these communities-composition, diversity, and burden-are consistently altered in lung disease, associate with host physiology and immunity, and can predict clinical outcomes. Although initial studies of the lung microbiome were descriptive, recent studies have leveraged advances in technology to identify metabolically active microbes and potential associations with their immunomodulatory by-products and lung disease. In this brief review, we discuss novel insights in airway disease and parenchymal lung disease, exploring host-microbiome interactions in disease pathogenesis. We also discuss complex interactions between gut and oropharyngeal microbiota and lung immunobiology. Our advancing knowledge of the lung microbiome will provide disease targets in acute and chronic lung disease and may facilitate the development of new therapeutic strategies.
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Affiliation(s)
- Jay H. Lipinksi
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Piyush Ranjan
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - David N. O’Dwyer
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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Walsh D, Bevan J, Harrison F. How Does Airway Surface Liquid Composition Vary in Different Pulmonary Diseases, and How Can We Use This Knowledge to Model Microbial Infections? Microorganisms 2024; 12:732. [PMID: 38674677 PMCID: PMC11052052 DOI: 10.3390/microorganisms12040732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Growth environment greatly alters many facets of pathogen physiology, including pathogenesis and antimicrobial tolerance. The importance of host-mimicking environments for attaining an accurate picture of pathogen behaviour is widely recognised. Whilst this recognition has translated into the extensive development of artificial cystic fibrosis (CF) sputum medium, attempts to mimic the growth environment in other respiratory disease states have been completely neglected. The composition of the airway surface liquid (ASL) in different pulmonary diseases is far less well characterised than CF sputum, making it very difficult for researchers to model these infection environments. In this review, we discuss the components of human ASL, how different lung pathologies affect ASL composition, and how different pathogens interact with these components. This will provide researchers interested in mimicking different respiratory environments with the information necessary to design a host-mimicking medium, allowing for better understanding of how to treat pathogens causing infection in these environments.
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Affiliation(s)
- Dean Walsh
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.H.)
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Zheng L, Liu C, Wang H, Zhang J, Mao L, Dong X, Hu S, Li N, Pi D, Qiu J, Xu F, Chen C, Zou Z. Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury. MICROBIOME 2024; 12:56. [PMID: 38494479 PMCID: PMC10946114 DOI: 10.1186/s40168-024-01772-6] [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: 06/07/2023] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Accumulating clinical evidence suggests that lung microbiome is closely linked to the progression of pulmonary diseases; however, it is still controversial which specimen type is preferred for the evaluation of lung microbiome. METHODS AND RESULTS To address this issue, we established a classical acute lung injury (ALI) mice model by intratracheal instillation of lipopolysaccharides (LPS). We found that the bacterial DNA obtained from the bronchoalveolar lavage fluid (BALF), intact lung tissue [Lung(i)], lung tissue after perfused [Lung(p)], and feces of one mouse were enough for 16S rRNA sequencing, except the BALF of mice treated with phosphate buffer saline (PBS), which might be due to the biomass of lung microbiome in the BALF were upregulated in the mice treated with LPS. Although the alpha diversity among the three specimens from lungs had minimal differences, Lung(p) had higher sample-to-sample variation compared with BALF and Lung(i). Consistently, PCoA analysis at phylum level indicated that BALF was similar to Lung(i), but not Lung(p), in the lungs of mice treated with LPS, suggesting that BALF and Lung(i) were suitable for the evaluation of lung microbiome in ALI. Importantly, Actinobacteria and Firmicutes were identified as the mostly changed phyla in the lungs and might be important factors involved in the gut-lung axis in ALI mice. Moreover, Actinobacteria and Proteobacteria might play indicative roles in the severity of lung injury. CONCLUSION This study shows both Lung(i) and BALF are suitable for the evaluation of murine lung microbiome in ALI, and several bacterial phyla, such as Actinobacteria, may serve as potential biomarkers for the severity of ALI. Video Abstract.
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Affiliation(s)
- Lijun Zheng
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Chengjun Liu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Hongjing Wang
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jun Zhang
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China
| | - Lejiao Mao
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xiaomei Dong
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Siyao Hu
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Na Li
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Dandan Pi
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Jingfu Qiu
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Feng Xu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Chengzhi Chen
- Department of Occupational and Environmental Health, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China
| | - Zhen Zou
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China.
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Taherkhani H, KavianFar A, Aminnezhad S, Lanjanian H, Ahmadi A, Azimzadeh S, Masoudi-Nejad A. Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome. Heliyon 2024; 10:e24775. [PMID: 38370212 PMCID: PMC10869780 DOI: 10.1016/j.heliyon.2024.e24775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.
