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Hu JC, Sethi S. New methods to detect bacterial or viral infections in patients with chronic obstructive pulmonary disease. Expert Rev Respir Med 2024:1-15. [PMID: 39175157 DOI: 10.1080/17476348.2024.2396413] [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: 04/08/2024] [Revised: 07/22/2024] [Accepted: 08/21/2024] [Indexed: 08/24/2024]
Abstract
INTRODUCTION Patients with chronic obstructive pulmonary disease (COPD) are frequently colonized and infected by respiratory pathogens. Identifying these infectious etiologies is critical for understanding the microbial dynamics of COPD and for the appropriate use of antimicrobials during exacerbations. AREAS COVERED Traditional methods, such as bacterial and viral cultures, have been standard in diagnosing respiratory infections. However, these methods have significant limitations, including lack of sensitivity and prolonged turnaround time. Modern molecular approaches offer rapid, sensitive, and specific detection, though they also come with their own challenges. This review explores and evaluates the clinical utility of the latest advancements in detecting bacterial and viral respiratory infections in COPD, encompassing molecular techniques, biomarkers, and emerging technologies. EXPERT OPINION In the evolving landscape of COPD management, integrating molecular diagnostics and emerging technologies holds great promise. The enhanced sensitivity of molecular techniques has significantly advanced our understanding of the role of microbes in COPD. However, many of these technologies have primarily been developed for pneumonia diagnosis or research applications, and their clinical utility in managing COPD requires further evaluation.
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Affiliation(s)
- John C Hu
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Sanjay Sethi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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2
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Chen YF, Hou HH, Chien N, Lu KZ, Lin CH, Liao YC, Lor KL, Chien JY, Chen CM, Chen CY, Cheng SL, Wang HC, Hsueh PR, Yu CJ. The clinical impacts of lung microbiome in bronchiectasis with fixed airflow obstruction: a prospective cohort study. Respir Res 2024; 25:308. [PMID: 39143556 PMCID: PMC11325704 DOI: 10.1186/s12931-024-02931-x] [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: 01/20/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Airflow obstruction is a hallmark of disease severity and prognosis in bronchiectasis. The relationship between lung microbiota, airway inflammation, and outcomes in bronchiectasis with fixed airflow obstruction (FAO) remains unclear. This study explores these interactions in bronchiectasis patients, with and without FAO, and compares them to those diagnosed with chronic obstructive pulmonary disease (COPD). METHODS This prospective observational study in Taiwan enrolled patients with either bronchiectasis or COPD. To analyze the lung microbiome and assess inflammatory markers, bronchoalveolar lavage (BAL) samples were collected for 16S rRNA gene sequencing. The study cohort comprised 181 patients: 86 with COPD, 46 with bronchiectasis, and 49 with bronchiectasis and FAO, as confirmed by spirometry. RESULTS Patients with bronchiectasis, with or without FAO, had similar microbiome profiles characterized by reduced alpha diversity and a predominance of Proteobacteria, distinctly different from COPD patients who exhibited more Firmicutes, greater diversity, and more commensal taxa. Furthermore, compared to COPD and bronchiectasis without FAO, bronchiectasis with FAO showed more severe disease and a higher risk of exacerbations. A significant correlation was found between the presence of Pseudomonas aeruginosa and increased airway neutrophilic inflammation such as Interleukin [IL]-1β, IL-8, and tumor necrosis factor-alpha [TNF]-α, as well as with higher bronchiectasis severity, which might contribute to an increased risk of exacerbations. Moreover, in bronchiectasis patients with FAO, the ROSE (Radiology, Obstruction, Symptoms, and Exposure) criteria were employed to classify individuals as either ROSE (+) or ROSE (-), based on smoking history. This classification highlighted differences in clinical features, inflammatory profiles, and slight microbiome variations between ROSE (-) and ROSE (+) patients, suggesting diverse endotypes within the bronchiectasis with FAO group. CONCLUSION Bronchiectasis patients with FAO may exhibit two distinct endotypes, as defined by ROSE criteria, characterized by greater disease severity and a lung microbiome more similar to bronchiectasis without FAO than to COPD. The significant correlation between Pseudomonas aeruginosa colonization and increased airway neutrophilic inflammation, as well as disease severity, underscores the clinical relevance of microbial patterns. This finding reinforces the potential role of these patterns in the progression and exacerbations of bronchiectasis with FAO.
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Affiliation(s)
- Yen-Fu Chen
- Department of Internal Medicine, National Taiwan University Hospital, Yun-Lin Branch, Yunlin County, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, 7 Chung-Shan South Road, Taipei, 100, Taiwan (ROC)
- Thoracic Medicine Center, Department of Medicine and Surgery, National Taiwan University Hospital Yunlin Branch, Yunlin County, Taiwan
| | - Hsin-Han Hou
- Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ning Chien
- Department of Medical Imaging, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Kai-Zen Lu
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chieh-Hua Lin
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, 350, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, 350, Taiwan
| | - Kuo-Lung Lor
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Jung-Yien Chien
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, 7 Chung-Shan South Road, Taipei, 100, Taiwan (ROC)
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chung-Ming Chen
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Chung-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital, Yun-Lin Branch, Yunlin County, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, 7 Chung-Shan South Road, Taipei, 100, Taiwan (ROC)
- Thoracic Medicine Center, Department of Medicine and Surgery, National Taiwan University Hospital Yunlin Branch, Yunlin County, Taiwan
| | - Shih-Lung Cheng
- Division of Thoracic Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan City 320, Taiwan
| | - Hao-Chien Wang
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- Ph.D Programme for Aging, College of Medicine, China Medical University, Taichung, Taiwan
| | - Chong-Jen Yu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, 7 Chung-Shan South Road, Taipei, 100, Taiwan (ROC).
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsin-Chu, Taiwan.
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3
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Huang SS, Qiu JY, Li SP, Ma YQ, He J, Han LN, Jiao LL, Xu C, Mao YM, Zhang YM. Microbial signatures predictive of short-term prognosis in severe pneumonia. Front Cell Infect Microbiol 2024; 14:1397717. [PMID: 39157177 PMCID: PMC11327560 DOI: 10.3389/fcimb.2024.1397717] [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: 03/08/2024] [Accepted: 07/15/2024] [Indexed: 08/20/2024] Open
Abstract
Objective This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis. Methods A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis. Results The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial α and β diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera. Conclusion Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.
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Affiliation(s)
- Shen-Shen Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Jia-Yong Qiu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shuang-Ping Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Ya-Qing Ma
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Jun He
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Li-Na Han
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Long-Long Jiao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Chong Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Yi-Min Mao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Yong-Mei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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Meldrum OW, Donaldson GC, Narayana JK, Xaverius Ivan F, Jaggi TK, Mac Aogáin M, Finney LJ, Allinson JP, Wedzicha JA, Chotirmall SH. Accelerated Lung Function Decline and Mucus-Microbe Evolution in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 210:298-310. [PMID: 38315959 PMCID: PMC11348959 DOI: 10.1164/rccm.202306-1060oc] [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: 06/20/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
Rationale: Progressive lung function loss is recognized in chronic obstructive pulmonary disease (COPD); however, no study concurrently evaluates how accelerated lung function decline relates to mucus properties and the microbiome in COPD. Objectives: Longitudinal assessment of mucus and microbiome changes accompanying accelerated lung function decline in patients COPD. Methods: This was a prospective, longitudinal assessment of the London COPD cohort exhibiting the greatest FEV1 decline (n = 30; accelerated decline; 156 ml/yr FEV1 loss) and with no FEV1 decline (n = 28; nondecline; 49 ml/yr FEV1 gain) over time. Lung microbiomes from paired sputum (total 116 specimens) were assessed by shotgun metagenomics and corresponding mucus profiles evaluated for biochemical and biophysical properties. Measurements and Main Results: Biochemical and biophysical mucus properties are significantly altered in the accelerated decline group. Unsupervised principal component analysis showed clear separation, with mucus biochemistry associated with accelerated decline, whereas biophysical mucus characteristics contributed to interindividual variability. When mucus and microbes are considered together, an accelerated decline mucus-microbiome association emerges, characterized by increased mucin (MUC5AC [mucin 5AC] and MUC5B [mucin 5B]) concentration and the presence of Achromobacter and Klebsiella. As COPD progresses, mucus-microbiome shifts occur, initially characterized by low mucin concentration and transition from viscous to elastic dominance accompanied by the commensals Veillonella, Gemella, Rothia, and Prevotella (Global Initiative for Chronic Obstructive Lung Disease [GOLD] A and B) before transition to increased mucus viscosity, mucins, and DNA concentration together with the emergence of pathogenic microorganisms including Haemophilus, Moraxella, and Pseudomonas (GOLD E). Conclusions: Mucus-microbiome associations evolve over time with accelerated lung function decline, symptom progression, and exacerbations affording fresh therapeutic opportunities for early intervention.
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Affiliation(s)
- Oliver W. Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Gavin C. Donaldson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | | | - Tavleen K. Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lydia J. Finney
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - James P. Allinson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton Hospital, London, United Kingdom; and
| | - Jadwiga A. Wedzicha
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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Wu J, Zhang Y, Duan J, Wei Y, Miao Y. A metagenomic next-generation sequencing (mNGS)-based analysis of bronchoalveolar lavage samples in patients with an acute exacerbation of chronic obstructive pulmonary disease. J Mol Histol 2024:10.1007/s10735-024-10225-1. [PMID: 39060894 DOI: 10.1007/s10735-024-10225-1] [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: 03/21/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
The role of the bronchoalveolar lavage fluid (BALF) microbiome in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) remains unclear. The advent of the metagenomic next-generation sequencing (mNGS) has made it possible to reveal the complex microbiome composition of the respiratory tract. This study aimed to explore whether there are differences in the BALF microbiome of AECOPD patients with different lung functions. We enrolled 55 AECOPD patients and divided them into a mild group (n = 31) and a severe group (n = 24) according to their lung function. We collected BALF and submitted it to mNGS and bioinformatics analysis. At the species level, mNGS identified 264 bacteria, 13 fungi and 12 viruses in the mild group, and 174 bacteria, 6 fungi and 6 viruses in the severe group. Mixed bacterial and viral infection occurred in both groups. At the genus level, Rothia and Veillonella were more abundant in the mild group, while Pseudomonas and Staphylococcus were more abundant in the severe group. At the species level, compared with the mild group, the relative abundance of Haemophilus influenzae and Pseudomonas aeruginosa was increased in the severe group. Besides, the BALF microbiome composition was similar between the two groups, and there was no significant difference in α and β diversity. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) (%) showed no significant correlation with the Shannon or Simpson index. The microbiome abundance was different between the mild and severe groups; however, microbiome diversity was similar between the two groups. Based on our findings, Haemophilus influenzae and Pseudomonas aeruginosa may be the pathogenic bacteria that cause the difference in lung function in patients with AECOPD.
