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Li NN, Kang K, Zhou Y, Liu YQ, Zhang QQ, Luo PY, Wang L, Man MY, Lv JF, Wang XB, Peng YH, Luan FY, Li Y, Zhang JN, Chong Y, Wang YQ, Wang CS, Zhao MY, Yu KJ. Throat microbiota drives alterations in pulmonary alveolar microbiota in patients with septic ARDS. Virulence 2024; 15:2350775. [PMID: 38736041 PMCID: PMC11093027 DOI: 10.1080/21505594.2024.2350775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/27/2024] [Indexed: 05/14/2024] Open
Abstract
OBJECTIVES The translocation of intestinal flora has been linked to the colonization of diverse and heavy lower respiratory flora in patients with septic ARDS, and is considered a critical prognostic factor for patients. METHODS On the first and third days of ICU admission, BALF, throat swab, and anal swab were collected, resulting in a total of 288 samples. These samples were analyzed using 16S rRNA analysis and the traceability analysis of new generation technology. RESULTS On the first day, among the top five microbiota species in abundance, four species were found to be identical in BALF and throat samples. Similarly, on the third day, three microbiota species were found to be identical in abundance in both BALF and throat samples. On the first day, 85.16% of microorganisms originated from the throat, 5.79% from the intestines, and 9.05% were unknown. On the third day, 83.52% of microorganisms came from the throat, 4.67% from the intestines, and 11.81% were unknown. Additionally, when regrouping the 46 patients, the results revealed a significant predominance of throat microorganisms in BALF on both the first and third day. Furthermore, as the disease progressed, the proportion of intestinal flora in BALF increased in patients with enterogenic ARDS. CONCLUSIONS In patients with septic ARDS, the main source of lung microbiota is primarily from the throat. Furthermore, the dynamic trend of the microbiota on the first and third day is essentially consistent.It is important to note that the origin of the intestinal flora does not exclude the possibility of its origin from the throat.
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Affiliation(s)
- Na-Na Li
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Kai Kang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yang Zhou
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yan-Qi Liu
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qian-Qian Zhang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Pei-Yao Luo
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lei Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ming-Yin Man
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
- Departments of Critical Care Medicine, Zhongshan Hospital of Xiamen University, Xiamen, Fujian, China
| | - Jia-Feng Lv
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xi-Bo Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ya-Hui Peng
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Fei-Yu Luan
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yue Li
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
- Departments of Critical Care Medicine, the Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jian-Nan Zhang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yang Chong
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yi-Qi Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chang-song Wang
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ming-yan Zhao
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Kai-jiang Yu
- Departments of Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
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Motta H, Reuwsaat JCV, Lopes FC, Viezzer G, Volpato FCZ, Barth AL, de Tarso Roth Dalcin P, Staats CC, Vainstein MH, Kmetzsch L. Comparative microbiome analysis in cystic fibrosis and non-cystic fibrosis bronchiectasis. Respir Res 2024; 25:211. [PMID: 38762736 PMCID: PMC11102160 DOI: 10.1186/s12931-024-02835-w] [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: 01/04/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Bronchiectasis is a condition characterized by abnormal and irreversible bronchial dilation resulting from lung tissue damage and can be categorized into two main groups: cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Both diseases are marked by recurrent infections, inflammatory exacerbations, and lung damage. Given that infections are the primary drivers of disease progression, characterization of the respiratory microbiome can shed light on compositional alterations and susceptibility to antimicrobial drugs in these cases compared to healthy individuals. METHODS To assess the microbiota in the two studied diseases, 35 subjects were recruited, comprising 10 NCFB and 13 CF patients and 12 healthy individuals. Nasopharyngeal swabs and induced sputum were collected, and total DNA was extracted. The DNA was then sequenced by the shotgun method and evaluated using the SqueezeMeta pipeline and R. RESULTS We observed reduced species diversity in both disease cohorts, along with distinct microbial compositions and profiles of antimicrobial resistance genes, compared to healthy individuals. The nasopharynx exhibited a consistent microbiota composition across all cohorts. Enrichment of members of the Burkholderiaceae family and an increased Firmicutes/Bacteroidetes ratio in the CF cohort emerged as key distinguishing factors compared to NCFB group. Staphylococcus aureus and Prevotella shahii also presented differential abundance in the CF and NCFB cohorts, respectively, in the lower respiratory tract. Considering antimicrobial resistance, a high number of genes related to antibiotic efflux were detected in both disease groups, which correlated with the patient's clinical data. CONCLUSIONS Bronchiectasis is associated with reduced microbial diversity and a shift in microbial and resistome composition compared to healthy subjects. Despite some similarities, CF and NCFB present significant differences in microbiome composition and antimicrobial resistance profiles, suggesting the need for customized management strategies for each disease.
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Affiliation(s)
- Heryk Motta
- Laboratório de Biologia Molecular de Patógenos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Júlia Catarina Vieira Reuwsaat
- Laboratório de Biologia Molecular de Patógenos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Cortez Lopes
- Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Graciele Viezzer
- Serviço de Pneumologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Fabiana Caroline Zempulski Volpato
- Laboratório de Pesquisa em Resistência Bacteriana, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Afonso Luís Barth
- Laboratório de Pesquisa em Resistência Bacteriana, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Paulo de Tarso Roth Dalcin
- Serviço de Pneumologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Medicina Interna, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Charley Christian Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marilene Henning Vainstein
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Microrganismos de Importância Médica e Biotecnológica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lívia Kmetzsch
- Laboratório de Biologia Molecular de Patógenos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Enríquez-Rodríguez CJ, Pascual-Guardia S, Casadevall C, Caguana-Vélez OA, Rodríguez-Chiaradia D, Barreiro E, Gea J. Proteomic Blood Profiles Obtained by Totally Blind Biological Clustering in Stable and Exacerbated COPD Patients. Cells 2024; 13:866. [PMID: 38786086 PMCID: PMC11119172 DOI: 10.3390/cells13100866] [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: 03/25/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Although Chronic Obstructive Pulmonary Disease (COPD) is highly prevalent, it is often underdiagnosed. One of the main characteristics of this heterogeneous disease is the presence of periods of acute clinical impairment (exacerbations). Obtaining blood biomarkers for either COPD as a chronic entity or its exacerbations (AECOPD) will be particularly useful for the clinical management of patients. However, most of the earlier studies have been characterized by potential biases derived from pre-existing hypotheses in one or more of their analysis steps: some studies have only targeted molecules already suggested by pre-existing knowledge, and others had initially carried out a blind search but later compared the detected biomarkers among well-predefined clinical groups. We hypothesized that a clinically blind cluster analysis on the results of a non-hypothesis-driven wide proteomic search would determine an unbiased grouping of patients, potentially reflecting their endotypes and/or clinical characteristics. To check this hypothesis, we included the plasma samples from 24 clinically stable COPD patients, 10 additional patients with AECOPD, and 10 healthy controls. The samples were analyzed through label-free liquid chromatography/tandem mass spectrometry. Subsequently, the Scikit-learn machine learning module and K-means were used for clustering the individuals based solely on their proteomic profiles. The obtained clusters were confronted with clinical groups only at the end of the entire procedure. Although our clusters were unable to differentiate stable COPD patients from healthy individuals, they segregated those patients with AECOPD from the patients in stable conditions (sensitivity 80%, specificity 79%, and global accuracy, 79.4%). Moreover, the proteins involved in the blind grouping process to identify AECOPD were associated with five biological processes: inflammation, humoral immune response, blood coagulation, modulation of lipid metabolism, and complement system pathways. Even though the present results merit an external validation, our results suggest that the present blinded approach may be useful to segregate AECOPD from stability in both the clinical setting and trials, favoring more personalized medicine and clinical research.