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Affiliation(s)
- Hamidreza Taherkhani
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Azadeh KavianFar
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Sargol Aminnezhad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Sadegh Azimzadeh
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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9
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Tangedal S, Nielsen R, Aanerud M, Drengenes C, Husebø GR, Lehmann S, Knudsen KS, Hiemstra PS, Eagan TM. Lower airway microbiota in COPD and healthy controls. Thorax 2024:thorax-2023-220455. [PMID: 38331579 DOI: 10.1136/thorax-2023-220455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The lower airway microbiota in patients with chronic obstructive pulmonary disease (COPD) are likely altered compared with the microbiota in healthy individuals. Information on how the microbiota is affected by smoking, use of inhaled corticosteroids (ICS) and COPD severity is still scarce. METHODS In the MicroCOPD Study, participant characteristics were obtained through standardised questionnaires and clinical measurements at a single centre from 2012 to 2015. Protected bronchoalveolar lavage samples from 97 patients with COPD and 97 controls were paired-end sequenced with the Illumina MiSeq System. Data were analysed in QIIME 2 and R. RESULTS Alpha-diversity was lower in patients with COPD than controls (Pielou evenness: COPD=0.76, control=0.80, p=0.004; Shannon entropy: COPD=3.98, control=4.34, p=0.01). Beta-diversity differed with smoking only in the COPD cohort (weighted UniFrac: permutational analysis of variance R2=0.04, p=0.03). Nine genera were differentially abundant between COPD and controls. Genera enriched in COPD belonged to the Firmicutes phylum. Pack years were linked to differential abundance of taxa in controls only (ANCOM-BC (Analysis of Compositions of Microbiomes with Bias Correction) log-fold difference/q-values: Haemophilus -0.05/0.048; Lachnoanaerobaculum -0.04/0.03). Oribacterium was absent in smoking patients with COPD compared with non-smoking patients (ANCOM-BC log-fold difference/q-values: -1.46/0.03). We found no associations between the microbiota and COPD severity or ICS. CONCLUSION The lower airway microbiota is equal in richness in patients with COPD to controls, but less even. Genera from the Firmicutes phylum thrive particularly in COPD airways. Smoking has different effects on diversity and taxonomic abundance in patients with COPD compared with controls. COPD severity and ICS use were not linked to the lower airway microbiota.
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Affiliation(s)
- Solveig Tangedal
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Rune Nielsen
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Marianne Aanerud
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Christine Drengenes
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Gunnar R Husebø
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sverre Lehmann
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Kristel S Knudsen
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tomas Ml Eagan
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
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10
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Melani AS, Croce S, Fabbri G, Messina M, Bargagli E. Inhaled Corticosteroids in Subjects with Chronic Obstructive Pulmonary Disease: An Old, Unfinished History. Biomolecules 2024; 14:195. [PMID: 38397432 PMCID: PMC10887366 DOI: 10.3390/biom14020195] [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: 12/11/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the major causes of disability and death. Maintenance use of inhaled bronchodilator(s) is the cornerstone of COPD pharmacological therapy, but inhaled corticosteroids (ICSs) are also commonly used. This narrative paper reviews the role of ICSs as maintenance treatment in combination with bronchodilators, usually in a single inhaler, in stable COPD subjects. The guidelines strongly recommend the addition of an ICS in COPD subjects with a history of concomitant asthma or as a step-up on the top of dual bronchodilators in the presence of hospitalization for exacerbation or at least two moderate exacerbations per year plus high blood eosinophil counts (≥300/mcl). This indication would only involve some COPD subjects. In contrast, in real life, triple inhaled therapy is largely used in COPD, independently of symptoms and in the presence of exacerbations. We will discuss the results of recent randomized controlled trials that found reduced all-cause mortality with triple inhaled therapy compared with dual inhaled long-acting bronchodilator therapy. ICS use is frequently associated with common local adverse events, such as dysphonia, oral candidiasis, and increased risk of pneumonia. Other side effects, such as systemic toxicity and unfavorable changes in the lung microbiome, are suspected mainly at higher doses of ICS in elderly COPD subjects with comorbidities, even if not fully demonstrated. We conclude that, contrary to real life, the use of ICS should be carefully evaluated in stable COPD patients.
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Affiliation(s)
- Andrea S. Melani
- Respiratory Diseases Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.C.); (G.F.); (M.M.); (E.B.)