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Affiliation(s)
- Junfang Wu
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yongqing Zhang
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Jinjin Duan
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yiqun Wei
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yi Miao
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China.
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6
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Li Y, Mao X, Shi P, Wan Z, Yang D, Ma T, Wang B, Wang J, Wang J, Zhu R. Microbiome-host interactions in the pathogenesis of acute exacerbation of chronic obstructive pulmonary disease. Front Cell Infect Microbiol 2024; 14:1386201. [PMID: 39091676 PMCID: PMC11291260 DOI: 10.3389/fcimb.2024.1386201] [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: 02/14/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Objective To explore the underlying mechanisms the airway microbiome contributes to Acute Exacerbation of Chronic Obstructive Pulmonary Disease(AECOPD). Methods We enrolled 31 AECOPD patients and 26 stable COPD patients, their sputum samples were collected for metagenomic and RNA sequencing, and then subjected to bioinformatic analyses. The expression of host genes was validated by Quantitative Real-time PCR(qPCR) using the same batch of specimens. Results Our results indicated a higher expression of Rothia mucilaginosa(p=0.015) in the AECOPD group and Haemophilus influenzae(p=0.005) in the COPD group. The Different expressed genes(DEGs) detected were significantly enriched in "type I interferon signaling pathway"(p<0.001, q=0.001) in gene function annotation, and "Cytosolic DNA-sensing pathway"(p=0.002, q=0.024), "Toll-like receptor signaling pathway"(p=0.006, q=0.045), and "TNF signaling pathway"(p=0.006, q=0.045) in KEGG enrichment analysis. qPCR amplification experiment verified that the expression of OASL and IL6 increased significantly in the AECOPD group. Conclusion Pulmonary bacteria dysbiosis may regulate the pathogenesis of AECOPD through innate immune system pathways like type I interferon signaling pathway and Toll-like receptor signaling pathway.
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Affiliation(s)
- Yao Li
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian, China
| | - Xiaoyan Mao
- Department of Intensive Care Unit, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Pengfei Shi
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian, China
| | - Zongren Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Dan Yang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Ting Ma
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Baolan Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Jipeng Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Jingjing Wang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rong Zhu
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian, China
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Tanabe N, Matsumoto H, Morimoto C, Hayashi Y, Sakamoto R, Oguma T, Nagasaki T, Sunadome H, Sato A, Sato S, Ohashi K, Tsukahara T, Hirai T. Mucus plugging on computed tomography and the sputum microbiome in patients with asthma, chronic obstructive pulmonary disease, and asthma-COPD overlap. Allergol Int 2024:S1323-8930(24)00055-8. [PMID: 39013753 DOI: 10.1016/j.alit.2024.05.004] [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: 03/13/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Despite clinical implications, the pathogenesis of mucus plugging in asthma, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap (ACO) remains unclear. We hypothesized that distinct airway microbiomes might affect mucus plugging differently among ACO, asthma, and COPD and among different extents of airway eosinophilic inflammation. METHODS The sputum microbiome, sputum cell differential count, and mucus plug score on computed tomography were cross-sectionally evaluated in patients with chronic airflow limitation. RESULTS Patients with ACO, asthma, or COPD were enrolled (n = 56, 10, and 25). Higher mucus plug scores were associated with a greater relative abundance of the phylum Proteobacteria (rho = 0.29) only in patients with ACO and a greater relative abundance of the phylum Actinobacteria (rho = 0.46) only in patients with COPD. In multivariable models including only patients with ACO, the presence of mucus plugs was associated with a greater relative abundance of the phylum Proteobacteria and the genus Haemophilus, independent of smoking status, airflow limitation, and emphysema severity. Moreover, the mucus score was associated with a greater relative abundance of the genus Streptococcus (rho = 0.46) in patients with a high sputum eosinophil count (n = 22) and with that of the genus Haemophilus (rho = 0.46) in those with a moderate sputum eosinophil count (n = 26). CONCLUSIONS The associations between mucus plugging and the microbiome in ACO differed from those in COPD and asthma. Greater relative abundances of the phylum Proteobacteria and genus Haemophilus may be involved in mucus plugging in patients with ACO and moderate airway eosinophilic inflammation.
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Affiliation(s)
- Naoya Tanabe
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Hisako Matsumoto
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Respiratory Medicine & Allergology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Chie Morimoto
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yusuke Hayashi
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Sakamoto
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Oguma
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tadao Nagasaki
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hironobu Sunadome
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Respiratory Care and Sleep Control Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsuyasu Sato
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Susumu Sato
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Respiratory Care and Sleep Control Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kai Ohashi
- Kyoto Institute of Nutrition & Pathology, Inc., Kyoto, Japan
| | | | - Toyohiro Hirai
- Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
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8
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Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation. Nat Med 2024; 30:1982-1993. [PMID: 38783139 PMCID: PMC11271406 DOI: 10.1038/s41591-024-02999-4] [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: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Hematopoietic cell transplantation (HCT) uses cytotoxic chemotherapy and/or radiation followed by intravenous infusion of stem cells to cure malignancies, bone marrow failure and inborn errors of immunity, hemoglobin and metabolism. Lung injury is a known complication of the process, due in part to disruption in the pulmonary microenvironment by insults such as infection, alloreactive inflammation and cellular toxicity. How microorganisms, immunity and the respiratory epithelium interact to contribute to lung injury is uncertain, limiting the development of prevention and treatment strategies. Here we used 278 bronchoalveolar lavage (BAL) fluid samples to study the lung microenvironment in 229 pediatric patients who have undergone HCT treated at 32 children's hospitals between 2014 and 2022. By leveraging paired microbiome and human gene expression data, we identified high-risk BAL compositions associated with in-hospital mortality (P = 0.007). Disadvantageous profiles included bacterial overgrowth with neutrophilic inflammation, microbiome contraction with epithelial fibroproliferation and profound commensal depletion with viral and staphylococcal enrichment, lymphocytic activation and cellular injury, and were replicated in an independent cohort from the Netherlands (P = 0.022). In addition, a broad array of previously occult pathogens was identified, as well as a strong link between antibiotic exposure, commensal bacterial depletion and enrichment of viruses and fungi. Together these lung-immune system-microorganism interactions clarify the important drivers of fatal lung injury in pediatric patients who have undergone HCT. Further investigation is needed to determine how personalized interpretation of heterogeneous pulmonary microenvironments may be used to improve pediatric HCT outcomes.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Courtney M Rowan
- Department of Pediatrics, Division of Critical Care Medicine, Indiana University, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Division of Pediatric Oncology Harvard Medical School Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, Benioff Children's Hospital Oakland, University of California, San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- Department of Pediatrics, Division of Critical Care Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Department of Pediatric Medicine, Division of Critical Care, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Division of Pediatric Oncology Harvard Medical School Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Department of Pediatrics, Division of Pediatric Critical Care, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Department of Pediatrics, Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Columbia University, New York, NY, USA
| | - Paul Castillo
- UF Health Shands Children's Hospital, University of Florida, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, Division of Critical Care Medicine, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Department of Pediatrics, Division of Infectious Diseases, Children's National Hospital, Washington DC, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Department of Pediatrics, Division of Pediatric Hematology/Oncology/BMT, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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9
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Sui Y, Song P, Chen G, Zuo S, Liu H, Guo J, Chang Z, Dai H, Liu F, Dong H. Gut microbiota and Tritrichomonas foetus infection: A study of prevalence and risk factors based on pet cats. Prev Vet Med 2024; 226:106162. [PMID: 38518658 DOI: 10.1016/j.prevetmed.2024.106162] [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: 10/22/2023] [Revised: 01/16/2024] [Accepted: 02/23/2024] [Indexed: 03/24/2024]
Abstract
Tritrichomonas foetus (T. foetus) is a protozoal pathogen that infects cats and constitutes a significant cause of chronic colitis and diarrhea. Perturbations in the gut microbiota (GM) are affected by Trichomonas infection. Furthermore, dysregulation of the host GM enhances Trichomonas pathogenicity. However, it remains unclear whether the occurrence of diarrhea is associated with a dysregulation in GM following T. foetus infection in cats. Hence, the primary objective of this investigation was to explore the correlation between T. foetus infection and dysregulation in GM by analyzing fecal samples obtained from pet cats in Henan Province, central China. We randomly collected 898 fecal samples from pet cats living in 11 prefectural cities within Henan Province, and T. foetus was screened with polymerase chain reaction (PCR) amplification based on the 18 S rRNA gene. Subsequently, six T. foetus-positive and six T. foetus-negative samples underwent analysis through 16 S rRNA gene sequencing to evaluate the gut microbiota's composition. The overall prevalence of T. foetus infection among the collected samples was found to be 6.01% (54/898). Notably, a higher prevalence of infection was observed in young, undewormed, unimmunized, and diarrheic pet cats. T. foetus infection was found to significantly alter the composition of the pet cat fecal microbiota, leading to dysfunctions. Moreover, it resulted in a substantial increase in the abundance of Bacteroidetes, Proteobacteria, and Phascolarctobacterium spp., while decreasing the ratio of Firmicutes to Bacteroidetes (F/B) and the abundance of Actinobacteria, Clostridiaceae_Clostridium spp., Phascolarctobacterium spp., SMB53 spp., and Blautia spp. We constructed ROC curves to assess the diagnostic value of specific bacterial taxa in discriminating T. foetus infection. The analysis revealed that Proteobacteria and Clostridiaceae_Clostridium spp. were the most reliable single predictors for T. foetus infection. This finding suggests that alterations in the GM may be strongly associated with T. foetus infections.
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Affiliation(s)
- Yuzhen Sui
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Pengtao Song
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Guizhen Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Shoujun Zuo
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Hu Liu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Jinjie Guo
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Zhihai Chang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Hongyu Dai
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China.
| | - Fang Liu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China.
| | - Haiju Dong
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China.