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Affiliation(s)
- Cesar Jessé Enríquez-Rodríguez
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
| | - Sergi Pascual-Guardia
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
| | - Carme Casadevall
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
| | - Oswaldo Antonio Caguana-Vélez
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
| | - Diego Rodríguez-Chiaradia
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
| | - Esther Barreiro
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
| | - Joaquim Gea
- Respiratory Medicine Department, Hospital del Mar—IMIM, 08003 Barcelona, Spain; (C.J.E.-R.); (S.P.-G.); (C.C.); (O.A.C.-V.); (D.R.-C.); (E.B.)
- MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- CIBERES, ISCiii, 08003 Barcelona, Spain
- BRN, 08003 Barcelona, Spain
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Chotirmall SH, Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology and treatment outcomes. AREAS COVERED We detail the dynamics of the airway microbiome, its influence in chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline searches between Jan 2010 and March 2024 were retrieved and summarized. The review examines clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, anti-inflammatories and antimicrobial strategies are discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management. EXPERT OPINION Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogen-centric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving cross-disciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials and therapeutic development pipelines.
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Affiliation(s)
- Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Micheál Mac Aogáin
- Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Shivani Singh
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY
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Pragman AA, Hodgson SW, Wu T, Zank A, Kelly RF, Reilly CS, Wendt CH. Tobacco use, self-reported professional dental cleaning habits, and lung adenocarcinoma diagnosis are associated with bronchial and lung microbiome alpha diversity. Respir Res 2024; 25:130. [PMID: 38500160 PMCID: PMC10949571 DOI: 10.1186/s12931-024-02750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/25/2024] [Indexed: 03/20/2024] Open
Abstract
RATIONALE The lung microbiome is an inflammatory stimulus whose role in the development of lung malignancies is incompletely understood. We hypothesized that the lung microbiome associates with multiple clinical factors, including the presence of a lung malignancy. OBJECTIVES To assess associations between the upper and lower airway microbiome and multiple clinical factors including lung malignancy. METHODS We conducted a prospective cohort study of upper and lower airway microbiome samples from 44 subjects undergoing lung lobectomy for suspected or confirmed lung cancer. Subjects provided oral (2), induced sputum, nasopharyngeal, bronchial, and lung tissue (3) samples. Pathologic diagnosis, age, tobacco use, dental care history, lung function, and inhaled corticosteroid use were associated with upper and lower airway microbiome findings. MEASUREMENTS AND MAIN RESULTS Older age was associated with greater Simpson diversity in the oral and nasopharyngeal sites (p = 0.022 and p = 0.019, respectively). Current tobacco use was associated with greater lung and bronchus Simpson diversity (p < 0.0001). Self-reported last profession dental cleaning more than 6 months prior (vs. 6 or fewer months prior) was associated with lower lung and bronchus Simpson diversity (p < 0.0001). Diagnosis of a lung adenocarcinoma (vs. other pathologic findings) was associated with lower bronchus and lung Simpson diversity (p = 0.024). Last professional dental cleaning, dichotomized as ≤ 6 months vs. >6 months prior, was associated with clustering among lung samples (p = 0.027, R2 = 0.016). Current tobacco use was associated with greater abundance of pulmonary pathogens Mycoplasmoides and Haemophilus in lower airway samples. Self-reported professional dental cleaning ≤ 6 months prior (vs. >6 months prior) was associated with greater bronchial Actinomyces and lung Streptococcus abundance. Lung adenocarcinoma (vs. no lung adenocarcinoma) was associated with lower Lawsonella abundance in lung samples. Inhaled corticosteroid use was associated with greater abundance of Haemophilus among oral samples and greater Staphylococcus among lung samples. CONCLUSIONS Current tobacco use, recent dental cleaning, and a diagnosis of adenocarcinoma are associated with lung and bronchial microbiome α-diversity, composition (β-diversity), and the abundance of several respiratory pathogens. These findings suggest that modifiable habits (tobacco use and dental care) may influence the lower airway microbiome. Larger controlled studies to investigate these potential associations are warranted.
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Affiliation(s)
- Alexa A Pragman
- Department of Medicine, Minneapolis VA Health Care System and University of Minnesota, 111F, 1 Veterans Dr, Minneapolis, MN, 55417, USA.
| | - Shane W Hodgson
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Tianhua Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Allison Zank
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Rosemary F Kelly
- Department of Surgery, Minneapolis VA Health Care System and University of Minnesota, Minneapolis, MN, USA
| | - Cavan S Reilly
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Chris H Wendt
- Department of Medicine, Minneapolis VA Health Care System and University of Minnesota, 111F, 1 Veterans Dr, Minneapolis, MN, 55417, USA
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Perotin JM, Muggeo A, Lecomte-Thenot Q, Brisebarre A, Dury S, Launois C, Ancel J, Dormoy V, Guillard T, Deslee G. High Blood Eosinophil Count at Stable State is Not Associated with Airway Microbiota Distinct Profile in COPD. Int J Chron Obstruct Pulmon Dis 2024; 19:765-771. [PMID: 38524398 PMCID: PMC10959750 DOI: 10.2147/copd.s453526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Purpose The heterogeneity of clinical features in COPD at stable state has been associated with airway microbiota. Blood eosinophil count (BEC) represents a biomarker for a pejorative evolution of COPD, including exacerbations and accelerated FEV1 decline. We aimed to analyse the associations between BEC and airway microbiota in COPD at stable state. Patients and Methods Adult COPD patients at stable state (RINNOPARI cohort) were included and characterised for clinical, functional, biological and morphological features. BEC at inclusion defined 2 groups of patients with low BEC <300/mm3 and high BEC ≥300/mm3. Sputa were collected and an extended microbiological culture was performed for the identification of viable airway microbiota. Results Fifty-nine subjects were included. When compared with the low BEC (n=40, 67.8%), the high BEC group (n=19, 32.2%) had more frequent exacerbations (p<0.001) and more pronounced cough and sputum (p<0.05). The global composition, the number of bacteria per sample and the α-diversity of the microbiota did not differ between groups, as well as the predominant phyla (Firmicutes), or the gender repartition. Conclusion In our study, high BEC in COPD at stable state was associated with a clinical phenotype including frequent exacerbation, but no distinct profile of viable airway microbiota compared with low BEC.