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11
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Cheng J, Zhou L, Wang H. Symbiotic microbial communities in various locations of the lung cancer respiratory tract along with potential host immunological processes affected. Front Cell Infect Microbiol 2024; 14:1296295. [PMID: 38371298 PMCID: PMC10873922 DOI: 10.3389/fcimb.2024.1296295] [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: 09/18/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Lung cancer has the highest mortality rate among all cancers worldwide. The 5-year overall survival rate for non-small cell lung cancer (NSCLC) is estimated at around 26%, whereas for small cell lung cancer (SCLC), the survival rate is only approximately 7%. This disease places a significant financial and psychological burden on individuals worldwide. The symbiotic microbiota in the human body has been significantly associated with the occurrence, progression, and prognosis of various diseases, such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. Studies have demonstrated that respiratory symbiotic microorganisms and their metabolites play a crucial role in modulating immune function and contributing to the pathophysiology of lung cancer through their interactions with the host. In this review, we provide a comprehensive overview of the microbial characteristics associated with lung cancer, with a focus on the respiratory tract microbiota from different locations, including saliva, sputum, bronchoalveolar lavage fluid (BALF), bronchial brush samples, and tissue. We describe the respiratory tract microbiota's biodiversity characteristics by anatomical region, elucidating distinct pathological features, staging, metastasis, host chromosomal mutations, immune therapies, and the differentiated symbiotic microbiota under the influence of environmental factors. Our exploration investigates the intrinsic mechanisms linking the microbiota and its host. Furthermore, we have also provided a comprehensive review of the immune mechanisms by which microbiota are implicated in the development of lung cancer. Dysbiosis of the respiratory microbiota can promote or inhibit tumor progression through various mechanisms, including DNA damage and genomic instability, activation and regulation of the innate and adaptive immune systems, and stimulation of epithelial cells leading to the upregulation of carcinogenesis-related pathways.
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Affiliation(s)
- Jiuling Cheng
- Respiratory Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lujia Zhou
- Henan Key Laboratory of Precision Diagnosis of Respiratory Infectious Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Key Laboratory of Precision Diagnosis of Respiratory Infectious Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Huaqi Wang
- Respiratory Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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12
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Taylor SL, Crabbé A, Hoffman LR, Chalmers JD, Rogers GB. Understanding the clinical implications of the "non-classical" microbiome in chronic lung disease: a viewpoint. Eur Respir J 2024; 63:2302281. [PMID: 38387999 DOI: 10.1183/13993003.02281-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Affiliation(s)
- Steven L Taylor
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Luke R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Geraint B Rogers
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
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13
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Liu K, Guo Q, Ding Y, Luo L, Huang J, Zhang Q. Alterations in nasal microbiota of patients with amyotrophic lateral sclerosis. Chin Med J (Engl) 2024; 137:162-171. [PMID: 37482646 PMCID: PMC10798702 DOI: 10.1097/cm9.0000000000002701] [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: 01/20/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Links between alterations in gut microbiota composition and amyotrophic lateral sclerosis (ALS) have previously been reported. This study aimed to examine the microbiota in the nasal cavity of ALS. METHODS Sixty-six ALS patients and 40 healthy caregivers who live in close proximity with patients were enrolled. High throughput metagenomic sequencing of the 16S ribosomal deoxyribonucleic acid (rDNA) gene V3-V4 region of nasal microbiota was used to characterize the alpha and beta diversity and relative abundance of bacterial taxa, predict function, and conduct correlation analysis between specific taxa and clinical features. RESULTS The nasal microbiome of ALS patients showed lower alpha diversity than that of corresponding healthy family members. Genera Gaiella , Sphingomonas , Polaribacter _1, Lachnospiraceae _NK4A136_group, Klebsiella , and Alistipes were differentially enriched in ALS patients compared to controls. Nasal microbiota composition in ALS patients significantly differed from that in healthy subjects (unweighted UniFrac P = 0.001), while Linear discriminant analysis Effect Size (LEfSe) analysis indicated that Bacteroidetes and Firmicutes dominated healthy nasal communities at the phylum level, whereas Actinobacteria was the predominant phylum and Thermoleophilia was the predominant class in ALS patients. Genus Faecalibacterium and Alistipes were positively correlated with ALS functional rating scale revised (ALSFRS-R; rs = 0.349, P = 0.020 and rs = 0.393, P = 0.008), while Prevotella -9 and Bacteroides operational taxonomic units (OTUs) were positively associated with lung function (FVC) in ALS patients ( rs = 0.304, P = 0.045, and rs = 0.300, P = 0.048, respectively). Prevotella -1 was positively correlated with white blood cell counts (WBC, rs = 0.347, P = 0.021), neutrophil percentage (Neu%, rs = 0.428, P = 0.004), and neutrophil-to-lymphocyte ratio (NLR, rs = 0.411, P = 0.006), but negatively correlated with lymphocyte percentage (Lym%, rs = -0.408, P = 0.006). In contrast, Streptococcus was negatively associated with Neu% ( rs = -0.445, P = 0.003) and NLR ( rs = -0.436, P = 0.003), while positively associated with Lym% ( rs = 0.437, P = 0.003). No significant differences in nasal microbiota richness and evenness were detected among the severe and mild ALS patients. CONCLUSIONS ALS is accompanied by altered nasal microbial community composition and diversity. The findings presented here highlight the need to understand how dysbiosis of nasal microbiota may contribute to the development of ALS.