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10
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Short B, Delaney C, Johnston W, Litherland GJ, Lockhart JC, Williams C, Mackay WG, Ramage G. Informed development of a multi-species biofilm in chronic obstructive pulmonary disease. APMIS 2024; 132:336-347. [PMID: 38379455 DOI: 10.1111/apm.13386] [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: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
Recent evidence indicates that microbial biofilm aggregates inhabit the lungs of COPD patients and actively contribute towards chronic colonization and repeat infections. However, there are no contextually relevant complex biofilm models for COPD research. In this study, a meta-analysis of the lung microbiome in COPD was used to inform development of an optimized biofilm model composed of genera highly associated with COPD. Bioinformatic analysis showed that although diversity matrices of COPD microbiomes were similar to healthy controls, and internal compositions made it possible to accurately differentiate between these cohorts (AUC = 0.939). Genera that best defined these patients included Haemophilus, Moraxella and Streptococcus. Many studies fail to account for fungi; therefore, Candida albicans was included in the creation of an interkingdom biofilm model. These organisms formed a biofilm capable of tolerating high concentrations of antimicrobial therapies with no significant reductions in viability. However, combined therapies of antibiotics and an antifungal resulted in significant reductions in viable cells throughout the biofilm (p < 0.05). This biofilm model is representative of the COPD lung microbiome and results from in vitro antimicrobial challenge experiments indicate that targeting both bacteria and fungi in these interkingdom communities will be required for more positive clinical outcomes.
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Affiliation(s)
- Bryn Short
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - Christopher Delaney
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - William Johnston
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
| | - Gary J Litherland
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - John C Lockhart
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - Craig Williams
- Microbiology Department, Lancaster Royal Infirmary, University of Lancaster, Lancaster, UK
| | - William G Mackay
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
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11
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Xiao W, Chen YL, Du LY, Wu J, Wang Z, Mao B, Wen FQ, Gibson PG, McDonald VM, Yu H, Fu JJ. Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations. Respir Res 2024; 25:173. [PMID: 38643126 PMCID: PMC11032604 DOI: 10.1186/s12931-024-02802-5] [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: 11/08/2023] [Accepted: 04/03/2024] [Indexed: 04/22/2024] Open
Abstract
RATIONALE Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome. OBJECTIVES To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes. METHODS We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data. RESULTS Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (≥ 2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota. CONCLUSIONS Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.
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Affiliation(s)
- Wei Xiao
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Yi-Long Chen
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Long-Yi Du
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
| | - Jiqiu Wu
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Bing Mao
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
| | - Fu-Qiang Wen
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Peter Gerard Gibson
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Vanessa M McDonald
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Juan-Juan Fu
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China.
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China.
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12
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [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: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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13
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Luo L, Tang J, Du X, Li N. Chronic obstructive pulmonary disease and the airway microbiome: A review for clinicians. Respir Med 2024; 225:107586. [PMID: 38460708 DOI: 10.1016/j.rmed.2024.107586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/30/2023] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex heterogeneous disease characterized by progressive airflow limitation and chronic inflammation. The progressive development and long-term repeated acute exacerbation of COPD make many patients still unable to control the deterioration of the disease after active treatment, and even eventually lead to death. An increasing number of studies have shown that the occurrence and development of COPD are closely related to the composition and changes of airway microbiome. This article reviews the interaction between COPD and airway microbiome, the potential mechanisms of interaction, and the treatment methods related to microbiome. We elaborated the internal correlation between airway microbiome and different stages of COPD, inflammatory endotypes, glucocorticoid and antibiotic treatment, analyze the pathophysiological mechanisms such as the "vicious cycle" hypothesis, abnormal inflammation-immune response of the host and the "natural selection" of COPD to airway microbiome, introduce the treatment of COPD related to microbiome and emphasize the predictive value of airway microbiome for the progression, exacerbation and prognosis of COPD, as well as the guiding role for clinical management of patients, in order to provide a new perspective for exploring the pathogenesis of COPD, and also provide clues and guidance for finding new treatment targets.
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Affiliation(s)
- Lingxin Luo
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China
| | - Junli Tang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China
| | - Xianzhi Du
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China
| | - Na Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China.
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14
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Enríquez-Rodríguez CJ, Casadevall C, Faner R, Castro-Costa A, Pascual-Guàrdia S, Seijó L, López-Campos JL, Peces-Barba G, Monsó E, Barreiro E, Cosío BG, Agustí A, Gea J. COPD: systemic proteomic profiles in frequent and infrequent exacerbators. ERJ Open Res 2024; 10:00004-2024. [PMID: 38529348 PMCID: PMC10962451 DOI: 10.1183/23120541.00004-2024] [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: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 03/27/2024] Open
Abstract
Background Some patients with COPD suffer frequent exacerbations (FE). We hypothesised that their systemic proteomic profile would be different from that of non-frequent exacerbators (NFE). The objective of the present study was to contrast the systemic proteomic profile in FE versus NFE. As a reference, we also determined the systemic proteomic profile of healthy controls (HC) and COPD patients during an actual episode of exacerbation (AE). Methods In the analysis we included 40 clinically stable COPD patients (20 FE and 20 NFE), and 20 HC and 10 AE patients. Their plasma samples were analysed by combining two complementary proteomic approaches: label-free liquid chromatography-tandem mass spectrometry and multiplex immunoassays. Gene Ontology annotation, pathway enrichment and network analyses were used to investigate molecular pathways associated with differentially abundant proteins/peptides (DAPs). Results Compared with HC, we identified 40 DAPs in FE, 10 in NFE and 63 in AE. Also compared to HC, pathway functional and protein-protein network analyses revealed dysregulation of inflammatory responses involving innate and antibody-mediated immunity in COPD, particularly in the FE group, as well as during an AE episode. Besides, we only identified alterations in the complement and coagulation cascades in AE. Conclusion There are specific plasma proteome profiles associated with FE, which are partially shared with findings observed during AE, albeit others are uniquely present during the actual episode of AE.
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Affiliation(s)
- Cesar Jessé Enríquez-Rodríguez
- Servei de Pneumologia, Hospital del Mar – IMIM, MELIS Dept, Universitat Pompeu Fabra and BRN, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- These authors contributed equally
| | - Carme Casadevall
- Servei de Pneumologia, Hospital del Mar – IMIM, MELIS Dept, Universitat Pompeu Fabra and BRN, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- These authors contributed equally
| | - Rosa Faner
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servei de Pneumologia (Institut Clínic de Respiratori), Hospital Clínic – Fundació Clínic per la Recerca Biomèdica, Universitat de Barcelona, Barcelona, Spain
| | - Ady Castro-Costa
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Neumología, Hospital 12 de Octubre, Madrid, Spain
| | - Sergi Pascual-Guàrdia
- Servei de Pneumologia, Hospital del Mar – IMIM, MELIS Dept, Universitat Pompeu Fabra and BRN, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Seijó
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Neumología, Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Clínica Universidad de Navarra, Madrid, Spain
| | - José Luis López-Campos
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Seville, Spain
| | - Germán Peces-Barba
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Neumología, Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eduard Monsó
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Neumología, Consorci Sanitari Parc Taulí, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Esther Barreiro
- Servei de Pneumologia, Hospital del Mar – IMIM, MELIS Dept, Universitat Pompeu Fabra and BRN, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Borja G. Cosío
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Neumología, Hospital Son Espases – Instituto de Investigación Sanitaria de Palma, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Alvar Agustí
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servei de Pneumologia (Institut Clínic de Respiratori), Hospital Clínic – Fundació Clínic per la Recerca Biomèdica, Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Gea
- Servei de Pneumologia, Hospital del Mar – IMIM, MELIS Dept, Universitat Pompeu Fabra and BRN, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- For a list of the members of the BIOMEPOC group see the Acknowledgements
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15
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Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN, Chotirmall SH. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024; 18:111-125. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology, and treatment outcomes. AREAS COVERED We detail the dynamics of the airway microbiome, its influence on chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline (January 2010-March 2024) were retrieved and summarized. We examine clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, antiinflammatories and antimicrobial strategies is discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management. EXPERT OPINION Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogencentric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving crossdisciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials, and therapeutic development pipelines.
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Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Shivani Singh
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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16
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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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17
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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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18
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van der Bie S, Haaksma ME, Vermin B, van Assema H, van Gorp ECM, Langerak T, Endeman H, Snijders D, van den Akker JPC, van Houten MA, van Lelyveld SFL, Goeijenbier M. A Systematic Review of the Pulmonary Microbiome in Patients with Acute Exacerbation COPD Requiring ICU Admission. J Clin Med 2024; 13:472. [PMID: 38256606 PMCID: PMC10816170 DOI: 10.3390/jcm13020472] [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: 11/30/2023] [Revised: 01/03/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is a major health concern. Acute exacerbations (AECOPD) may require intensive care unit (ICU) admission and mechanical ventilation. Acute infections and chronic colonization of the respiratory system are known to precipitate AECOPD. Detailed knowledge of the respiratory microbiome could lead to effective treatment and prevention of exacerbations. Objective: The aim of this review is to summarize the available evidence on the respiratory microbiome of patients with a severe AECOPD requiring mechanical ventilation and intensive care admission. Methods: A systematic literature search was conducted to identify the published papers until January 2023. The collected data were then subjected to qualitative analysis. After the first analysis, a secondary focused review of the most recent publications studying the relationship between microbiome and mortality in AECOPD was performed. Results: Out of 120 screened articles six articles were included in this review. Potentially pathogenic microorganisms (PPMs) were identified in 30% to 72% of the patients with community-acquired bacteria, gram-negative enteric bacilli, Stenotrophomonas and Pseudomonas being the most frequently isolated. During hospitalization, 21% of patients experienced colonization by PPMs. Adequate antimicrobial therapy resulted in the eradication of 77% of the identified PPMs. However, 24% of the bacteria displayed multi-drug resistance leading to prolonged or failure of eradication. Conclusion: PPMs are prevalent in a significant proportion of patients experiencing an AECOPD. The most identified PPMs include community-acquired pathogens and gram-negative enteric bacilli. Notably, no differences in mortality or duration of ventilation were observed between patients with and without isolated PPMs. However, the included studies did not investigate the virome of the patients, which may influence the microbiome and the outcome of infection. Therefore, further research is essential to comprehensively investigate the complete microbial and viral composition of the lower respiratory system in COPD patients admitted to the ICU.