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Affiliation(s)
- Jeanne-Marie Perotin
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Anaëlle Muggeo
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, Reims, France
| | - Quentin Lecomte-Thenot
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, Reims, France
| | - Audrey Brisebarre
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
| | - Sandra Dury
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Claire Launois
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Julien Ancel
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Valérian Dormoy
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
| | - Thomas Guillard
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, Reims, France
| | - Gaëtan Deslee
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
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Pragman AA, Hodgson SW, Wu T, Zank A, Reilly CS, Wendt CH. Sputum microbiome α-diversity is a key feature of the COPD frequent exacerbator phenotype. ERJ Open Res 2024; 10:00595-2023. [PMID: 38333651 PMCID: PMC10851948 DOI: 10.1183/23120541.00595-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 02/10/2024] Open
Abstract
Background The lung microbiome is an inflammatory stimulus whose role in COPD pathogenesis is incompletely understood. We hypothesised that the frequent exacerbator phenotype is associated with decreased α-diversity and increased lung inflammation. Our objective was to assess correlations between the frequent exacerbator phenotype, the microbiome and inflammation longitudinally during exacerbation-free periods. Methods We conducted a case-control longitudinal observational study of the frequent exacerbator phenotype and characteristics of the airway microbiome. 81 subjects (41 frequent and 40 infrequent exacerbators) provided nasal, oral and sputum microbiome samples at two visits over 2-4 months. Exacerbation phenotype, relevant clinical factors and sputum cytokine values were associated with microbiome findings. Results The frequent exacerbator phenotype was associated with lower sputum microbiome α-diversity (p=0.0031). This decrease in α-diversity among frequent exacerbators was enhanced when the sputum bacterial culture was positive (p<0.001). Older age was associated with decreased sputum microbiome α-diversity (p=0.0030). Between-visit β-diversity was increased among frequent exacerbators and those who experienced a COPD exacerbation between visits (p=0.025 and p=0.014, respectively). Sputum cytokine values did not differ based on exacerbation phenotype or other clinical characteristics. Interleukin (IL)-17A was negatively associated with α-diversity, while IL-6 and IL-8 were positively associated with α-diversity (p=0.012, p=0.012 and p=0.0496, respectively). IL-22, IL-17A and IL-5 levels were positively associated with Moraxella abundance (p=0.027, p=0.0014 and p=0.0020, respectively). Conclusions Even during exacerbation-free intervals, the COPD frequent exacerbator phenotype is associated with decreased sputum microbiome α-diversity and increased β-diversity. Decreased sputum microbiome α-diversity and Moraxella abundance are associated with lung inflammation.
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Affiliation(s)
- Alexa A. Pragman
- Department of Medicine, Minneapolis VA Health Care System and Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Shane W. Hodgson
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Tianhua Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Allison Zank
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Cavan S. Reilly
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Chris H. Wendt
- Department of Medicine, Minneapolis VA Health Care System and Department of Medicine, University of Minnesota, Minneapolis, MN, USA
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Gea J, Enríquez-Rodríguez CJ, Agranovich B, Pascual-Guardia S. Update on metabolomic findings in COPD patients. ERJ Open Res 2023; 9:00180-2023. [PMID: 37908399 PMCID: PMC10613990 DOI: 10.1183/23120541.00180-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/15/2023] [Indexed: 11/02/2023] Open
Abstract
COPD is a heterogeneous disorder that shows diverse clinical presentations (phenotypes and "treatable traits") and biological mechanisms (endotypes). This heterogeneity implies that to carry out a more personalised clinical management, it is necessary to classify each patient accurately. With this objective, and in addition to clinical features, it would be very useful to have well-defined biological markers. The search for these markers may either be done through more conventional laboratory and hypothesis-driven techniques or relatively blind high-throughput methods, with the omics approaches being suitable for the latter. Metabolomics is the science that studies biological processes through their metabolites, using various techniques such as gas and liquid chromatography, mass spectrometry and nuclear magnetic resonance. The most relevant metabolomics studies carried out in COPD highlight the importance of metabolites involved in pathways directly related to proteins (peptides and amino acids), nucleic acids (nitrogenous bases and nucleosides), and lipids and their derivatives (especially fatty acids, phospholipids, ceramides and eicosanoids). These findings indicate the relevance of inflammatory-immune processes, oxidative stress, increased catabolism and alterations in the energy production. However, some specific findings have also been reported for different COPD phenotypes, demographic characteristics of the patients, disease progression profiles, exacerbations, systemic manifestations and even diverse treatments. Unfortunately, the studies carried out to date have some limitations and shortcomings and there is still a need to define clear metabolomic profiles with clinical utility for the management of COPD and its implicit heterogeneity.
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Affiliation(s)
- Joaquim Gea
- Respiratory Medicine Department, Hospital del Mar – IMIM, Barcelona, Spain
- MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
- CIBERES, ISCIII, Barcelona, Spain
| | - César J. Enríquez-Rodríguez
- Respiratory Medicine Department, Hospital del Mar – IMIM, Barcelona, Spain
- MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Bella Agranovich
- Rappaport Institute for Research in the Medical Sciences, Technion University, Haifa, Israel
| | - Sergi Pascual-Guardia
- Respiratory Medicine Department, Hospital del Mar – IMIM, Barcelona, Spain
- MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
- CIBERES, ISCIII, Barcelona, Spain
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9
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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: 0] [Impact Index Per Article: 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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10
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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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11
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Gea J, Enríquez-Rodríguez CJ, Pascual-Guardia S. Metabolomics in COPD. Arch Bronconeumol 2023; 59:311-321. [PMID: 36717301 DOI: 10.1016/j.arbres.2022.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 01/20/2023]
Abstract
The clinical presentation of chronic obstructive pulmonary disease (COPD) is highly heterogeneous. Attempts have been made to define subpopulations of patients who share clinical characteristics (phenotypes and treatable traits) and/or biological characteristics (endotypes), in order to offer more personalized care. Assigning a patient to any of these groups requires the identification of both clinical and biological markers. Ideally, biological markers should be easily obtained from blood or urine, but these may lack specificity. Biomarkers can be identified initially using conventional or more sophisticated techniques. However, the more sophisticated techniques should be simplified in the future if they are to have clinical utility. The -omics approach offers a methodology that can assist in the investigation and identification of useful markers in both targeted and blind searches. Specifically, metabolomics is the science that studies biological processes involving metabolites, which can be intermediate or final products. The metabolites associated with COPD and their specific phenotypic and endotypic features have been studied using various techniques. Several compounds of particular interest have emerged, namely, several types of lipids and derivatives (mainly phospholipids, but also ceramides, fatty acids and eicosanoids), amino acids, coagulation factors, and nucleic acid components, likely to be involved in their function, protein catabolism, energy production, oxidative stress, immune-inflammatory response and coagulation disorders. However, clear metabolomic profiles of the disease and its various manifestations that may already be applicable in clinical practice still need to be defined.