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Affiliation(s)
- Kaixiong Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Qifu Guo
- Department of Neurology, Fujian Institute of Neurology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Ying Ding
- Department of Neurology, Fujian Institute of Neurology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Li Luo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Jianchai Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Qijie Zhang
- Department of Neurology, Fujian Institute of Neurology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
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14
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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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15
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Pragman AA. Investigating a Causal Role for Lung Microbiome Dysbiosis in Early Chronic Obstructive Pulmonary Disease Pathogenesis. Am J Respir Crit Care Med 2023; 208:1019-1021. [PMID: 37703423 PMCID: PMC10867932 DOI: 10.1164/rccm.202309-1599ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Affiliation(s)
- Alexa A Pragman
- Department of Medicine Minneapolis Veterans Affairs Medical Center Minneapolis, Minnesota and Department of Medicine University of Minnesota Minneapolis, Minnesota
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16
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Sulaiman I, Wu BG, Chung M, Isaacs B, Tsay JCJ, Holub M, Barnett CR, Kwok B, Kugler MC, Natalini JG, Singh S, Li Y, Schluger R, Carpenito J, Collazo D, Perez L, Kyeremateng Y, Chang M, Campbell CD, Hansbro PM, Oppenheimer BW, Berger KI, Goldring RM, Koralov SB, Weiden MD, Xiao R, D’Armiento J, Clemente JC, Ghedin E, Segal LN. Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2023; 208:1101-1114. [PMID: 37677136 PMCID: PMC10867925 DOI: 10.1164/rccm.202210-1865oc] [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: 10/18/2022] [Accepted: 09/07/2023] [Indexed: 09/09/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity, mortality, and healthcare costs. Cigarette smoke is a causative factor; however, not all heavy smokers develop COPD. Microbial colonization and infections are contributing factors to disease progression in advanced stages. Objectives: We investigated whether lower airway dysbiosis occurs in mild-to-moderate COPD and analyzed possible mechanistic contributions to COPD pathogenesis. Methods: We recruited 57 patients with a >10 pack-year smoking history: 26 had physiological evidence of COPD, and 31 had normal lung function (smoker control subjects). Bronchoscopy sampled the upper airways, lower airways, and environmental background. Samples were analyzed by 16S rRNA gene sequencing, whole genome, RNA metatranscriptome, and host RNA transcriptome. A preclinical mouse model was used to evaluate the contributions of cigarette smoke and dysbiosis on lower airway inflammatory injury. Measurements and Main Results: Compared with smoker control subjects, microbiome analyses showed that the lower airways of subjects with COPD were enriched with common oral commensals. The lower airway host transcriptomics demonstrated differences in markers of inflammation and tumorigenesis, such as upregulation of IL-17, IL-6, ERK/MAPK, PI3K, MUC1, and MUC4 in mild-to-moderate COPD. Finally, in a preclinical murine model exposed to cigarette smoke, lower airway dysbiosis with common oral commensals augments the inflammatory injury, revealing transcriptomic signatures similar to those observed in human subjects with COPD. Conclusions: Lower airway dysbiosis in the setting of smoke exposure contributes to inflammatory injury early in COPD. Targeting the lower airway microbiome in combination with smoking cessation may be of potential therapeutic relevance.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Benjamin G. Wu
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Bradley Isaacs
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Jun-Chieh J. Tsay
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Meredith Holub
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Hartford Health Care, Hartford, Connecticut
| | - Clea R. Barnett
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Benjamin Kwok
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | - Jake G. Natalini
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rosemary Schluger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Joseph Carpenito
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Destiny Collazo
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Luisanny Perez
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yaa Kyeremateng
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Miao Chang
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Christina D. Campbell
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Sydney, New South Wales, Australia
| | | | - Kenneth I. Berger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | | | - Michael D. Weiden
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rui Xiao
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jeanine D’Armiento
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, New York
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17
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Kim BG, Yu JY, Kim SY, Kim DH, Jhun BW. Changes in sputum microbiota during treatment for nontuberculous mycobacterial pulmonary disease. Sci Rep 2023; 13:19764. [PMID: 37957253 PMCID: PMC10643529 DOI: 10.1038/s41598-023-47230-5] [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: 09/18/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