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Affiliation(s)
- Sjoerd van der Bie
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Mark E. Haaksma
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Ben Vermin
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Hidde van Assema
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Eric C. M. van Gorp
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Thomas Langerak
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Henrik Endeman
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
| | - Dominic Snijders
- Department of Pulmonology, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marlies A. van Houten
- Department of Pediatric Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marco Goeijenbier
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
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19
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Chen R, Zhan Y, Lin Z, Wu X, Zhou J, Yang Z, Zheng J. Effect of YuPingFeng granules on clinical symptoms of stable COPD: study protocol for a multicenter, double-blind, and randomized controlled trial. BMC Complement Med Ther 2024; 24:25. [PMID: 38191338 PMCID: PMC10773120 DOI: 10.1186/s12906-023-04271-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 11/22/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Reducing current clinical symptoms and the risks of future exacerbations is the main goal of stable COPD management. Traditional Chinese medicine has unique advantages in chronic disease management. YuPingFeng (YPF), as a classical prescription, has been proven to reduce the risk of exacerbations, but there is a lack of high-quality evidence for the assessment of clinical symptoms and quality of life, particularly for the assessment of treatment response of microecology and immunity. METHODS/DESIGN This is a prospective, multicentre, randomized, double-blind, placebo-controlled clinical trial. A total of 316 eligible subjects with moderate to severe COPD will be randomized 1:1 to receive YPF or placebo. Participants will receive either YPF or a placebo at 5 g three times daily for 52 weeks. The primary outcome will be the change in the COPD Assessment Test (CAT) score after 52 weeks of treatment. Secondary outcomes will include changes in the St George's Respiratory Questionnaire (SGRQ) score and clinical symptom score, among others. Outcomes will be measured at each visit. The study will continue for 52 weeks and will include six visits to each subject (at day 0 and weeks 4,12,24,36 and 52). In the event of exacerbations, subjects will be required to go back to the hospital once on the first day of exacerbation or when their condition permits. DISCUSSION This trial will provide research methods to evaluate the clinical efficacy, safety, and the possible mechanism of YPF in the treatment of stable moderate-to-severe COPD patients. In addition, we hope to provide more possibilities for TCM to participate in the management of stable COPD. TRIAL REGISTRATION The trial was registered at the Chinese Clinical Trials Registry on 3 June 2022 (ChiCTR2200060476; date recorded: 3/6/2022, https://www.chictr.org.cn/ ).
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Affiliation(s)
- Ruifeng Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 9998078 China
| | - Yangqing Zhan
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
| | - Zhengshi Lin
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
| | - Xiao Wu
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
| | - Jinchao Zhou
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
| | - Zifeng Yang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 9998078 China
- Guangzhou Laboratory, Guangzhou, 510230 China
| | - Jinping Zheng
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou, 510230 China
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20
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Lea S, Higham A, Beech A, Singh D. How inhaled corticosteroids target inflammation in COPD. Eur Respir Rev 2023; 32:230084. [PMID: 37852657 PMCID: PMC10582931 DOI: 10.1183/16000617.0084-2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/05/2023] [Indexed: 10/20/2023] Open
Abstract
Inhaled corticosteroids (ICS) are the most commonly used anti-inflammatory drugs for the treatment of COPD. COPD has been previously described as a "corticosteroid-resistant" condition, but current clinical trial evidence shows that selected COPD patients, namely those with increased exacerbation risk plus higher blood eosinophil count (BEC), can benefit from ICS treatment. This review describes the components of inflammation modulated by ICS in COPD and the reasons for the variation in response to ICS between individuals. There are corticosteroid-insensitive inflammatory pathways in COPD, such as bacteria-induced macrophage interleukin-8 production and resultant neutrophil recruitment, but also corticosteroid-sensitive pathways including the reduction of type 2 markers and mast cell numbers. The review also describes the mechanisms whereby ICS can skew the lung microbiome, with reduced diversity and increased relative abundance, towards an excess of proteobacteria. BEC is a biomarker used to enable the selective use of ICS in COPD, but the clinical outcome in an individual is decided by a complex interacting network involving the microbiome and airway inflammation.
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Affiliation(s)
- Simon Lea
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Andrew Higham
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Augusta Beech
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Dave Singh
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
- Medicines Evaluation Unit, Manchester University NHS Foundation Trust, Manchester, UK
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21
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Souza VGP, Forder A, Pewarchuk ME, Telkar N, de Araujo RP, Stewart GL, Vieira J, Reis PP, Lam WL. The Complex Role of the Microbiome in Non-Small Cell Lung Cancer Development and Progression. Cells 2023; 12:2801. [PMID: 38132121 PMCID: PMC10741843 DOI: 10.3390/cells12242801] [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: 11/01/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
In recent years, there has been a growing interest in the relationship between microorganisms in the surrounding environment and cancer cells. While the tumor microenvironment predominantly comprises cancer cells, stromal cells, and immune cells, emerging research highlights the significant contributions of microbial cells to tumor development and progression. Although the impact of the gut microbiome on treatment response in lung cancer is well established, recent investigations indicate complex roles of lung microbiota in lung cancer. This article focuses on recent findings on the human lung microbiome and its impacts in cancer development and progression. We delve into the characteristics of the lung microbiome and its influence on lung cancer development. Additionally, we explore the characteristics of the intratumoral microbiome, the metabolic interactions between lung tumor cells, and how microorganism-produced metabolites can contribute to cancer progression. Furthermore, we provide a comprehensive review of the current literature on the lung microbiome and its implications for the metastatic potential of tumor cells. Additionally, this review discusses the potential for therapeutic modulation of the microbiome to establish lung cancer prevention strategies and optimize lung cancer treatment.
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Affiliation(s)
- Vanessa G. P. Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | | | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rachel Paes de Araujo
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Juliana Vieira
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
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22
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Earle K, Valero C, Conn DP, Vere G, Cook PC, Bromley MJ, Bowyer P, Gago S. Pathogenicity and virulence of Aspergillus fumigatus. Virulence 2023; 14:2172264. [PMID: 36752587 PMCID: PMC10732619 DOI: 10.1080/21505594.2023.2172264] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 02/09/2023] Open
Abstract
Pulmonary infections caused by the mould pathogen Aspergillus fumigatus are a major cause of morbidity and mortality globally. Compromised lung defences arising from immunosuppression, chronic respiratory conditions or more recently, concomitant viral or bacterial pulmonary infections are recognised risks factors for the development of pulmonary aspergillosis. In this review, we will summarise our current knowledge of the mechanistic basis of pulmonary aspergillosis with a focus on emerging at-risk populations.
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Affiliation(s)
- Kayleigh Earle
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Clara Valero
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Daniel P. Conn
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - George Vere
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Peter C. Cook
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Michael J. Bromley
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Bowyer
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Sara Gago
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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23
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Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299130. [PMID: 38077035 PMCID: PMC10705623 DOI: 10.1101/2023.11.29.23299130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes. In this multicenter study, we collected 278 bronchoalveolar lavage (BAL) samples from 229 patients treated at 32 children's hospitals between 2014-2022. Using paired metatranscriptomes and human gene expression data, we identified 4 patient clusters with varying BAL composition. Among those requiring respiratory support prior to sampling, in-hospital mortality varied from 22-60% depending on the cluster (p=0.007). The most common patient subtype, Cluster 1, showed a moderate quantity and high diversity of commensal microbes with robust metabolic activity, low rates of infection, gene expression indicating alveolar macrophage predominance, and low mortality. The second most common cluster showed a very high burden of airway microbes, gene expression enriched for neutrophil signaling, frequent bacterial infections, and moderate mortality. Cluster 3 showed significant depletion of commensal microbes, a loss of biodiversity, gene expression indicative of fibroproliferative pathways, increased viral and fungal pathogens, and high mortality. Finally, Cluster 4 showed profound microbiome depletion with enrichment of Staphylococci and viruses, gene expression driven by lymphocyte activation and cellular injury, and the highest mortality. BAL clusters were modeled with a random forest classifier and reproduced in a geographically distinct validation cohort of 57 patients from The Netherlands, recapitulating similar cluster-based mortality differences (p=0.022). Degree of antibiotic exposure was strongly associated with depletion of BAL microbes and enrichment of fungi. Potential pathogens were parsed from all detected microbes by analyzing each BAL microbe relative to the overall microbiome composition, which yielded increased sensitivity for numerous previously occult pathogens. These findings support personalized interpretation of the pulmonary microenvironment in pediatric HCT, which may facilitate biology-targeted interventions to improve outcomes.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children`s Hospital at Westmead, Sydney, Australia
| | - Courtney M Rowan
- Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Division of Critical Care, Department of Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Division of Pediatric Critical Care, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Paul Castillo
- University of Florida, Gainesville, UF Health Shands Children's Hospital, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Children's National Hospital, Washington, District of Columbia, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Division of Pediatric Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Departments of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Popovic D, Kulas J, Tucovic D, Popov Aleksandrov A, Glamoclija J, Sokovic Bajic S, Tolinacki M, Golic N, Mirkov I. Lung microbiota changes during pulmonary Aspergillus fumigatus infection in rats. Microbes Infect 2023; 25:105186. [PMID: 37479024 DOI: 10.1016/j.micinf.2023.105186] [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: 09/12/2022] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Since the realization that the lungs are not sterile but are normally inhabited by various bacterial species, studies have been conducted to define healthy lung microbiota and to investigate whether it changes during lung diseases, infections, and inflammation. Using next-generation sequencing, we investigated bacterial microbiota from whole lungs in two rat strains (previously shown to differ in gut microbiota composition) in a healthy state and during pulmonary infection caused by the opportunistic fungus Aspergillus fumigatus. No differences in alpha diversity indices and microbial composition between DA and AO rats before infection were noted. Fungal infection caused dysbiosis in both rat strains, characterized by increased alpha diversity indices and unchanged beta diversity. The relative abundance of genera and species was increased in DA but decreased in AO rats during infection. Changes in lung microbiota coincided with inflammation (in both rat strains) and oxidative stress (in DA rats). Disparate response of lung microbiota in DA and AO rats to pulmonary fungal infection might render these two rat strains differentially susceptible to a subsequent inflammatory insult.
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Affiliation(s)
- Dusanka Popovic
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Jelena Kulas
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Dina Tucovic
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Aleksandra Popov Aleksandrov
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Jasmina Glamoclija
- Mycology Laboratory, Department Plant Physiology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000 Belgrade, Serbia
| | - Svetlana Sokovic Bajic
- Group for Probiotics and Microbiota-host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Maja Tolinacki
- Group for Probiotics and Microbiota-host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Natasa Golic
- Group for Probiotics and Microbiota-host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Ivana Mirkov
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia.