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Affiliation(s)
- Joaquim Gea
- Servicio de Neumología, Hospital del Mar - IMIM, Barcelona, Spain; Dpt. MELIS, Universitat Pompeu Fabra, Barcelona, Spain; CIBERES, ISCIII, Barcelona, Spain.
| | - César J Enríquez-Rodríguez
- Servicio de Neumología, Hospital del Mar - IMIM, Barcelona, Spain; Dpt. MELIS, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergi Pascual-Guardia
- Servicio de Neumología, Hospital del Mar - IMIM, Barcelona, Spain; Dpt. MELIS, Universitat Pompeu Fabra, Barcelona, Spain; CIBERES, ISCIII, Barcelona, Spain
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12
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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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13
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Millares L, Monso E. The Microbiome in COPD: Emerging Potential for Microbiome-Targeted Interventions. Int J Chron Obstruct Pulmon Dis 2022; 17:1835-1845. [PMID: 35983167 PMCID: PMC9380728 DOI: 10.2147/copd.s371958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
The aim of interventions over the respiratory microbiome in COPD is to preserve the original microbial flora, focusing in taxa with a demonstrated impact on the prognosis of the disease. Inhaled therapy is the main treatment for COPD, and chronic corticosteroid use is recommended for patients with frequent exacerbations. This therapy, however, increases both the bronchial microbial load and the abundance of potentially pathogenic bacteria in patients with low peripheral eosinophil counts, and to minimize its use in patients without peripheral eosinophilia, when possible, may avoid increases in bacterial loads of microorganisms as Haemophilus influenzae and Streptococcus pneumoniae. In exacerbations antibiotics determine a decrease in the microbial diversity, a change that persists during stability periods in frequent exacerbators. High-diversity bronchial microbiomes are enriched in non-dominant genera and determine low exacerbation frequencies and survival improvement. Limiting the antibiotic use to the treatment of exacerbations which would clearly benefit would favor the diversity of the respiratory microbiome and may have a positive impact on quality of life and survival. Oral antiseptics have shown and effect on the bronchial microbiome that was associated with improvements in quality of life, and the gut microbiome may be also modified through the oral administration of probiotics or prebiotics, that potentially may determine decreases in lung inflammation and bronchial hyperreactivity. High fiber diets also favor the production of anti-inflammatory molecules by the digestive flora, which would reach the respiratory system through the bloodstream. Interventional approaches favoring the preservation of the respiratory microbiome in COPD need first to select accurately the patients who would benefit from long-term inhaled corticosteroids and antibiotic treatments during exacerbations, under the hypothesis that keeping a respiratory microbiome close to the healthy subject would favor the respiratory health. Additionally, high fiber diets may be able to modify the gut microbiome and influence the respiratory system through the gut-lung axis. Therapeutic approaches targeting the microbiome to improve COPD, however, still require clinical validation and the identification of patient subtypes who would benefit the most with their use.
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Affiliation(s)
- Laura Millares
- Airway Inflammation Research Group, Parc Taulí Research and Innovation Institute - I3PT - Parc Taulí Foundation, Sabadell, Barcelona, Spain.,Catalan Institute of Oncology - ICO, Badalona, Barcelona, Spain
| | - Eduard Monso
- Airway Inflammation Research Group, Parc Taulí Research and Innovation Institute - I3PT - Parc Taulí Foundation, Sabadell, Barcelona, Spain.,Catalan Institute of Oncology - ICO, Badalona, Barcelona, Spain.,Biomedical Research Network on Respiratory Diseases (CIBERES), Carlos III Health Institute (ISCIII), Madrid, Spain.,Autonomous University of Barcelona - UAB, Cerdanyola del Vallès, Barcelona, Spain
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14
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Gorgone M, Singhvi D, Nouraie SM, Finkelman M, Zhang Y, Pu J, Chandra D, Zhang Y, Kitsios GD, Morris A, Sciurba FC, Bon J. Circulating 1,3-Beta-D-Glucan is Associated with Lung Function, Respiratory Symptoms, and Mediators of Matrix Degradation in Chronic Obstructive Pulmonary Disease. CHRONIC OBSTRUCTIVE PULMONARY DISEASES (MIAMI, FLA.) 2022; 9:325-335. [PMID: 35550241 PMCID: PMC9448008 DOI: 10.15326/jcopdf.2022.0290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Introduction Factors beyond cigarette smoke likely contribute to chronic obstructive pulmonary disease (COPD) pathogenesis. Prior studies demonstrate fungal colonization of the respiratory tract and increased epithelial barrier permeability in COPD. We sought to determine whether 1,3-beta-d-glucan (BDG), a polysaccharide component of the fungal cell wall, is detectable in the plasma of individuals with COPD and associates with clinical outcomes and matrix degradation proteins. Methods BDG was measured in the plasma of current and former smokers with COPD. High BDG was defined as a value greater than the 95th percentile of BDG in smokers without airflow obstruction. Pulmonary function, emphysema, and symptoms were compared between COPD participants with high versus low BDG. The relationship between plasma BDG, matrix metalloproteinases (MMP) 1, 7, and 9, and tissue inhibitor of matrix metalloproteinases (TIMP) 1, 2, and 4 was assessed adjusting for age, sex, and smoking status. Results COPD participants with high BDG plasma levels (19.8%) had lower forced expiratory volume in 1 second to forced vital capacity ratios (median 31.9 versus 39.3, p=0.025), higher St George's Respiratory Questionnaire symptom scores (median 63.6 versus 57.4, p=0.016), and greater prevalence of sputum production (69.4% versus 52.0%) and exacerbations (69.4% versus 48%) compared to COPD participants with low BDG. BDG levels directly correlated with MMP1 (r=0.27, p<0.001) and TIMP1 (r=0.16, p=0.022) in unadjusted and adjusted analyses. Conclusions Elevated plasma BDG levels correlate with worse lung function, greater respiratory morbidity, and circulating markers of matrix degradation in COPD. These findings suggest that targeting dysbiosis or enhancing epithelial barrier integrity may have disease-modifying effects in COPD.
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Affiliation(s)
- Matthew Gorgone
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- *Authors contributed equally
| | - Deepti Singhvi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- *Authors contributed equally
| | - Seyed Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Malcolm Finkelman
- Associates of Cape Cod Incorporated, East Falmouth, Massachusetts, United States
| | - Yonglong Zhang
- Associates of Cape Cod Incorporated, East Falmouth, Massachusetts, United States
| | - Jiantao Pu
- Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Divay Chandra
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Frank C. Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Jessica Bon
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States
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15
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Russo C, Colaianni V, Ielo G, Valle MS, Spicuzza L, Malaguarnera L. Impact of Lung Microbiota on COPD. Biomedicines 2022; 10:biomedicines10061337. [PMID: 35740358 PMCID: PMC9219765 DOI: 10.3390/biomedicines10061337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
There is a fine balance in maintaining healthy microbiota composition, and its alterations due to genetic, lifestyle, and environmental factors can lead to the onset of respiratory dysfunctions such as chronic obstructive pulmonary disease (COPD). The relationship between lung microbiota and COPD is currently under study. Little is known about the role of the microbiota in patients with stable or exacerbated COPD. Inflammation in COPD disorders appears to be characterised by dysbiosis, reduced lung activity, and an imbalance between the innate and adaptive immune systems. Lung microbiota intervention could ameliorate these disorders. The microbiota’s anti-inflammatory action could be decisive in the onset of pathologies. In this review, we highlight the feedback loop between microbiota dysfunction, immune response, inflammation, and lung damage in relation to COPD status in order to encourage the development of innovative therapeutic goals for the prevention and management of this disease.