Limited data exist on longitudinal changes in the sputum bacterial microbiome during treatment in nontuberculous mycobacterial pulmonary disease (NTM-PD) patients. We prospectively collected serial sputum samples from 14 NTM-PD patients during treatment, at the start (n = 14) and at 1 (n = 10), 3 (n = 10), 6 (n = 12), and 12 (n = 7) months. The bacterial microbiome changes were analyzed using 16S rRNA sequences (V3-V4 regions). Subgroup analysis included culture conversion (n = 9) and treatment refractory (n = 5) groups. In all patients, sputum alpha-diversity (ACE, Chao1, and Jackknife) significantly decreased during antibiotic treatment at 1, 3, 6, and 12 months compared to treatment initiation levels. Within the culture conversion group, genus/species-level beta-diversity showed differences at 1, 3, 6, and 12 months compared to treatment initiation (all p < 0.05). However, in the refractory group, there were no differences in beta-diversity at the genus/species levels in the sputum at any time point. In the linear discriminant analysis (LDA) effect sizes (LEfSe) analysis, the culture conversion group exhibited decreasing taxa at various levels (phylum/genus/species), but no significant increase in taxa was observed. LEfSe analysis of the refractory patient group revealed multiple taxa decreased during treatment. However, proportions of Veillonella dispar (LDA = 4.78), Fusobacterium periodonticum (LDA = 4.35), and Pseudomonas aeruginosa (LDA = 2.92) increased as the treatment period progressed in the refractory group. Sputum microbiota diversity decreases during NTM-PD treatment. In the culture conversion group, most taxa decrease, while some increase in the refractory group. These findings suggest that a distinct respiratory microbial community may exist in refractory NTM-PD patients compared to responsive antibiotic-treated patients.
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Affiliation(s)
- Bo-Guen Kim
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Jin Young Yu
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, South Korea
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, South Korea.
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18
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Zhao Y, Sun H, Chen Y, Niu Q, Dong Y, Li M, Yuan Y, Yang X, Sun Q. Butyrate protects against MRSA pneumonia via regulating gut-lung microbiota and alveolar macrophage M2 polarization. mBio 2023; 14:e0198723. [PMID: 37754570 PMCID: PMC10653920 DOI: 10.1128/mbio.01987-23] [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: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Pneumonia caused by methicillin-resistant Staphylococcus aureus (MRSA) continues to carry a high burden in terms of mortality. With the roles of gut microbiota in mediating lung diseases being gradually uncovered, the details of the molecular mechanism of the "gut-lung axis" mediated by beneficial microorganisms and small-molecule metabolites have gradually attracted the attention of researchers. However, further studies are still necessary to determine the efficacy of microbial-based interventions. Our findings indicate that sodium butyrate (NaB) alleviates MRSA-induced pulmonary inflammation by improving gut-lung microbiota and promoting M2 polarization of alveolar macrophages. Therefore, the preventive administration of NaB might be explored as an effective strategy to control MRSA pneumonia.
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Affiliation(s)
- Yan Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haoming Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiwei Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiang Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiting Dong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ye Yuan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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19
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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20
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Gea J, Enríquez-Rodríguez CJ, Agranovich B, Pascual-Guardia S. Update on metabolomic findings in COPD patients. ERJ Open Res 2023; 9:00180-2023. [PMID: 37908399 PMCID: PMC10613990 DOI: 10.1183/23120541.00180-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/15/2023] [Indexed: 11/02/2023] Open
Abstract
COPD is a heterogeneous disorder that shows diverse clinical presentations (phenotypes and "treatable traits") and biological mechanisms (endotypes). This heterogeneity implies that to carry out a more personalised clinical management, it is necessary to classify each patient accurately. With this objective, and in addition to clinical features, it would be very useful to have well-defined biological markers. The search for these markers may either be done through more conventional laboratory and hypothesis-driven techniques or relatively blind high-throughput methods, with the omics approaches being suitable for the latter. Metabolomics is the science that studies biological processes through their metabolites, using various techniques such as gas and liquid chromatography, mass spectrometry and nuclear magnetic resonance. The most relevant metabolomics studies carried out in COPD highlight the importance of metabolites involved in pathways directly related to proteins (peptides and amino acids), nucleic acids (nitrogenous bases and nucleosides), and lipids and their derivatives (especially fatty acids, phospholipids, ceramides and eicosanoids). These findings indicate the relevance of inflammatory-immune processes, oxidative stress, increased catabolism and alterations in the energy production. However, some specific findings have also been reported for different COPD phenotypes, demographic characteristics of the patients, disease progression profiles, exacerbations, systemic manifestations and even diverse treatments. Unfortunately, the studies carried out to date have some limitations and shortcomings and there is still a need to define clear metabolomic profiles with clinical utility for the management of COPD and its implicit heterogeneity.