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Mao X, Li Y, Shi P, Zhu Z, Sun J, Xue Y, Wan Z, Yang D, Ma T, Wang J, Zhu R. Analysis of sputum microbial flora in chronic obstructive pulmonary disease patients with different phenotypes during acute exacerbations. Microb Pathog 2023; 184:106335. [PMID: 37673353 DOI: 10.1016/j.micpath.2023.106335] [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: 06/22/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Increasing studies have shown that the imbalance of the respiratory microbial flora is related to the occurrence of COPD, the severity and frequency of exacerbations and mortality.However, it remains unclear how the sputum microbial flora differs during exacerbations in COPD patients manifesting emphysema phenotype, chronic bronchitis with emphysema phenotype and asthma-COPD overlap phenotype. METHODS Sputum samples were obtained from 29 COPD patients experiencing acute exacerbations who had not received antibiotics or systemic corticosteroids within the past four weeks.Patients were divided into three groups;emphysema phenotype(E);chronic bronchitis with emphysema phenotype(B+E) and asthma-COPD overlap phenotype(ACO).We utilized metagenomic Next Generation Sequencing (mNGS) technology to analyze the sputum microbial flora in COPD patients with different phenotypes during exacerbations. RESULTS There was no significant difference in alpha diversity and beta diversity among three groups.The microbial flora composition was similar in all three groups during exacerbations except for a significant increase in Streptococcus mitis in ACO.Through network analysis,we found Candidatus Saccharibacteria oral taxon TM7x and Fusobacterium necrophorum were the core nodes of the co-occurrence network in ACO and E respectively.They were positively correlated with some species and play a synergistic role.In B+E,Haemophilus pittmaniae and Klebsiella pneumoniae had a synergistic effect.Besides,some species among the three groups play a synergistic or antagonistic role.Through Spearman analysis,we found the relative abundance of Streptococcus mitis was negatively correlated with the number of hospitalizations in the past year(r = -0.410,P = 0.027).We also observed that the relative abundance of Prevotella and Prevotella melaninogenica was negatively correlated with age(r = -0.534,P = 0.003;r = -0.567,P = 0.001),while the relative abundance of Streptococcus oralis and Actinomyces odontolyticus was positively correlated with age(r = 0.570,P = 0.001;r = 0.480,P = 0.008).In addition,the relative abundance of Prevotella melaninogenica was negatively correlated with peripheral blood neutrophil ratio and neutrophil to lymphocyte ratio(r = -0.479,P = 0.009;r = -0.555,P = 0.002),while the relative abundance of Streptococcus sanguinis was positively correlated with peripheral blood neutrophil ratio and neutrophil to lymphocyte ratio (r = 0.450,P = 0.014;r = 0.501,P = 0.006).There was also a significant positive correlation between Oribacterium and blood eosinophil counts(r = 0.491,P = 0.007). CONCLUSION Overall,we analyzed the sputum microbiota of COPD patients with different phenotypes and its relationship with clinical indicators, and explored the relationships between microbiota and inflammation in COPD.We hope to alter the prognosis of patients by inhibiting specific bacterial taxa related to inflammation and using guide individualized treatment in the future research.
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Affiliation(s)
- Xiaoyan Mao
- Department of Intensive Care Unit, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, Jiangsu, 223002, China
| | - Yao Li
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China
| | - Pengfei Shi
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China
| | - Ziwei Zhu
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China
| | - Juan Sun
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Yu Xue
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Zongren Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Dan Yang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Ting Ma
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Jipeng Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Rong Zhu
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China.
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Hazra D, SM F, Chawla K, Sintchenko V, Martinez E, Magazine R, Siddalingaiah N. The altered sputum microbiome profile in patients with moderate and severe COPD exacerbations, compared to the healthy group in the Indian population. F1000Res 2023; 12:528. [PMID: 37928173 PMCID: PMC10624950 DOI: 10.12688/f1000research.132220.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2023] [Indexed: 11/07/2023] Open
Abstract
Background: Microbial culture-independent sequencing techniques have advanced our understanding of host-microbiome interactions in health and disease. The purpose of this study was to explore the dysbiosis of airway microbiota in patients with moderate or severe chronic obstructive pulmonary disease (COPD) and compare them with healthy controls. Methods: The COPD patients were investigated for disease severity based on airflow limitations and divided into moderate (50%≤FEV1<80% predicted) and severe groups (FEV1<50% predicted). Spontaneous sputum samples were collected and, the V3-V4 regions of the 16S rRNA coding gene were sequenced to examine the microbiome profile of COPD and healthy participants. Results: A total of 45 sputum samples were collected from 17 severe COPD, 12 moderate COPD cases, and 16 healthy volunteers. The bacterial alpha diversity (Shannon and Simpson's index) significantly decreased in the moderate and severe COPD groups, compared to healthy samples. A significantly higher proportion of Firmicutes and Actinobacteria were present in moderate COPD, and Proteobacteria numbers were comparatively increased in severe COPD. In healthy samples, Bacteroidetes and Fusobacteria were more abundant in comparison to both the COPD groups. Among the most commonly detected 20 bacterial genera, Streptococcus was predominant among the COPD sputum samples, whereas Prevotella was the top genus in healthy controls. Linear discriminant analysis (LDA>2) revealed that marker genera like Streptococcus and Rothia were abundant in moderate COPD. For severe COPD, the genera Pseudomonasand Leptotrichia were most prevalent, whereas Fusobacterium and Prevotella were dominant in the healthy group. Conclusions: Our findings suggest a significant dysbiosis of the respiratory microbiome in COPD patients. The decreased microbial diversity may influence the host immune response and provide microbiological biomarkers for the diagnosis and monitoring of COPD.
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Affiliation(s)
- Druti Hazra
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Fayaz SM
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wale, 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, 2145, Australia
| | - Elena Martinez
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, 2145, Australia
| | - Rahul Magazine
- Department of Respiratory Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Nayana Siddalingaiah
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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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: 3] [Impact Index Per Article: 3.0] [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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Brettoni C, Muzzi A, Rondini S, Weynants V, Rossi Paccani S. Ex-vivo RNA expression analysis of vaccine candidate genes in COPD sputum samples. Respir Res 2023; 24:243. [PMID: 37798723 PMCID: PMC10552247 DOI: 10.1186/s12931-023-02525-z] [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: 01/19/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a lung disease characterised by airflow-limiting inflammation and mucus production. Acute exacerbations are a major cause of COPD-related morbidity and mortality and are mostly associated with bacterial or viral infections. A vaccine targeting non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat), the main bacteria associated with exacerbations, was tested in a Phase 2 trial. We assessed "ex-vivo" expression of vaccine candidate and housekeeping genes pd, pe, pilA, gapA, ompP6 of NTHi, and uspA2, parE, polA of Mcat in sputum samples of COPD patients and determined whether expression of the vaccine candidate genes pd, pe, pilA (NTHi) and uspA2 (Mcat) differed between stable and exacerbation samples. METHODS A single-centre, prospective, observational cohort study was conducted where 123 COPD patients were seen on enrolment, followed monthly for 2 years, and reviewed after onset of acute exacerbations. We selected 69 patients with sputum samples positive for NTHi or Mcat by PCR during at least one stable and one exacerbation visit. mRNA was isolated from the sputum, and expression of NTHi and Mcat genes was analysed with RT-PCR. Statistical analyses compared mRNA concentrations between stable and exacerbation samples and in relationship to COPD severity and exacerbation frequency. RESULTS The vaccine candidate genes were variably expressed in sputum samples, suggesting they are expressed in the lung. Absolute and relative expression of all NTHi vaccine candidate genes and Mcat uspA2 were similar between exacerbation and stable samples. Expression of pd and pilA was slightly associated with the number of exacerbations in the year before enrolment, and uspA2 with the disease severity status at enrolment. CONCLUSIONS The NTHi-Mcat vaccine candidate genes were expressed in sputum samples, and each gene had a specific level of expression. No statistically significant differences in gene expression were detectable between stable and exacerbation samples. However, the history of COPD exacerbations was slightly associated with the expression of pd, pilA and uspA2. Trial registration NCT01360398 ( https://www. CLINICALTRIALS gov ).
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Flahaut M, Leprohon P, Pham NP, Gingras H, Bourbeau J, Papadopoulou B, Maltais F, Ouellette M. Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis. Sci Rep 2023; 13:16622. [PMID: 37789055 PMCID: PMC10547696 DOI: 10.1038/s41598-023-43821-4] [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: 02/03/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our objective was to investigate associations between respiratory health in Inuit communities and their airway microbiome. Oropharyngeal samples were collected during the Qanuilirpitaa? 2017 Inuit Health Survey and subjected to metagenomic analyses. Participants were assigned to a bronchial obstruction group or a control group based on their clinical history and their pulmonary function, as monitored by spirometry. The Inuit microbiota composition was found to be distinct from other studied populations. Within the Inuit microbiota, differences in diversity measures tend to distinguish the two groups. Bacterial taxa found to be more abundant in the control group included candidate probiotic strains, while those enriched in the bronchial obstruction group included opportunistic pathogens. Crossing taxa affiliation method and machine learning consolidated our finding of distinct core microbiomes between the two groups. More microbial metabolic pathways were enriched in the control participants and these were often involved in vitamin and anti-inflammatory metabolism, while a link could be established between the enriched pathways in the disease group and inflammation. Overall, our results suggest a link between microbial abundance, interactions and metabolic activities and respiratory health in the Inuit population.
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Affiliation(s)
- Mathilde Flahaut
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Jean Bourbeau
- Department of Medicine, Division of Respiratory Medicine, McGill University Health Center, Montréal, QC, Canada
| | - Barbara Papadopoulou
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - François Maltais
- Groupe de Recherche en Santé Respiratoire, Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada.
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Tamiya H, Mitani A, Abe M, Nagase T. Putative Bidirectionality of Chronic Obstructive Pulmonary Disease and Periodontal Disease: A Review of the Literature. J Clin Med 2023; 12:5935. [PMID: 37762876 PMCID: PMC10531527 DOI: 10.3390/jcm12185935] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/24/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The prevalence of chronic obstructive pulmonary disease (COPD) is increasing worldwide and is currently the third leading cause of death globally. The long-term inhalation of toxic substances, mainly cigarette smoke, deteriorates pulmonary function over time, resulting in the development of COPD in adulthood. Periodontal disease is an inflammatory condition that affects most adults and is caused by the bacteria within dental plaque. These bacteria dissolve the gums around the teeth and the bone that supports them, ultimately leading to tooth loss. Periodontal disease and COPD share common risk factors, such as aging and smoking. Other similarities include local chronic inflammation and links with the onset and progression of systemic diseases such as ischemic heart disease and diabetes mellitus. Understanding whether interventions for periodontal disease improve the disease trajectory of COPD (and vice versa) is important, given our rapidly aging society. This review focuses on the putative relationship between COPD and periodontal disease while exploring current evidence and future research directions.