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Affiliation(s)
- Cristina Russo
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
| | - Valeria Colaianni
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
| | - Giuseppe Ielo
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (G.I.); (L.S.)
| | - Maria Stella Valle
- Laboratory of Neuro-Biomechanics, Section of Physiology, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, 95123 Catania, Italy
- Correspondence: (M.S.V.); (L.M.)
| | - Lucia Spicuzza
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (G.I.); (L.S.)
| | - Lucia Malaguarnera
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
- Correspondence: (M.S.V.); (L.M.)
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16
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Mancabelli L, Milani C, Fontana F, Lugli GA, Tarracchini C, Turroni F, van Sinderen D, Ventura M. Mapping bacterial diversity and metabolic functionality of the human respiratory tract microbiome. J Oral Microbiol 2022; 14:2051336. [PMID: 35309410 PMCID: PMC8933033 DOI: 10.1080/20002297.2022.2051336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background The Human Respiratory Tract (HRT) is colonized by various microbial taxa, known as HRT microbiota, in a manner that is indicative of mutualistic interaction between such microorganisms and their host. Aim To investigate the microbial composition of the HRT and its possible correlation with the different compartments of the respiratory tract. Methods In the current study, we performed an in-depth meta‐analysis of 849 HRT samples from public shotgun metagenomic datasets obtained through several distinct collection methods. Results The statistical robustness provided by this meta-analysis allowed the identification of 13 possible HRT-specific Community State Types (CSTs), which appear to be specific to each anatomical region of the respiratory tract. Furthermore, functional characterization of the metagenomic datasets revealed specific microbial metabolic features correlating with the different compartments of the respiratory tract. Conclusion The meta-analysis here performed suggested that the variable presence of certain bacterial species seems to be linked to a location-related abundance gradient in the HRT and seems to be characterized by a specific microbial metabolic capability.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
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17
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Tiew PY, Mac Aogáin M, Chotirmall SH. The current understanding and future directions for sputum microbiome profiling in chronic obstructive pulmonary disease. Curr Opin Pulm Med 2022; 28:121-133. [PMID: 34839338 DOI: 10.1097/mcp.0000000000000850] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Next-generation sequencing (NGS) has deepened our understanding of the respiratory microbiome in health and disease. The number of microbiome studies employing sputum as an airway surrogate has continued to increase over the past decade to include multiple large multicentre and longitudinal studies of the microbiome in chronic obstructive pulmonary disease (COPD). In this review, we summarize the recent advances to our understanding of the bacteriome, virome and mycobiome in COPD. RECENT FINDINGS Diverse microbiome profiles are reported in COPD. The neutrophilic Haemophilus-predominant bacteriome remains a prominent COPD phenotype, relatively stable over time and during exacerbations. Studies of the virome remain limited but reveal a potential involvement of viruses and bacteriophages particularly during COPD exacerbations and advancing disease severity. Mycobiome signatures, even in stable COPD are associated with poorer clinical outcomes including mortality. SUMMARY The sputum microbiome in COPD is being increasingly recognized for its clinical relevance, even in the stable state. Future studies integrating microbial kingdoms holistically (i.e. bacterial, viral and fungal) will provide deeper insight into its functionality including the relevance of microbial interactions and effect of treatment on microbiome-associated clinical outcomes.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Ireland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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18
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Martinez-Garcia MA, Miravitlles M. The Impact of Chronic Bronchial Infection in COPD: A Proposal for Management. Int J Chron Obstruct Pulmon Dis 2022; 17:621-630. [PMID: 35355582 PMCID: PMC8958724 DOI: 10.2147/copd.s357491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022] Open
Abstract
Up to 50% of patients with chronic obstructive pulmonary disease (COPD) in stable state may carry potentially pathogenic microorganisms (PPMs) in their airways. The presence of PPMs has been associated with increased symptoms, increased risk and severity of exacerbations, a faster decline in lung function and impairment in quality of life. Although some clinical trials have demonstrated a reduction in exacerbations in patients chronically treated with systemic antibiotics, particularly macrolides, the selection of patients was based on the previous frequency of exacerbations and not on the presence of PPMs in their airways. Therefore, unlike in bronchiectasis, there is a lack of evidence-based recommendations for assessment and treatment of the presence of PPMs in either single or repeated isolations in COPD. In this article, we propose that chronic bronchial infection (CBI) in COPD be defined as the isolation of the same PPM in at least three sputum samples separated by more than one month; we review the impact of CBI on the natural course of COPD and suggest a course of action in patients with a single isolation of a PPM or suspected CBI. Antibiotic treatment in stable COPD should be recommended based on four main criteria: a) the presence of comorbid bronchiectasis, b) the demonstration of a single or multiple isolation of the same PPM, c) the clinical impact of CBI on the patients, and d) the type of PPM, either Pseudomonas aeruginosa or non-pseudomonal PPM. These recommendations are derived from evidence generated in patients with bronchiectasis and, until new evidence specifically obtained in COPD is available, they may help in the management of these challenging patients with COPD. Existing evidence suggests that inhaled therapy is insufficient to manage patients with moderate-to-severe COPD, frequent exacerbations, and CBI. New studies must be conducted in this particularly demanding population.
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Affiliation(s)
- Miguel Angel Martinez-Garcia
- Pneumology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Marc Miravitlles
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Pneumology Department, Hospital Universitari Vall d´Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Correspondence: Marc Miravitlles, Pneumology Department, Vall d’Hebron Barcelona Hospital Campus, P. Vall d’Hebron 119-129, Barcelona, 08035, Spain, Tel +34932746083, Email
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19
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Zhao Y, Chen J, Hao Y, Wang B, Wang Y, Liu Q, Zhao J, Li Y, Wang P, Wang X, Zhang P, Zhang L. Predicting the recurrence of chronic rhinosinusitis with nasal polyps using nasal microbiota. Allergy 2022; 77:540-549. [PMID: 34735742 DOI: 10.1111/all.15168] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/11/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Recent studies have revealed that the nasal microbiota in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) is profoundly altered and is correlated with systemic inflammation. However, little is known regarding whether the microbiota can be utilized to predict nasal polyp recurrence. This study is aimed to determine whether altered nasal microbiota constituents could be used as biomarkers to predict CRSwNP recurrence. METHODS Nasal microbiota constituents were quantified and characterized using bacterial 16S ribosomal RNA gene sequencing. Selected features for least absolute shrinkage and selection operator regression-based predictors were the nasal microbiota community composition and CRSwNP patient clinical characteristics. The primary outcome was recurrence, which was determined post-admission. RESULTS By distinguishing recurrence-associated nasal microbiota taxa and exploiting the distinct nasal microbiota abundance between patients with recurrent and non-recurrent CRSwNP, we developed a predictive classifier for the diagnosis of nasal polyps' recurrence with 91.4% accuracy. CONCLUSIONS Key taxonomical features of the nasal microbiome could predict recurrence in CRSwNP patients. The nasal microbiome is an understudied source of clinical variation in CRSwNP and represents a novel therapeutic target for future prevention and treatment.