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Affiliation(s)
- Joaquim Gea
- Respiratory Medicine Department, Hospital del Mar – IMIM, Barcelona, Spain
- MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
- CIBERES, ISCIII, Barcelona, Spain
| | - César J. Enríquez-Rodríguez
- Respiratory Medicine Department, Hospital del Mar – IMIM, Barcelona, Spain
- MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Bella Agranovich
- Rappaport Institute for Research in the Medical Sciences, Technion University, Haifa, Israel
| | - Sergi Pascual-Guardia
- Respiratory Medicine Department, Hospital del Mar – IMIM, Barcelona, Spain
- MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
- CIBERES, ISCIII, Barcelona, Spain
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21
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Fan LC, McConn K, Plataki M, Kenny S, Williams NC, Kim K, Quirke JA, Chen Y, Sauler M, Möbius ME, Chung KP, Area Gomez E, Choi AM, Xu JF, Cloonan SM. Alveolar type II epithelial cell FASN maintains lipid homeostasis in experimental COPD. JCI Insight 2023; 8:e163403. [PMID: 37606038 PMCID: PMC10543729 DOI: 10.1172/jci.insight.163403] [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: 07/19/2022] [Accepted: 07/10/2023] [Indexed: 08/23/2023] Open
Abstract
Alveolar epithelial type II (AEC2) cells strictly regulate lipid metabolism to maintain surfactant synthesis. Loss of AEC2 cell function and surfactant production are implicated in the pathogenesis of the smoking-related lung disease chronic obstructive pulmonary disease (COPD). Whether smoking alters lipid synthesis in AEC2 cells and whether altering lipid metabolism in AEC2 cells contributes to COPD development are unclear. In this study, high-throughput lipidomic analysis revealed increased lipid biosynthesis in AEC2 cells isolated from mice chronically exposed to cigarette smoke (CS). Mice with a targeted deletion of the de novo lipogenesis enzyme, fatty acid synthase (FASN), in AEC2 cells (FasniΔAEC2) exposed to CS exhibited higher bronchoalveolar lavage fluid (BALF) neutrophils, higher BALF protein, and more severe airspace enlargement. FasniΔAEC2 mice exposed to CS had lower levels of key surfactant phospholipids but higher levels of BALF ether phospholipids, sphingomyelins, and polyunsaturated fatty acid-containing phospholipids, as well as increased BALF surface tension. FasniΔAEC2 mice exposed to CS also had higher levels of protective ferroptosis markers in the lung. These data suggest that AEC2 cell FASN modulates the response of the lung to smoke by regulating the composition of the surfactant phospholipidome.
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Affiliation(s)
- Li-Chao Fan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Keith McConn
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Maria Plataki
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Sarah Kenny
- School of Medicine, Trinity Biomedical Sciences Institute, and
| | | | - Kihwan Kim
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | - Yan Chen
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Kuei-Pin Chung
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Laboratory Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Estela Area Gomez
- Division of Neuromuscular Medicine, Department of Neurology, Columbia University Irving Medical Center, Neurological Institute, New York, New York, USA
- Center for Biological Research “Margarita Salas”, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Augustine M.K. Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Jin-Fu Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Suzanne M. Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- School of Medicine, Trinity Biomedical Sciences Institute, and
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22
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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23
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Calverley PMA, Walker PP. Contemporary Concise Review 2022: Chronic obstructive pulmonary disease. Respirology 2023; 28:428-436. [PMID: 36922031 DOI: 10.1111/resp.14489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/17/2023]
Abstract
International respiratory organizations now recommend using lower limit of normal and standardized residuals to diagnose airflow obstruction and COPD though using a fixed ratio <0.7 is simpler and robustly predicts important clinical outcomes. The most common COPD comorbidities are coronary artery calcification, emphysema and bronchiectasis. COPD patients with psychological (high anxiety and depression) and cachectic (underweight and osteoporotic) comorbidity have higher mortality and exacerbate more. Serum eosinophil count remains an important COPD biomarker and we have greater clarity about normal eosinophil levels in COPD and the wider population. Criteria for entry into COPD clinical trials continue to exclude many patients, in particular those at greater risk of exacerbation and death. The effect of hyperinflation on cardiac function impacts COPD mortality and is an important target for successful lung volume reduction procedures.