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Affiliation(s)
- Hiroyuki Tamiya
- Division for Health Service Promotion, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- The Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Akihisa Mitani
- The Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Masanobu Abe
- Department of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Takahide Nagase
- The Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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Gan Y, Zhao G, Wang Z, Zhang X, Wu MX, Lu M. Bacterial Membrane Vesicles: Physiological Roles, Infection Immunology, and Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301357. [PMID: 37357142 PMCID: PMC10477901 DOI: 10.1002/advs.202301357] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/19/2023] [Indexed: 06/27/2023]
Abstract
Bacterial or fungal membrane vesicles, traditionally considered as microbial metabolic wastes, are secreted mainly from the outer membrane or cell membrane of microorganisms. However, recent studies have shown that these vesicles play essential roles in direct or indirect communications among microorganisms and between microorganisms and hosts. This review aims to provide an updated understanding of the physiological functions and emerging applications of bacterial membrane vesicles, with a focus on their biogenesis, mechanisms of adsorption and invasion into host cells, immune stimulatory effects, and roles in the much-concerned problem of bacterial resistance. Additionally, the potential applications of these vesicles as biomarkers, vaccine candidates, and drug delivery platforms are discussed.
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Affiliation(s)
- Yixiao Gan
- Department of Transfusion MedicineHuashan HospitalFudan UniversityShanghai200040P. R. China
| | - Gang Zhao
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200240P. R. China
| | - Zhicheng Wang
- Department of Transfusion MedicineHuashan HospitalFudan UniversityShanghai200040P. R. China
| | - Xingcai Zhang
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
| | - Mei X. Wu
- Wellman Center for PhotomedicineMassachusetts General HospitalDepartment of DermatologyHarvard Medical School, 50 Blossom StreetBostonMA02114USA
| | - Min Lu
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200240P. R. China
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O’Shaughnessy M, Sheils O, Baird AM. The Lung Microbiome in COPD and Lung Cancer: Exploring the Potential of Metal-Based Drugs. Int J Mol Sci 2023; 24:12296. [PMID: 37569672 PMCID: PMC10419288 DOI: 10.3390/ijms241512296] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) and lung cancer 17 are two of the most prevalent and debilitating respiratory diseases worldwide, both associated with high morbidity and mortality rates. As major global health concerns, they impose a substantial burden on patients, healthcare systems, and society at large. Despite their distinct aetiologies, lung cancer and COPD share common risk factors, clinical features, and pathological pathways, which have spurred increasing research interest in their co-occurrence. One area of particular interest is the role of the lung microbiome in the development and progression of these diseases, including the transition from COPD to lung cancer. Exploring novel therapeutic strategies, such as metal-based drugs, offers a potential avenue for targeting the microbiome in these diseases to improve patient outcomes. This review aims to provide an overview of the current understanding of the lung microbiome, with a particular emphasis on COPD and lung cancer, and to discuss the potential of metal-based drugs as a therapeutic strategy for these conditions, specifically concerning targeting the microbiome.
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Affiliation(s)
- Megan O’Shaughnessy
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Orla Sheils
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
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Belizário J, Garay-Malpartida M, Faintuch J. Lung microbiome and origins of the respiratory diseases. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100065. [PMID: 37456520 PMCID: PMC10339129 DOI: 10.1016/j.crimmu.2023.100065] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The studies on the composition of the human microbiomes in healthy individuals, its variability in the course of inflammation, infection, antibiotic therapy, diets and different pathological conditions have revealed their intra and inter-kingdom relationships. The lung microbiome comprises of major species members of the phylum Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Proteobacteria, which are distributed in ecological niches along nasal cavity, nasopharynx, oropharynx, trachea and in the lungs. Commensal and pathogenic species are maintained in equilibrium as they have strong relationships. Bacterial overgrowth after dysbiosis and/or imbalanced of CD4+ helper T cells, CD8+ cytotoxic T cells and regulatory T cells (Treg) populations can promote lung inflammatory reactions and distress, and consequently acute and chronic respiratory diseases. This review is aimed to summarize the latest advances in resident lung microbiome and its participation in most common pulmonary infections and pneumonia, community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), immunodeficiency associated pneumonia, SARS-CoV-2-associated pneumonia, acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). We briefly describe physiological and immunological mechanisms that selectively create advantages or disadvantages for relative growth of pathogenic bacterial species in the respiratory tract. At the end, we propose some directions and analytical methods that may facilitate the identification of key genera and species of resident and transient microbes involved in the respiratory diseases' initiation and progression.
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Affiliation(s)
- José Belizário
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Miguel Garay-Malpartida
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Joel Faintuch
- Department of Gastroenterology of the Clinics Hospital of the University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, São Paulo, CEP 05403-000, Brazil
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Cai S, Gao J, Liu X, Yang J, Feng D, Li G, Li S, Yang H, Wang Z, Yi X, Zhou Y. Seasonal Dynamics of the Upper Respiratory Tract Microbiome in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2023; 18:1267-1276. [PMID: 37362620 PMCID: PMC10290470 DOI: 10.2147/copd.s403198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Increasing evidence suggests that seasonal changes can trigger the alternation of airway microbiome. However, the dynamics of the upper airway bacterial ecology of chronic obstructive pulmonary disease (COPD) patients across different seasons remains unclear. Methods In this study, we present a 16S ribosomal RNA survey of the airway microbiome on 72 swab samples collected in different months (March, May, July, September, and November) in 2019 from 18 COPD patients and from six resampled patients in November in 2020. Results Our study uncovered a dynamic airway microbiota where changes appeared to be associated with seasonal alternation in COPD patients. Twelve clusters of temporal patterns were displayed by differential and clustering analysis along the time course, systematically revealing distinct microbial taxa that prefer to grow in cool and warm seasons, respectively. Moreover, the upper airway microbiome composition was relatively stable in the same season in different years. Discussion Given the tight association between airway microbiome and COPD disease progression, this study can provide useful information for clinically understanding the seasonal trend of disease phenotypes in COPD patients.
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Affiliation(s)
- Shuping Cai
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guang Dong, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, the Seventh Affiliated Hospital of SUN YAT-SEN University, Shenzhen, Guang Dong, People’s Republic of China
| | - Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guang Dong, People’s Republic of China
| | - Xiaomin Liu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guang Dong, People’s Republic of China
| | - Junhao Yang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guang Dong, People’s Republic of China
| | - Dingyun Feng
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guang Dong, People’s Republic of China
| | - Guijun Li
- Department of Pulmonary and Critical Care Medicine, the Seventh Affiliated Hospital of SUN YAT-SEN University, Shenzhen, Guang Dong, People’s Republic of China
| | - Sijia Li
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guang Dong, People’s Republic of China
| | - Hailing Yang
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guang Dong, People’s Republic of China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guang Dong, People’s Republic of China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guang Dong, People’s Republic of China
| | - Yuqi Zhou
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guang Dong, People’s Republic of China
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Du S, Shang L, Zou X, Deng X, Sun A, Mu S, Zhao J, Wang Y, Feng X, Li B, Wang C, Liu S, Lu B, Liu Y, Zhang R, Tong Y, Cao B. Azithromycin Exposure Induces Transient Microbial Composition Shifts and Decreases the Airway Microbiota Resilience from Outdoor PM 2.5 Stress in Healthy Adults: a Randomized, Double-Blind, Placebo-Controlled Trial. Microbiol Spectr 2023; 11:e0206622. [PMID: 37093053 PMCID: PMC10269807 DOI: 10.1128/spectrum.02066-22] [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: 06/03/2022] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Inappropriate antibiotic prescriptions are common for patients with upper respiratory tract infections (URTIs). Few data exist regarding the effects of antibiotic administration on airway microbiota among healthy adults. We conducted a randomized, double-blind, placebo-controlled trial to characterize the airway microbiota longitudinally in healthy adults using 16S rRNA gene sequencing and quantification. Both the induced sputum and oral wash samples were collected over a 60-day period following a 3-day intervention with 500 mg azithromycin or placebo. Environmental information, including air quality data (particulate matter [PM2.5] and PM10, air quality index [AQI] values), were also collected during the study. A total of 48 healthy volunteers were enrolled and randomly assigned into two groups. Azithromycin did not alter bacterial load but significantly reduced species richness and Shannon index. Azithromycin exposure resulted in a decrease in the detection rate and relative abundance of different genera belonging to Veillonellaceae, Leptotrichia, Fusobacterium, Neisseria, and Haemophilus. In contrast, the relative abundance of taxa belonging to Streptococcus increased immediately after azithromycin intervention. The shifts in the diversity of the microbiology composition took between 14 and 60 days to recover, depending on the measure used: either UniFrac phylogenetic distance or α-diversity. Outdoor environmental perturbations, especially the high concentration of PM2.5, contributed to novel variability in microbial community composition of the azithromycin group at D30 (30 days after baseline). The network analysis found that azithromycin altered the microbial interactions within airway microbiota. The influence was still obvious at D14 when the relative abundance of most taxa had returned to the baseline level. Compared to the sputum microbiota, oral cavity microbiota had a different pattern of change over time. The induced sputum microbial data can represent the airway microbiota composition in healthy adults. Azithromycin may have transient effects in the airway microbiota of healthy adults and decrease the airway microbiota resilience against outdoor environmental stress. The influence of azithromycin on microbial interactions is noteworthy, although the airway microbiota has returned to a near-baseline level. IMPORTANCE The influence of antibiotic administration on the airway microbiota of healthy adults remains unknown. This study is a randomized, double-blind, placebo-controlled trial aiming to investigate the microbial shifts in airways after exposure to azithromycin among heathy adults. We find that azithromycin changes the airway microbial community composition of healthy adults and decreases the airway microbiota resilience against outdoor environmental stress. This study depicts the longitudinal recovery trajectory of airway microbiota after the antibiotic perturbation and may provide reference for appropriate antibiotic prescription.