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Affiliation(s)
- Yan Zhao
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
- Beijing Key Laboratory of Nasal Diseases and Beijing Laboratory of Allergic Diseases Beijing Institute of Otolaryngology Beijing China
| | - Junru Chen
- Reproductive and Genetic Hospital of CITIC‐Xiangya Changsha China
| | - Yun Hao
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
| | - Boqian Wang
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
| | - Yue Wang
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
| | - Qinghua Liu
- Department of Otorhinolaryngology Head and Neck Surgery Fujian Provincial Hospital Fuzhou China
| | - Jinming Zhao
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
| | - Ying Li
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
- Beijing Key Laboratory of Nasal Diseases and Beijing Laboratory of Allergic Diseases Beijing Institute of Otolaryngology Beijing China
| | - Ping Wang
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
- Beijing Key Laboratory of Nasal Diseases and Beijing Laboratory of Allergic Diseases Beijing Institute of Otolaryngology Beijing China
| | - Xiangdong Wang
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
- Beijing Key Laboratory of Nasal Diseases and Beijing Laboratory of Allergic Diseases Beijing Institute of Otolaryngology Beijing China
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health Beijing China
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery Beijing Tongren HospitalCapital Medical University Beijing China
- Beijing Key Laboratory of Nasal Diseases and Beijing Laboratory of Allergic Diseases Beijing Institute of Otolaryngology Beijing China
- Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
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20
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Ng J, Pacheco-Rodriguez G, Begley L, Huang YJ, Poli S, Perrella MA, Rosas IO, Moss J, El-Chemaly S. The lung microbiome in end-stage Lymphangioleiomyomatosis. Respir Res 2021; 22:277. [PMID: 34702264 PMCID: PMC8549264 DOI: 10.1186/s12931-021-01873-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Lymphangioleiomyomatosis (LAM) is a progressive cystic lung disease with mortality driven primarily by respiratory failure. Patients with LAM frequently have respiratory infections, suggestive of a dysregulated microbiome. Here we demonstrate that end-stage LAM patients have a distinct microbiome signature compared to patients with end-stage chronic obstructive pulmonary disease.
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Affiliation(s)
- Julie Ng
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Gustavo Pacheco-Rodriguez
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lesa Begley
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yvonne J Huang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sergio Poli
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
- Department of Internal Medicine, Mount Sinai Medical Center, Miami, FL, USA
| | - Mark A Perrella
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Ivan O Rosas
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souheil El-Chemaly
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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21
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Abstract
The healthy lung was long thought of as sterile, but recent advances using molecular sequencing approaches have detected bacteria at low levels. Healthy lung bacteria largely reflect communities present in the upper respiratory tract that enter the lung via microaspiration, which is balanced by mechanical and immune clearance and likely involves limited local replication. The nature and dynamics of the lung microbiome, therefore, differ from those of ecological niches with robust self-sustaining microbial communities. Aberrant populations (dysbiosis) have been demonstrated in many pulmonary diseases not traditionally considered microbial in origin, and potential pathways of microbe-host crosstalk are emerging. The question now is whether and how dysbiotic microbiota contribute to initiation or perpetuation of injury. The fungal microbiome and virome are less well studied. This Review highlights features of the lung microbiome, unique considerations in studying it, examples of dysbiosis in selected disease, emerging concepts in lung microbiome-host interactions, and critical areas for investigation.
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22
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Wang Z, Locantore N, Haldar K, Ramsheh MY, Beech AS, Ma W, Brown JR, Tal-Singer R, Barer MR, Bafadhel M, Donaldson GC, Wedzicha JA, Singh D, Wilkinson TMA, Miller BE, Brightling CE. Inflammatory Endotype-associated Airway Microbiome in Chronic Obstructive Pulmonary Disease Clinical Stability and Exacerbations: A Multicohort Longitudinal Analysis. Am J Respir Crit Care Med 2021; 203:1488-1502. [PMID: 33332995 PMCID: PMC8483235 DOI: 10.1164/rccm.202009-3448oc] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Rationale: Understanding the role of the airway microbiome in chronic obstructive pulmonary disease (COPD) inflammatory endotypes may help to develop microbiome-based diagnostic and therapeutic approaches. Objectives: To understand the association of the airway microbiome with neutrophilic and eosinophilic COPD at stability and during exacerbations. Methods: An integrative analysis was performed on 1,706 sputum samples collected longitudinally from 510 patients with COPD recruited at four UK sites of the BEAT-COPD (Biomarkers to Target Antibiotic and Systemic COPD), COPDMAP (Chronic Obstructive Pulmonary Disease Medical Research Council/Association of the British Pharmaceutical Industry), and AERIS (Acute Exacerbation and Respiratory Infections in COPD) cohorts. The microbiome was analyzed using COPDMAP and AERIS as a discovery data set and BEAT-COPD as a validation data set. Measurements and Main Results: The airway microbiome in neutrophilic COPD was heterogeneous, with two primary community types differentiated by the predominance of Haemophilus. The Haemophilus-predominant subgroup had elevated sputum IL-1β and TNFα (tumor necrosis factor α) and was relatively stable over time. The other neutrophilic subgroup with a balanced microbiome profile had elevated sputum and serum IL-17A and was temporally dynamic. Patients in this state at stability were susceptible to the greatest microbiome shifts during exacerbations. This subgroup can temporally switch to both neutrophilic Haemophilus-predominant and eosinophilic states that were otherwise mutually exclusive. Time-series analysis on the microbiome showed that the temporal trajectories of Campylobacter and Granulicatella were indicative of intrapatient switches from neutrophilic to eosinophilic inflammation, in track with patient sputum eosinophilia over time. Network analysis revealed distinct host-microbiome interaction patterns among neutrophilic Haemophilus-predominant, neutrophilic balanced microbiome, and eosinophilic subgroups. Conclusions: The airway microbiome can stratify neutrophilic COPD into subgroups that justify different therapies. Neutrophilic and eosinophilic COPD are interchangeable in some patients. Monitoring temporal variability of the airway microbiome may track patient inflammatory status over time.
