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Widder S, Zhao J, Carmody LA, Zhang Q, Kalikin LM, Schloss PD, LiPuma JJ. Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways. THE ISME JOURNAL 2022; 16:905-914. [PMID: 34689185 PMCID: PMC8941020 DOI: 10.1038/s41396-021-01129-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022]
Abstract
Bacterial infection and inflammation of the airways are the leading causes of morbidity and mortality in persons with cystic fibrosis (CF). The ecology of the bacterial communities inhabiting CF airways is poorly understood, especially with respect to how community structure, dynamics, and microbial metabolic activity relate to clinical outcomes. In this study, the bacterial communities in 818 sputum samples from 109 persons with CF were analyzed by sequencing bacterial 16S rRNA gene amplicons. We identified eight alternative community types (pulmotypes) by using a Dirichlet multinomial mixture model and studied their temporal dynamics in the cohort. Across patients, the pulmotypes displayed chronological patterns in the transition among each other. Furthermore, significant correlations between pulmotypes and patient clinical status were detected by using multinomial mixed effects models, principal components regression, and statistical testing. Constructing pulmotype-specific metabolic activity profiles, we found that pulmotype microbiota drive distinct community functions including mucus degradation or increased acid production. These results indicate that pulmotypes are the result of ordered, underlying drivers such as predominant metabolism, ecological competition, and niche construction and can form the basis for quantitative, predictive models supporting clinical treatment decisions.
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Affiliation(s)
- Stefanie Widder
- Department of Medicine 1, Research Laboratory of Infection Biology, Medical University of Vienna, Vienna, Austria.
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Qingyang Zhang
- Department of Mathematical Science, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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2
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Hardouin P, Chiron R, Marchandin H, Armengaud J, Grenga L. Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives. Genes (Basel) 2021; 12:892. [PMID: 34207804 PMCID: PMC8227082 DOI: 10.3390/genes12060892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, triggering dysfunction of the anion channel in several organs including the lung and gut. The main cause of morbidity and mortality is chronic infection. The microbiota is now included among the additional factors that could contribute to the exacerbation of patient symptoms, to treatment outcome, and more generally to the phenotypic variability observed in CF patients. In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host-microbiota interactions. In this context, proteomics targets the key effectors of the responses from organisms, and thus their phenotypes. Recent advances are promising in terms of gaining insights into the CF microbiota and its relation with the host. This review provides an overview of the contributions made by proteomics and metaproteomics to our knowledge of the complex host-microbiota partnership in CF. Considering the strengths and weaknesses of proteomics-based approaches in profiling the microbiota in the context of other diseases, we illustrate their potential and discuss possible strategies to overcome their limitations in monitoring both the respiratory and intestinal microbiota in sample from patients with CF.
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Affiliation(s)
- Pauline Hardouin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols-sur-Cèze, France;
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Raphael Chiron
- HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France;
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
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3
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Hyperinflammation and airway surface liquid dehydration in cystic fibrosis: purinergic system as therapeutic target. Inflamm Res 2021; 70:633-649. [PMID: 33904934 DOI: 10.1007/s00011-021-01464-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE AND DESIGN The exacerbate inflammatory response contributes to the progressive loss of lung function in cystic fibrosis (CF), a genetic disease that affects the osmotic balance of mucus and mucociliary clearance, resulting in a microenvironment that favors infection and inflammation. The purinergic system, an extracellular signaling pathway characterized by nucleotides, enzymes and receptors, may have a protective role in the disease, through its action in airway surface liquid (ASL) and anti-inflammatory response. MATERIALS AND METHODS To make up this review, studies covering topics of CF, inflammation, ASL and purinergic system were selected from the main medical databases, such as Pubmed and ScienceDirect. CONCLUSION We propose several ways to modulate the purinergic system as a potential therapy for CF, like inhibition of P2X7, activation of P2Y2, A2A and A2B receptors and blocking of adenosine deaminase. Among them, we postulate that the most suitable strategy is to block the action of adenosine deaminase, which culminates in the increase of Ado levels that presents anti-inflammatory actions and improves mucociliary clearance. Furthermore, it is possible to maintain the physiological levels of ATP to control the hydration of ASL. These therapies could correct the main mechanisms that contribute to the progression of CF.
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4
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Magryś A. Microbiota: A Missing Link in The Pathogenesis of Chronic Lung Inflammatory Diseases. Pol J Microbiol 2021; 70:25-32. [PMID: 33815524 PMCID: PMC8008760 DOI: 10.33073/pjm-2021-013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic respiratory diseases account for high morbidity and mortality, with asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF) being the most prevalent globally. Even though the diseases increase in prevalence, the exact underlying mechanisms have still not been fully understood. Despite their differences in nature, pathophysiologies, and clinical phenotypes, a growing body of evidence indicates that the presence of lung microbiota can shape the pathogenic processes underlying chronic inflammation, typically observed in the course of the diseases. Therefore, the characterization of the lung microbiota may shed new light on the pathogenesis of these diseases. Specifically, in chronic respiratory tract diseases, the human microbiota may contribute to the disease’s development and severity. The present review explores the role of the microbiota in the area of chronic pulmonary diseases, especially COPD, asthma, and CF.