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Affiliation(s)
- Sisi Du
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Lianhan Shang
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohui Zou
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Deng
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Aihua Sun
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Shengrui Mu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Jiankang Zhao
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yimin Wang
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Jin Yin-tan Hospital, Wuhan, Hubei, China
| | - Xiaoxuan Feng
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Binbin Li
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Chunlei Wang
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Shuai Liu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Binghuai Lu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yingmei Liu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Rongrong Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Bin Cao
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
- Changping Laboratory, Beijing, China
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Kim BG, Kang N, Kim SY, Kim DH, Kim H, Kwon OJ, Huh HJ, Lee NY, Jhun BW. The lung microbiota in nontuberculous mycobacterial pulmonary disease. PLoS One 2023; 18:e0285143. [PMID: 37235629 DOI: 10.1371/journal.pone.0285143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The role of bacterial microbiota in the pathogenesis of nontuberculous mycobacterial pulmonary disease (NTM-PD) is unclear. We aimed to compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients. METHODS We analyzed lung tissues from 23 NTM-PD patients who underwent surgical lung resection. Lung tissues were collected in pairs from each patient, with one sample from a disease-involved site and the other from a non-involved site. Lung tissue microbiome libraries were constructed using 16S rRNA gene sequences (V3-V4 regions). RESULTS Sixteen (70%) patients had Mycobacterium avium complex (MAC)-PD, and the remaining seven (30%) had Mycobacterium abscessus-PD. Compared to non-involved sites, involved sites showed greater species richness (ACE, Chao1, and Jackknife analyses, all p = 0.001); greater diversity on the Shannon index (p = 0.007); and genus-level differences (Jensen-Shannon, PERMANOVA p = 0.001). Analysis of taxonomic biomarkers using linear discriminant analysis (LDA) effect sizes (LEfSe) demonstrated that several genera, including Limnohabitans, Rahnella, Lachnospira, Flavobacterium, Megamonas, Gaiella, Subdoligranulum, Rheinheimera, Dorea, Collinsella, and Phascolarctobacterium, had significantly greater abundance in involved sites (LDA >3.00, p <0.05, and q <0.05). In contrast, Acinetobacter had significantly greater abundance at non-involved sites (LDA = 4.27, p<0.001, and q = 0.002). Several genera were differentially distributed between lung tissues from MAC-PD (n = 16) and M. abscessus-PD (n = 7), and between nodular bronchiectatic form (n = 12) and fibrocavitary form (n = 11) patients. However, there was no genus with a significant q-value. CONCLUSIONS We identified differential microbial distributions between disease-invaded and normal lung tissues from NTM-PD patients, and microbial diversity was significantly higher in disease-invaded tissues. TRIAL REGISTRATION Clinical Trial registration number: NCT00970801.
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Affiliation(s)
- Bo-Guen Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Noeul Kang
- Division of Pulmonary and Critical Care Medicine, 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, Seoul, South Korea
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Wang R, Huang C, Yang W, Wang C, Wang P, Guo L, Cao J, Huang L, Song H, Zhang C, Zhang Y, Shi G. Respiratory microbiota and radiomics features in the stable COPD patients. Respir Res 2023; 24:131. [PMID: 37173744 PMCID: PMC10176953 DOI: 10.1186/s12931-023-02434-1] [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: 11/21/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUNDS The respiratory microbiota and radiomics correlate with the disease severity and prognosis of chronic obstructive pulmonary disease (COPD). We aim to characterize the respiratory microbiota and radiomics features of COPD patients and explore the relationship between them. METHODS Sputa from stable COPD patients were collected for bacterial 16 S rRNA gene sequencing and fungal Internal Transcribed Spacer (ITS) sequencing. Chest computed tomography (CT) and 3D-CT analysis were conducted for radiomics information, including the percentages of low attenuation area below - 950 Hounsfield Units (LAA%), wall thickness (WT), and intraluminal area (Ai). WT and Ai were adjusted by body surface area (BSA) to WT/[Formula: see text] and Ai/BSA, respectively. Some key pulmonary function indicators were collected, which included forced expiratory volume in one second (FEV1), forced vital capacity (FVC), diffusion lung carbon monoxide (DLco). Differences and correlations of microbiomics with radiomics and clinical indicators between different patient subgroups were assessed. RESULTS Two bacterial clusters dominated by Streptococcus and Rothia were identified. Chao and Shannon indices were higher in the Streptococcus cluster than that in the Rothia cluster. Principal Co-ordinates Analysis (PCoA) indicated significant differences between their community structures. Higher relative abundance of Actinobacteria was detected in the Rothia cluster. Some genera were more common in the Streptococcus cluster, mainly including Leptotrichia, Oribacterium, Peptostreptococcus. Peptostreptococcus was positively correlated with DLco per unit of alveolar volume as a percentage of predicted value (DLco/VA%pred). The patients with past-year exacerbations were more in the Streptococcus cluster. Fungal analysis revealed two clusters dominated by Aspergillus and Candida. Chao and Shannon indices of the Aspergillus cluster were higher than that in the Candida cluster. PCoA showed distinct community compositions between the two clusters. Greater abundance of Cladosporium and Penicillium was found in the Aspergillus cluster. The patients of the Candida cluster had upper FEV1 and FEV1/FVC levels. In radiomics, the patients of the Rothia cluster had higher LAA% and WT/[Formula: see text] than those of the Streptococcus cluster. Haemophilus, Neisseria and Cutaneotrichosporon positively correlated with Ai/BSA, but Cladosporium negatively correlated with Ai/BSA. CONCLUSIONS Among respiratory microbiota in stable COPD patients, Streptococcus dominance was associated with an increased risk of exacerbation, and Rothia dominance was relevant to worse emphysema and airway lesions. Peptostreptococcus, Haemophilus, Neisseria and Cutaneotrichosporon probably affected COPD progression and potentially could be disease prediction biomarkers.
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Affiliation(s)
- Rong Wang
- Department of Pulmonary and Critical Care Medicine, the Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming, 650032, People's Republic of China
- Medical School, Kunming University of Science and Technology, Kunming, 650500, People's Republic of China
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Wenjie Yang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Cui Wang
- Department of Pulmonary and Critical Care Medicine, the Third People's Hospital of Kunshan, Suzhou, 215300, People's Republic of China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Leixin Guo
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Jin Cao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Lin Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Hejie Song
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, the Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming, 650032, People's Republic of China.
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China.
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Karakasidis E, Kotsiou OS, Gourgoulianis KI. Lung and Gut Microbiome in COPD. J Pers Med 2023; 13:jpm13050804. [PMID: 37240974 DOI: 10.3390/jpm13050804] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/06/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide. The association between lung and gut microbiomes in the pathogenesis of COPD has been recently uncovered. The goal of this study was to discuss the role of the lung and gut microbiomes in COPD pathophysiology. A systematic search of the PubMed database for relevant articles submitted up to June 2022 was performed. We examined the association between the lung and gut microbiome dysbiosis, reflected in bronchoalveolar lavage (BAL), lung tissue, sputum, and feces samples, and the pathogenesis and progression of COPD. It is evident that the lung and gut microbiomes affect each other and both play a vital role in the pathogenesis of COPD. However, more research needs to be carried out to find the exact associations between microbiome diversity and COPD pathophysiology and exacerbation genesis. Another field that research should focus on is the impact of treatment interventions targeting the human microbiome in preventing COPD genesis and progression.
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Affiliation(s)
- Efstathios Karakasidis
- Department of Respiratory Medicine, School of Health Science, University of Thessaly, Biopolis, 41110 Larissa, Greece
| | - Ourania S Kotsiou
- Department of Respiratory Medicine, School of Health Science, University of Thessaly, Biopolis, 41110 Larissa, Greece
- Department of Human Pathophysiology, Faculty of Nursing, School of Health Science, University of Thessaly, Gaiopolis, 41110 Larissa, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, School of Health Science, University of Thessaly, Biopolis, 41110 Larissa, Greece
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Chen D, Zeng Q, Liu L, Zhou Z, Qi W, Yu S, Zhao L. Global Research Trends on the Link Between the Microbiome and COPD: A Bibliometric Analysis. Int J Chron Obstruct Pulmon Dis 2023; 18:765-783. [PMID: 37180751 PMCID: PMC10167978 DOI: 10.2147/copd.s405310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023] Open
Abstract
Background The pathogenesis of chronic obstructive pulmonary disease (COPD) has been studied in relation to the microbiome, providing space for more targeted interventions and new treatments. Numerous papers on the COPD microbiome have been reported in the last 10 years, yet few publications have used bibliometric methods to evaluate this area. Methods We searched the Web of Science Core Collection for all original research articles in the field of COPD microbiome from January 2011 to August 2022 and used CiteSpace for visual analysis. Results A total of 505 relevant publications were obtained, and the number of global publications in this field is steadily increasing every year, with China and the USA occupying the first two spots in international publications. Imperial College London and the University of Leicester produced the most publications. Brightling C from the UK was the most prolific writer, while Huang Y and Sze M from the USA were first and second among the authors cited. The American Journal of Respiratory and Critical Care Medicine had the highest frequency of citations. The top 10 institutions, cited authors and journals are mostly from the UK and the US. In the ranking of citations, the first article was a paper published by Sze M on changes in the lung tissue's microbiota in COPD patients. The keywords "exacerbation", "gut microbiota", "lung microbiome", "airway microbiome", "bacterial colonization", and "inflammation" were identified as cutting-edge research projects for 2011-2022. Conclusion Based on the visualization results, in the future, we can use the gut-lung axis as the starting point to explore the immunoinflammatory mechanism of COPD, and study how to predict the effects of different treatments of COPD by identifying the microbiota, and how to achieve the optimal enrichment of beneficial bacteria and the optimal consumption of harmful bacteria to improve COPD.
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Affiliation(s)
- Daohong Chen
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Qian Zeng
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Lu Liu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Ziyang Zhou
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Wenchuan Qi
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Shuguang Yu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Ling Zhao
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
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Cao Y, Chen X, Shu L, Shi L, Wu M, Wang X, Deng K, Wei J, Yan J, Feng G. Analysis of the correlation between BMI and respiratory tract microbiota in acute exacerbation of COPD. Front Cell Infect Microbiol 2023; 13:1161203. [PMID: 37180432 PMCID: PMC10166817 DOI: 10.3389/fcimb.2023.1161203] [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: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
Objective To investigate the distribution differences in the respiratory tract microbiota of AECOPD patients in different BMI groups and explore its guiding value for treatment. Methods Sputum samples of thirty-eight AECOPD patients were collected. The patients were divided into low, normal and high BMI group. The sputum microbiota was sequenced by 16S rRNA detection technology, and the distribution of sputum microbiota was compared. Rarefaction curve, α-diversity, principal coordinate analysis (PCoA) and measurement of sputum microbiota abundance in each group were performed and analyzed by bioinformatics methods. Results 1. The rarefaction curve in each BMI group reached a plateau. No significant differences were observed in the OTU total number or α-diversity index of microbiota in each group. PCoA showed significant differences in the distance matrix of sputum microbiota between the three groups, which was calculated by the Binary Jaccard and the Bray Curtis algorithm. 2. At the phylum level, most of the microbiota were Proteobacteria, Bacteroidetes Firmicutes, Actinobacteria, and Fusobacteria. At the genus level, most were Streptococcus, Prevotella, Haemophilus, Neisseria and Bacteroides. 3. At the phylum level, the abundance of Proteobacteria in the low group was significantly higher than that in normal and high BMI groups, the abundances of Firmicutes in the low and normal groups were significantly lower than that in high BMI groups. At the genus level, the abundance of Haemophilus in the low group was significantly higher than that in high BMI group, and the abundances of Streptococcus in the low and normal BMI groups were significantly lower than that in the high BMI group. Conclusions 1. The sputum microbiota of AECOPD patients in different BMI groups covered almost all microbiota, and BMI had no significant association with total number of respiratory tract microbiota or α-diversity in AECOPD patients. However, there was a significant difference in the PCoA between different BMI groups. 2. The microbiota structure of AECOPD patients differed in different BMI groups. Gram-negative bacteria (G-) in the respiratory tract of patients predominated in the low BMI group, while gram-positive bacteria (G+) predominated in the high BMI group.