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Affiliation(s)
- Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | | | - Koirobi Haldar
- Human Genetics, Research and Development, GlaxoSmithKline, Collegeville, Pennsylvania
| | | | - Augusta S. Beech
- Department of Respiratory Sciences, Institute for Lung Health, Leicester National Institute for Health Research Biomedical Research Centre, University of Leicester, Leicester, United Kingdom
| | - Wei Ma
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - James R. Brown
- Institute of Statistics and Big Data, Renmin University of China, Beijing, China
| | - Ruth Tal-Singer
- Chronic Obstructive Pulmonary Disease Foundation, Research Department, Washington, District of Columbia
| | - Michael R. Barer
- Human Genetics, Research and Development, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Mona Bafadhel
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gavin C. Donaldson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
| | - Jadwiga A. Wedzicha
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
| | - Dave Singh
- Department of Respiratory Sciences, Institute for Lung Health, Leicester National Institute for Health Research Biomedical Research Centre, University of Leicester, Leicester, United Kingdom
| | - Tom M. A. Wilkinson
- National Institute for Health Research Southampton Respiratory Biomedical Research Unit, University Hospital Southampton National Health Service Foundation Trust, Southampton, United Kingdom
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23
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Opron K, Begley LA, Erb-Downward JR, Freeman C, Madapoosi S, Alexis NE, Barjaktarevic I, Graham Barr R, Bleecker ER, Bowler RP, Christenson SA, Comellas AP, Cooper CB, Couper DJ, Doerschuk CM, Dransfield MT, Han MK, Hansel NN, Hastie AT, Hoffman EA, Kaner RJ, Krishnan J, O'Neal WK, Ortega VE, Paine R, Peters SP, Michael Wells J, Woodruff PG, Martinez FJ, Curtis JL, Huffnagle GB, Huang YJ. Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort. NPJ Biofilms Microbiomes 2021; 7:14. [PMID: 33547327 PMCID: PMC7865064 DOI: 10.1038/s41522-021-00185-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/07/2021] [Indexed: 01/12/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is heterogeneous in development, progression, and phenotypes. Little is known about the lung microbiome, sampled by bronchoscopy, in milder COPD and its relationships to clinical features that reflect disease heterogeneity (lung function, symptom burden, and functional impairment). Using bronchoalveolar lavage fluid collected from 181 never-smokers and ever-smokers with or without COPD (GOLD 0-2) enrolled in the SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS), we find that lung bacterial composition associates with several clinical features, in particular bronchodilator responsiveness, peak expiratory flow rate, and forced expiratory flow rate between 25 and 75% of FVC (FEF25–75). Measures of symptom burden (COPD Assessment Test) and functional impairment (six-minute walk distance) also associate with disparate lung microbiota composition. Drivers of these relationships include members of the Streptococcus, Prevotella, Veillonella, Staphylococcus, and Pseudomonas genera. Thus, lung microbiota differences may contribute to airway dysfunction and airway disease in milder COPD.
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Affiliation(s)
- Kristopher Opron
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lesa A Begley
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John R Erb-Downward
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christine Freeman
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA.,Research Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Siddharth Madapoosi
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Neil E Alexis
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | | | | | | | - David J Couper
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - MeiLan K Han
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | - Wanda K O'Neal
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | | | | | - Jeffrey L Curtis
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA.,Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Gary B Huffnagle
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yvonne J Huang
- Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA.
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24
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Short B, Carson S, Devlin AC, Reihill JA, Crilly A, MacKay W, Ramage G, Williams C, Lundy FT, McGarvey LP, Thornbury KD, Martin SL. Non-typeable Haemophilus influenzae chronic colonization in chronic obstructive pulmonary disease (COPD). Crit Rev Microbiol 2021; 47:192-205. [PMID: 33455514 DOI: 10.1080/1040841x.2020.1863330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Haemophilus influenzae is the most common cause of bacterial infection in the lungs of chronic obstructive pulmonary disease (COPD) patients and contributes to episodes of acute exacerbation which are associated with increased hospitalization and mortality. Due to the ability of H. influenzae to adhere to host epithelial cells, initial colonization of the lower airways can progress to a persistent infection and biofilm formation. This is characterized by changes in bacterial behaviour such as reduced cellular metabolism and the production of an obstructive extracellular matrix (ECM). Herein we discuss the multiple mechanisms by which H. influenzae contributes to the pathogenesis of COPD. In particular, mechanisms that facilitate bacterial adherence to host airway epithelial cells, biofilm formation, and microbial persistence through immune system evasion and antibiotic tolerance will be discussed.
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Affiliation(s)
- Bryn Short
- University of the West of Scotland, Paisley, United Kingdom
| | - Stephen Carson
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Anna-Claire Devlin
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - James A Reihill
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Anne Crilly
- University of the West of Scotland, Paisley, United Kingdom
| | - William MacKay
- University of the West of Scotland, Paisley, United Kingdom
| | - Gordon Ramage
- Glasgow Biofilm Research Group, Oral Sciences, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Craig Williams
- University of the West of Scotland, Paisley, United Kingdom
| | - Fionnuala T Lundy
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Lorcan P McGarvey
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Keith D Thornbury
- Smooth Muscle Research Group, Dundalk Institute of Technology, Dundalk, Ireland
| | - S Lorraine Martin
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
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25
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Tiew PY, Jaggi TK, Chan LLY, Chotirmall SH. The airway microbiome in COPD, bronchiectasis and bronchiectasis-COPD overlap. CLINICAL RESPIRATORY JOURNAL 2020; 15:123-133. [PMID: 33063421 DOI: 10.1111/crj.13294] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To review the airway microbiome in chronic obstructive pulmonary disease (COPD), bronchiectasis and bronchiectasis-COPD overlap (BCO). DATA SOURCE AND STUDY SELECTION Relevant studies were selected from PubMed, Google scholar, EMBASE and Web of Science. All studies involving human microbiomes, published in the English language, and using the search terms "COPD", "Chronic Obstructive Pulmonary Disease", "Bronchiectasis", "BCO" or "Bronchiectasis and COPD overlap", AND "microbiome", "mycobiome" or "metagenomics" were included. RESULTS Despite variability in sampling methods and specimen types used, microbiome composition remains relatively comparable in COPD and bronchiectasis with prominence of Proteobacteria, Firmicutes and Bacteroidetes. Alterations to airway microbiomes occur in association to disease severity and/or exacerbations in COPD and bronchiectasis. Decreased alpha diversity and Haemophilus-predominant microbiomes are associated with poorer survival in COPD, while, in bronchiectasis, Pseudomonas-predominant microbiomes demonstrate high exacerbation frequency and greater symptom burden while Aspergillus-dominant mycobiome profiles associate with exacerbations. The role of the microbiome in BCO remains understudied. CONCLUSION Use of next-generation sequencing has revolutionised our detection and understanding of the airway microbiome in chronic respiratory diseases such as COPD and bronchiectasis. Targeted amplicon sequencing reveals important associations between the respiratory microbiome and disease outcome while metagenomics may elucidate functional pathways. How best to apply this information into patient care, monitoring and treatment, however, remains challenging and necessitates further study.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Tavleen K Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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26
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Liu J, Ran Z, Wang F, Xin C, Xiong B, Song Z. Role of pulmonary microorganisms in the development of chronic obstructive pulmonary disease. Crit Rev Microbiol 2020; 47:1-12. [PMID: 33040638 DOI: 10.1080/1040841x.2020.1830748] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic obstructive respiratory disease characterized by irreversible airway limitation and persistent respiratory symptoms. The main clinical symptoms of COPD are dyspnoea, chronic cough, and sputum. COPD is often accompanied by other respiratory diseases, which can cause worsening of the disease. COPD patients with dyspnoea and aggravation of cough and sputum symptoms represent acute exacerbations of COPD (AECOPD). There is mounting evidence suggesting that dysbiosis of pulmonary microbiota participates in the disease. However, investigations of dysbiosis of pulmonary microbiota and the disease are still in initial phases. To screen, diagnose, and treat this respiratory disease, integrating data from different studies can improve our understanding of the occurrence and development of COPD and AECOPD. In this review, COPD epidemiology and the primary triggering mechanism are explored. Emerging knowledge regarding the association of inflammation, caused by pulmonary microbiome imbalance, and changes in lung microbiome flora species involved in the development of the disease are also highlighted. These data will further our understanding of the pathogenesis of COPD and AECOPD and may yield novel strategies for the use of pulmonary microbiota as a potential therapeutic intervention.