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Affiliation(s)
- Peter M A Calverley
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Paul P Walker
- School of Health and Life Sciences, University of Liverpool, Liverpool, UK
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24
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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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25
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Gea J, Enríquez-Rodríguez CJ, Pascual-Guardia S. Metabolomics in COPD. Arch Bronconeumol 2023; 59:311-321. [PMID: 36717301 DOI: 10.1016/j.arbres.2022.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 01/20/2023]
Abstract
The clinical presentation of chronic obstructive pulmonary disease (COPD) is highly heterogeneous. Attempts have been made to define subpopulations of patients who share clinical characteristics (phenotypes and treatable traits) and/or biological characteristics (endotypes), in order to offer more personalized care. Assigning a patient to any of these groups requires the identification of both clinical and biological markers. Ideally, biological markers should be easily obtained from blood or urine, but these may lack specificity. Biomarkers can be identified initially using conventional or more sophisticated techniques. However, the more sophisticated techniques should be simplified in the future if they are to have clinical utility. The -omics approach offers a methodology that can assist in the investigation and identification of useful markers in both targeted and blind searches. Specifically, metabolomics is the science that studies biological processes involving metabolites, which can be intermediate or final products. The metabolites associated with COPD and their specific phenotypic and endotypic features have been studied using various techniques. Several compounds of particular interest have emerged, namely, several types of lipids and derivatives (mainly phospholipids, but also ceramides, fatty acids and eicosanoids), amino acids, coagulation factors, and nucleic acid components, likely to be involved in their function, protein catabolism, energy production, oxidative stress, immune-inflammatory response and coagulation disorders. However, clear metabolomic profiles of the disease and its various manifestations that may already be applicable in clinical practice still need to be defined.
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Affiliation(s)
- Joaquim Gea
- Servicio de Neumología, Hospital del Mar - IMIM, Barcelona, Spain; Dpt. MELIS, Universitat Pompeu Fabra, Barcelona, Spain; CIBERES, ISCIII, Barcelona, Spain.
| | - César J Enríquez-Rodríguez
- Servicio de Neumología, Hospital del Mar - IMIM, Barcelona, Spain; Dpt. MELIS, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergi Pascual-Guardia
- Servicio de Neumología, Hospital del Mar - IMIM, Barcelona, Spain; Dpt. MELIS, Universitat Pompeu Fabra, Barcelona, Spain; CIBERES, ISCIII, Barcelona, Spain
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26
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Kayongo A, Robertson NM, Siddharthan T, Ntayi ML, Ndawula JC, Sande OJ, Bagaya BS, Kirenga B, Mayanja-Kizza H, Joloba ML, Forslund SK. Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease. Front Immunol 2023; 13:1085551. [PMID: 36741369 PMCID: PMC9890194 DOI: 10.3389/fimmu.2022.1085551] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) has significantly contributed to global mortality, with three million deaths reported annually. This impact is expected to increase over the next 40 years, with approximately 5 million people predicted to succumb to COPD-related deaths annually. Immune mechanisms driving disease progression have not been fully elucidated. Airway microbiota have been implicated. However, it is still unclear how changes in the airway microbiome drive persistent immune activation and consequent lung damage. Mechanisms mediating microbiome-immune crosstalk in the airways remain unclear. In this review, we examine how dysbiosis mediates airway inflammation in COPD. We give a detailed account of how airway commensal bacteria interact with the mucosal innate and adaptive immune system to regulate immune responses in healthy or diseased airways. Immune-phenotyping airway microbiota could advance COPD immunotherapeutics and identify key open questions that future research must address to further such translation.