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Affiliation(s)
- Yang Cao
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaolin Chen
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Shu
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Shi
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mingjing Wu
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xueli Wang
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kaili Deng
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Wei
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiaxin Yan
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ganzhu Feng
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [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: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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Xue Q, Xie Y, He Y, Yu Y, Fang G, Yu W, Wu J, Li J, Zhao L, Deng X, Li R, Wang F, Zheng Y, Gao Z. Lung microbiome and cytokine profiles in different disease states of COPD: a cohort study. Sci Rep 2023; 13:5715. [PMID: 37029178 PMCID: PMC10080507 DOI: 10.1038/s41598-023-32901-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/04/2023] [Indexed: 04/09/2023] Open
Abstract
Increasing evidence indicates that respiratory tract microecological disorders may play a role in the pathogenesis of chronic obstructive pulmonary disease (COPD). Understanding the composition of the respiratory microbiome in COPD and its relevance to respiratory immunity will help develop microbiome-based diagnostic and therapeutic approaches. One hundred longitudinal sputum samples from 35 subjects with acute exacerbation of COPD (AECOPD) were analysed for respiratory bacterial microbiome using 16S ribosomal RNA amplicon sequencing technology, and the sputum supernatant was analysed for 12 cytokines using a Luminex liquid suspension chip. Unsupervised hierarchical clustering was employed to evaluate the existence of distinct microbial clusters. In AECOPD, the respiratory microbial diversity decreased, and the community composition changed significantly. The abundances of Haemophilus, Moraxella, Klebsiella, and Pseudomonas increased significantly. Significant positive correlations between the abundance of Pseudomonas and TNF-α, abundance of Klebsiella and the percentage of eosinophils were observed. Furthermore, COPD can be divided into four clusters based on the respiratory microbiome. AECOPD-related cluster was characterized by the enrichment of Pseudomonas and Haemophilus and a high level of TNF-α. Lactobacillus and Veillonella are enriched in therapy-related phenotypes and may play potential probiotic roles. There are two inflammatory endotypes in the stable state: Gemella is associated with the Th2 inflammatory endotypes, whereas Prevotella is associated with the Th17 inflammatory endotypes. Nevertheless, no differences in clinical manifestations were found between these two endotypes. The sputum microbiome is associated with the disease status of COPD, allowing us to distinguish different inflammatory endotypes. Targeted anti-inflammatory and anti-infective therapies may improve the long-term prognosis of COPD.
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Affiliation(s)
- Qing Xue
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Yu Xie
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
- Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yan Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Guiju Fang
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Jianhui Wu
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Jiwei Li
- Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361101, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Xinyu Deng
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Ran Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Fang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.
- Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361101, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.
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43
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Zhu Y, Chang D. Interactions between the lung microbiome and host immunity in chronic obstructive pulmonary disease. Chronic Dis Transl Med 2023. [DOI: 10.1002/cdt3.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Affiliation(s)
- Yixing Zhu
- Graduate School of The PLA General Hospital Beijing China
| | - De Chang
- Department of Respiratory and Critical Care Medicine, Eighth Medical Center, Department of Respiratory and Critical Care Seventh Medical Center Chinese PLA General Hospital Beijing China
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44
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Zhao L, Luo JL, Ali MK, Spiekerkoetter E, Nicolls MR. The Human Respiratory Microbiome: Current Understandings and Future Directions. Am J Respir Cell Mol Biol 2023; 68:245-255. [PMID: 36476129 PMCID: PMC9989478 DOI: 10.1165/rcmb.2022-0208tr] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.
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Affiliation(s)
- Lan Zhao
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California.,VA Palo Alto Health Care System, Palo Alto, California; and
| | - Jun-Li Luo
- The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Mohammed Khadem Ali
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California
| | - Edda Spiekerkoetter
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California
| | - Mark R Nicolls
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California.,VA Palo Alto Health Care System, Palo Alto, California; and
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45
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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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Hernández-Terán A, Vega-Sánchez AE, Mejía-Nepomuceno F, Serna-Muñoz R, Rodríguez-Llamazares S, Salido-Guadarrama I, Romero-Espinoza JA, Guadarrama-Pérez C, Sandoval-Gutierrez JL, Campos F, Mondragón-Rivero EN, Ramírez-Venegas A, Castillejos-López M, Téllez-Navarrete NA, Pérez-Padilla R, Vázquez-Pérez JA. Microbiota composition in the lower respiratory tract is associated with severity in patients with acute respiratory distress by influenza. Virol J 2023; 20:19. [PMID: 36726151 PMCID: PMC9891757 DOI: 10.1186/s12985-023-01979-3] [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: 09/23/2022] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
Several factors are associated with the severity of the respiratory disease caused by the influenza virus. Although viral factors are one of the most studied, in recent years the role of the microbiota and co-infections in severe and fatal outcomes has been recognized. However, most of the work has focused on the microbiota of the upper respiratory tract (URT), hindering potential insights from the lower respiratory tract (LRT) that may help to understand the role of the microbiota in Influenza disease. In this work, we characterized the microbiota of the LRT of patients with Influenza A using 16S rRNA sequencing. We tested if patients with different outcomes (deceased/recovered) and use of antibiotics differ in their microbial community composition. We found important differences in the diversity and composition of the microbiota between deceased and recovered patients. In particular, we detected a high abundance of opportunistic pathogens such as Granulicatella, in patients either deceased or with antibiotic treatment. Also, we found antibiotic treatment correlated with lower diversity of microbial communities and with lower probability of survival in Influenza A patients. Altogether, the loss of microbial diversity could generate a disequilibrium in the community, potentially compromising the immune response increasing viral infectivity, promoting the growth of potentially pathogenic bacteria that, together with altered biochemical parameters, can be leading to severe forms of the disease. Overall, the present study gives one of the first characterizations of the diversity and composition of microbial communities in the LRT of Influenza patients and its relationship with clinical variables and disease severity.
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Affiliation(s)
- Alejandra Hernández-Terán
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Angel E. Vega-Sánchez
- grid.419179.30000 0000 8515 3604Servicio de Urgencias Médicas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Fidencio Mejía-Nepomuceno
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Ricardo Serna-Muñoz
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Sebastián Rodríguez-Llamazares
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Iván Salido-Guadarrama
- grid.419218.70000 0004 1773 5302Departamento de Bioinformática y Análisis Estadísticos, Instituto Nacional de Perinatología Isidro Espinosa De los Reyes, INPER, Ciudad de Mexico, Mexico
| | - Jose A. Romero-Espinoza
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Cristobal Guadarrama-Pérez
- grid.419179.30000 0000 8515 3604Servicio de Urgencias Médicas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Jose L. Sandoval-Gutierrez
- grid.419179.30000 0000 8515 3604Servicio Auxiliar de Diagnóstico y Paramédicos, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Fernando Campos
- grid.419179.30000 0000 8515 3604Unidad de Terapia Intensiva, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Erika N. Mondragón-Rivero
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Alejandra Ramírez-Venegas
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Manuel Castillejos-López
- grid.419179.30000 0000 8515 3604Departamento de Unidad de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Norma A. Téllez-Navarrete
- grid.419179.30000 0000 8515 3604Laboratorio de Inmunología Integrativa, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Rogelio Pérez-Padilla
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Joel A. Vázquez-Pérez
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
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The Lung Microbiome: A New Frontier for Lung and Brain Disease. Int J Mol Sci 2023; 24:ijms24032170. [PMID: 36768494 PMCID: PMC9916971 DOI: 10.3390/ijms24032170] [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: 12/03/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Due to the limitations of culture techniques, the lung in a healthy state is traditionally considered to be a sterile organ. With the development of non-culture-dependent techniques, the presence of low-biomass microbiomes in the lungs has been identified. The species of the lung microbiome are similar to those of the oral microbiome, suggesting that the microbiome is derived passively within the lungs from the oral cavity via micro-aspiration. Elimination, immigration, and relative growth within its communities all contribute to the composition of the lung microbiome. The lung microbiome is reportedly altered in many lung diseases that have not traditionally been considered infectious or microbial, and potential pathways of microbe-host crosstalk are emerging. Recent studies have shown that the lung microbiome also plays an important role in brain autoimmunity. There is a close relationship between the lungs and the brain, which can be called the lung-brain axis. However, the problem now is that it is not well understood how the lung microbiota plays a role in the disease-specifically, whether there is a causal connection between disease and the lung microbiome. The lung microbiome includes bacteria, archaea, fungi, protozoa, and viruses. However, fungi and viruses have not been fully studied compared to bacteria in the lungs. In this review, we mainly discuss the role of the lung microbiome in chronic lung diseases and, in particular, we summarize the recent progress of the lung microbiome in multiple sclerosis, as well as the lung-brain axis.
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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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49
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Di Simone SK, Rudloff I, Nold-Petry CA, Forster SC, Nold MF. Understanding respiratory microbiome-immune system interactions in health and disease. Sci Transl Med 2023; 15:eabq5126. [PMID: 36630485 DOI: 10.1126/scitranslmed.abq5126] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Interactions between the developing microbiome and maturing immune system in early life are critical for establishment of a homeostasis beneficial to both host and commensals. The lung harbors a diverse community of microbes associated with health and local or systemic disease. We discuss how early life colonization and community changes correlate with immune development and health and disease throughout infancy, childhood, and adult life. We highlight key advances in microbiology, immunology, and computational biology that allow investigation of the functional relevance of interactions between the respiratory microbiome and host immune system, which may unlock the potential for microbiome-based therapeutics.
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Affiliation(s)
- Sara K Di Simone
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia.,Centre for Innate Immunity and Infectious Disease, Hudson Institute of Medical Research, Melbourne 3168, Australia
| | - Ina Rudloff
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia
| | - Claudia A Nold-Petry
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Disease, Hudson Institute of Medical Research, Melbourne 3168, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne 3168, Australia
| | - Marcel F Nold
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne 3168, Australia
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50
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The association between the respiratory tract microbiome and clinical outcomes in patients with COPD. Microbiol Res 2023; 266:127244. [DOI: 10.1016/j.micres.2022.127244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
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