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Affiliation(s)
- Jiexing Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhuonan Ran
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Fen Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Caiyan Xin
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Bin Xiong
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China.,Molecular Biotechnology Platform, Public Center of Experimental Technology, Southwest Medical University, Luzhou, PR China
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27
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Leiten EO, Nielsen R, Wiker HG, Bakke PS, Martinsen EMH, Drengenes C, Tangedal S, Husebø GR, Eagan TML. The airway microbiota and exacerbations of COPD. ERJ Open Res 2020; 6:00168-2020. [PMID: 32904583 PMCID: PMC7456643 DOI: 10.1183/23120541.00168-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
Aim The aim of this study was to investigate whether the compositionality of the lower airway microbiota predicts later exacerbation risk in persons with COPD in a cohort study. Materials and methods We collected lower airways microbiota samples by bronchoalveolar lavage and protected specimen brushes, and oral wash samples from 122 participants with COPD. Bacterial DNA was extracted from all samples, before we sequenced the V3-V4 region of the 16S RNA gene. The frequency of moderate and severe COPD exacerbations was surveyed in telephone interviews and in a follow-up visit. Compositional taxonomy and α and β diversity were compared between participants with and without later exacerbations. Results The four most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria and Fusobacteria in both groups, and the four most abundant genera were Streptococcus, Veillonella, Prevotella and Gemella. The relative abundances of different taxa showed a large variation between samples and individuals, and no statistically significant difference of either compositional taxonomy, or α or β diversity could be found between participants with and without COPD exacerbations within follow-up. Conclusion The findings from the current study indicate that individual differences in the lower airway microbiota in persons with COPD far outweigh group differences between frequent and nonfrequent COPD exacerbators, and that the compositionality of the microbiota is so complex as to present large challenges for use as a biomarker of later exacerbations. Contrary to previous reports, in this study there were no significant associations between the lung microbiota in stable COPD and COPD exacerbation frequencyhttps://bit.ly/2ZVcNdG
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Affiliation(s)
| | - Rune Nielsen
- Dept of Clinical Science, University of Bergen, Bergen, Norway.,Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Harald Gotten Wiker
- Dept of Clinical Science, University of Bergen, Bergen, Norway.,Dept of Microbiology, Haukeland University Hospital, Bergen, Norway
| | | | | | - Christine Drengenes
- Dept of Clinical Science, University of Bergen, Bergen, Norway.,Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Solveig Tangedal
- Dept of Clinical Science, University of Bergen, Bergen, Norway.,Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Gunnar Reksten Husebø
- Dept of Clinical Science, University of Bergen, Bergen, Norway.,Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tomas Mikal Lind Eagan
- Dept of Clinical Science, University of Bergen, Bergen, Norway.,Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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28
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Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) is a heterogeneous syndrome and may comprise several different phenotypes that are driven by different molecular mechanisms (endotypes). Several different clinical, genetic, and inflammatory phenotypes of COPD have been recognized and this may lead to more precise effective therapies. AREAS COVERED The different clinical phenotypes, including smoking versus nonsmoking COPD, small airway disease versus emphysema, non-exacerbators versus frequent exacerbators are discussed. Rare genetic endotypes (alpha1-antitrypsin deficiency, telomerase polymorphisms), and inflammatory phenotypes (eosinophilic versus neutrophilic) are also recognized in stable and exacerbating patients and have implications for the choice of therapy. EXPERT OPINION Clinical phenotypes have so far not proved to be very useful in selecting more personalized therapy for COPD. Even with genetic endotypes, this has not led to improved therapy. More promising is the recognition that COPD patients who have increased sputum or blood eosinophils tend to have more frequent exacerbations and inhaled corticosteroids are more effective in preventing exacerbation. Increased blood eosinophils have proved to be a useful biomarker now used to target ICS more effectively. Furthermore, COPD patients with low eosinophils are more likely to get pneumonia with ICS and to have lower airway bacterial colonization.
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Affiliation(s)
- Peter J Barnes
- National Heart and Lung Institute, Imperial College London , London, UK
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29
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Lira-Lucio JA, Falfán-Valencia R, Ramírez-Venegas A, Buendía-Roldán I, Rojas-Serrano J, Mejía M, Pérez-Rubio G. Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases. Microorganisms 2020; 8:E1059. [PMID: 32708647 PMCID: PMC7409050 DOI: 10.3390/microorganisms8071059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The lung microbiome composition has critical implications in the regulation of innate and adaptive immune responses. Next-generation sequencing techniques have revolutionized the understanding of pulmonary physiology and pathology. Currently, it is clear that the lung is not a sterile place; therefore, the investigation of the participation of the pulmonary microbiome in the presentation, severity, and prognosis of multiple pathologies, such as asthma, chronic obstructive pulmonary disease, and interstitial lung diseases, contributes to a better understanding of the pathophysiology. Dysregulation of microbiota components in the microbiome-host interaction is associated with multiple lung pathologies, severity, and prognosis, making microbiome study a useful tool for the identification of potential therapeutic strategies. This review integrates the findings regarding the activation and regulation of the innate and adaptive immune response pathways according to the microbiome, including microbial patterns that could be characteristic of certain diseases. Further studies are required to verify whether the microbial profile and its metabolites can be used as biomarkers of disease progression or poor prognosis and to identify new therapeutic targets that restore lung dysbiosis safely and effectively.
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Affiliation(s)
- Juan Alberto Lira-Lucio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
| | - Alejandra Ramírez-Venegas
- Tobacco Smoking and COPD Research Department, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Jorge Rojas-Serrano
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-S.); (M.M.)
| | - Mayra Mejía
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-S.); (M.M.)
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
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Criner GJ. Rebuttal From Dr Criner. Chest 2020; 157:1079-1080. [PMID: 32386635 DOI: 10.1016/j.chest.2020.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/07/2020] [Accepted: 01/18/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Gerard J Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA.
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