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Affiliation(s)
- Agnieszka Magryś
- Chair and Department of Medical Microbiology, Medical University of Lublin, Lublin, Poland
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Liessi N, Pedemonte N, Armirotti A, Braccia C. Proteomics and Metabolomics for Cystic Fibrosis Research. Int J Mol Sci 2020; 21:ijms21155439. [PMID: 32751630 PMCID: PMC7432297 DOI: 10.3390/ijms21155439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/18/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
The aim of this review article is to introduce the reader to the state-of-the-art of the contribution that proteomics and metabolomics sciences are currently providing for cystic fibrosis (CF) research: from the understanding of cystic fibrosis transmembrane conductance regulator (CFTR) biology to biomarker discovery for CF diagnosis. Our work particularly focuses on CFTR post-translational modifications and their role in cellular trafficking as well as on studies that allowed the identification of CFTR molecular interactors. We also show how metabolomics is currently helping biomarker discovery in CF. The most recent advances in these fields are covered by this review, as well as some considerations on possible future scenarios for new applications.
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Affiliation(s)
- Nara Liessi
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
| | - Andrea Armirotti
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
- Correspondence: ; Tel.: +39-010-2896-938
| | - Clarissa Braccia
- D3PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
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Saiman L. Improving outcomes of infections in cystic fibrosis in the era of CFTR modulator therapy. Pediatr Pulmonol 2019; 54 Suppl 3:S18-S26. [PMID: 31715086 DOI: 10.1002/ppul.24522] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022]
Abstract
Currently, available single and dual-combination cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies have favorably altered the life course of individuals with cystic fibrosis (CF) by decreasing morbidities and increasing survival. However, even with CFTR modulator use, questions and challenges remain to optimize the management of lung infections. This review (a) identifies these ongoing challenges and discusses the current understanding of the potential impact of CFTR modulator therapy on infections; (b) describes ongoing research to optimize detection, diagnosis, and treatment of CF microorganisms; and (c) discusses strategies to develop new anti-infective therapies. The CF Foundation has launched the Infection Research Initiative to fund research that will improve our understanding of the complex microbial ecology within the CF lung, improve detection of CF pathogens, optimize current treatment, including long-term chronic therapies, and develop new anti-infective therapies. Ongoing clinical trials to determine the optimal duration of treatment of pulmonary exacerbations and to diagnose and treat nontuberculous mycobacteria represent clinical research paradigms that could be used to answer other complex treatment questions. The anti-infective pipeline includes both existing anti-infective and non-anti-infective agents, many of which are proposed to have unique mechanisms of action in CF. Future studies plan to evaluate short- and long-term clinical effectiveness and impact on infections, of the next generation of CFTR modulator therapy, the highly effective triple-combination therapy, for individuals with CF, homozygous or heterozygous for F508del.
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Affiliation(s)
- Lisa Saiman
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
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Tunney MM, Payne JE, McGrath SJ, Einarsson GG, Ingram RJ, Gilpin DF, Juarez-Perez V, Elborn JS. Activity of hypothiocyanite and lactoferrin (ALX-009) against respiratory cystic fibrosis pathogens in sputum. J Antimicrob Chemother 2019; 73:3391-3397. [PMID: 30219825 DOI: 10.1093/jac/dky357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/10/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives To determine the antimicrobial activity of ALX-009, a combination of bovine lactoferrin and hypothiocyanite, in sputum against Pseudomonas aeruginosa and Burkholderia cepacia complex (Bcc), key pathogens causing infection in the lungs of cystic fibrosis (CF) patients. Methods The antimicrobial activity of ALX-009 against clinical respiratory P. aeruginosa isolates was determined by time-kill assay. Sputum from CF patients was treated with ALX-009, either alone or in combination with tobramycin, and the effect on P. aeruginosa, Bcc and total sputum density was determined. Results Time-kill assay indicated that ALX-009 was bactericidal at 24 h against 4/4 P. aeruginosa isolates under aerobic conditions, and against 3/4 isolates under anaerobic conditions. ALX-009 was also bactericidal against P. aeruginosa in sputum samples at 6 h (n = 22/24 samples) and 24 h (n = 14/24 samples), and demonstrated significantly greater activity than tobramycin at both timepoints. Activity against Bcc in sputum samples (n = 9) was also demonstrated, but the magnitude of change in Bcc density was less than for P. aeruginosa. To determine the effect of treating sputum with two doses of ALX-009, similar to current regimens for inhaled antibiotics, aliquots of a further 10 sputum samples positive for P. aeruginosa were treated with one (t = 0 h) or two doses (t = 0 h, t = 12 h) of ALX-009; treatment with two doses resulted in bactericidal activity in 7/10 samples at 34 h compared with only 3/10 samples when treatment was with one dose. Conclusions ALX-009 demonstrates promise as a novel antimicrobial that could be used to decrease P. aeruginosa density in the lungs of people with CF.