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Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Medicine, Center for Emerging Pathogens, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, United States
| | | | - Trishul Siddharthan
- Division of Pulmonary Medicine, School of Medicine, University of Miami, Miami, FL, United States
| | - Moses Levi Ntayi
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Josephine Caren Ndawula
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Obondo J. Sande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bernard S. Bagaya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany,Experimental and Clinical Research Center, a cooperation of Charité - Universitatsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany,Charité-Universitatsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,*Correspondence: Sofia K. Forslund,
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27
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Goeteyn E, Grassi L, Van den Bossche S, Rigauts C, Vande Weygaerde Y, Van Braeckel E, Maes T, Bracke KR, Crabbé A. Commensal bacteria of the lung microbiota synergistically inhibit inflammation in a three-dimensional epithelial cell model. Front Immunol 2023; 14:1176044. [PMID: 37168857 PMCID: PMC10164748 DOI: 10.3389/fimmu.2023.1176044] [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: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 05/13/2023] Open
Abstract
Patients with chronic lung disease suffer from persistent inflammation and are typically colonized by pro-inflammatory pathogenic bacteria. Besides these pathogens, a wide variety of commensal species is present in the lower airways but their role in inflammation is unclear. Here, we show that the lung microbiota contains several species able to inhibit activation of the pro-inflammatory NF-κB pathway and production of interleukin 8 (IL-8), triggered by lipopolysaccharide (LPS) or H2O2, in a physiologically relevant three-dimensional (3D) lung epithelial cell model. We demonstrate that the minimal dose needed for anti-inflammatory activity differs between species (with the lowest dose needed for Rothia mucilaginosa), and depends on the type of pro-inflammatory stimulus and read out. Furthermore, we evaluated synergistic activity between pairs of anti-inflammatory bacteria on the inhibition of the NF-κB pathway and IL-8 secretion. Synergistic anti-inflammatory activity was observed for 4/10 tested consortia. These findings indicate that various microbiota members can influence lung inflammation either alone or as a consortium. This information can contribute to a better understanding of the lung microbiota in chronic lung disease development and process, and could open up new avenues for treatment.
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Affiliation(s)
- Ellen Goeteyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Lucia Grassi
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | | | - Charlotte Rigauts
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Yannick Vande Weygaerde
- Cystic Fibrosis Reference Centre, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Eva Van Braeckel
- Cystic Fibrosis Reference Centre, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Lung Research Lab, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Tania Maes
- Lung Research Lab, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ken R. Bracke
- Lung Research Lab, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
- *Correspondence: Aurélie Crabbé,
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28
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Hamidou Soumana I, Ryu MH, Leitao Filho FS, Yang J, Orach J, Nislow C, Leung JM, Rider CF, Carlsten C. Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers. ENVIRONMENTAL RESEARCH 2023; 216:114826. [PMID: 36403657 DOI: 10.1016/j.envres.2022.114826] [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: 09/06/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m3 PM2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.
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Affiliation(s)
- Illiassou Hamidou Soumana
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Min Hyung Ryu
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Julia Yang
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Juma Orach
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Francis Rider
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Carlsten
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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29
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Narayana JK, Tsaneva-Atanasova K, Chotirmall SH. Microbiomics Focused Data Integration: A Fresh Solve for the Rubik's Cube of Endophenotyping? Am J Respir Crit Care Med 2022; 206:365-368. [PMID: 35584334 DOI: 10.1164/rccm.202205-0860ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jayanth Kumar Narayana
- Lee Kong Chian School of Medicine, Translational Respiratory Research Laboratory, Singapore, Singapore
| | - Krasimira Tsaneva-Atanasova
- University of Exeter, 3286, Living Systems Institute and Department of Mathematics, Exeter, United Kingdom of Great Britain and Northern Ireland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Translational Respiratory Research Laboratory, Singapore, Singapore;
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Singh S, Natalini JG, Segal LN. Lung microbial-host interface through the lens of multi-omics. Mucosal Immunol 2022; 15:837-845. [PMID: 35794200 PMCID: PMC9391302 DOI: 10.1038/s41385-022-00541-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023]
Abstract
In recent years, our understanding of the microbial world within us has been revolutionized by the use of culture-independent techniques. The use of multi-omic approaches can now not only comprehensively characterize the microbial environment but also evaluate its functional aspects and its relationship with the host immune response. Advances in bioinformatics have enabled high throughput and in-depth analyses of transcripts, proteins and metabolites and enormously expanded our understanding of the role of the human microbiome in different conditions. Such investigations of the lower airways have specific challenges but as the field develops, new approaches will be facilitated. In this review, we focus on how integrative multi-omics can advance our understanding of the microbial environment and its effects on the host immune tone in the lungs.
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Affiliation(s)
- Shivani Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jake G. Natalini
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY,NYU Langone Lung Transplant Institute, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
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