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Affiliation(s)
- Michael M Tunney
- Halo Research Group, Queen's University Belfast, Belfast, UK.,School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Joanna E Payne
- Halo Research Group, Queen's University Belfast, Belfast, UK.,Centre for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Stephanie J McGrath
- Halo Research Group, Queen's University Belfast, Belfast, UK.,School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Gisli G Einarsson
- Halo Research Group, Queen's University Belfast, Belfast, UK.,Centre for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Rebecca J Ingram
- Centre for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Deirdre F Gilpin
- Halo Research Group, Queen's University Belfast, Belfast, UK.,School of Pharmacy, Queen's University Belfast, Belfast, UK
| | | | - J Stuart Elborn
- Halo Research Group, Queen's University Belfast, Belfast, UK.,Centre for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, UK.,Imperial College London and Royal Brompton Hospital, London, UK
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Abstract
PURPOSE OF REVIEW To compile data from the past 10 years regarding the role of modifying genes in cystic fibrosis (CF). RECENT FINDINGS CF is a model disease for understanding of the action of modifying genes. Although it is a monogenic (CFTR) autosomal recessive disease, CF presents with wide phenotypic variability. In CF, variability occurs with different intensity among patients by each organ, being organ-specific, resulting from the mutual interaction of environmental and genetic factors, including CFTR mutations and various other genes, most of which are associated with inflammatory processes. In individuals, using precision medicine, gene modification studies have revealed individualized responses to drugs depending on particular CFTR mutations and modifying genes, most of which are alternative ion channels. SUMMARY Studies of modifying genes in CF allow: understanding of clinical variability among patients with the same CFTR genotype; evaluation of precision medicine; understanding of environmental and genetic effects at the organ level; understanding the involvement of genetic variants in inflammatory responses; improvements in genetic counseling; understanding the involvement of genetic variants in inflammatory responses in lung diseases, such as asthma; and understanding the individuality of the person with the disease.
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Taylor SL, O'Farrell HE, Simpson JL, Yang IA, Rogers GB. The contribution of respiratory microbiome analysis to a treatable traits model of care. Respirology 2018; 24:19-28. [PMID: 30282116 DOI: 10.1111/resp.13411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/13/2018] [Accepted: 09/09/2018] [Indexed: 12/15/2022]
Abstract
The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.
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Affiliation(s)
- Steven L Taylor
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Hannah E O'Farrell
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Jodie L Simpson
- Respiratory and Sleep Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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10
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Acosta N, Heirali A, Somayaji R, Surette MG, Workentine ML, Sibley CD, Rabin HR, Parkins MD. Sputum microbiota is predictive of long-term clinical outcomes in young adults with cystic fibrosis. Thorax 2018; 73:1016-1025. [PMID: 30135091 DOI: 10.1136/thoraxjnl-2018-211510] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND Complex polymicrobial communities infect cystic fibrosis (CF) lower airways. Generally, communities with low diversity, dominated by classical CF pathogens, associate with worsened patient status at sample collection. However, it is not known if the microbiome can predict future outcomes. We sought to determine if the microbiome could be adapted as a biomarker for patient prognostication. METHODS We retrospectively assessed prospectively collected sputum from a cohort of 104 individuals aged 18-22 to determine factors associated with progression to early end-stage lung disease (eESLD; death/transplantation <25 years) and rapid pulmonary function decline (>-3%/year FEV1 over the ensuing 5 years). Illumina MiSeq paired-end sequencing of the V3-V4 region of the 16S rRNA was used to define the airway microbiome. RESULTS Based on the primary outcome analysed, 17 individuals (16%) subsequently progressed to eESLD. They were more likely to have sputum with low alpha diversity, dominated by specific pathogens including Pseudomonas. Communities with abundant Streptococcus were observed to be protective. Microbial communities clustered together by baseline lung disease stage and subsequent progression to eESLD. Multivariable analysis identified baseline lung function and alpha diversity as independent predictors of eESLD. For the secondary outcomes, 58 and 47 patients were classified as rapid progressors based on absolute and relative definitions of lung function decline, respectively. Patients with low alpha diversity were similarly more likely to be classified as experiencing rapid lung function decline over the ensuing 5 years when adjusted for baseline lung function. CONCLUSIONS We observed that the diversity of microbial communities in CF airways is predictive of progression to eESLD and disproportionate lung function decline and may therefore represent a novel biomarker.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Alya Heirali
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada.,Department of Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | | | - Christopher D Sibley
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
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11
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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