4.8 Review

The lung microbiome: progress and promise

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Article Allergy

The sputum microbiome, airway inflammation, and mortality in chronic obstructive pulmonary disease

Alison J. Dicker et al.

Summary: The study found that the sputum microbiome of COPD patients is closely related to disease severity, frequent exacerbations, blood eosinophil levels, etc., and different dominant microbiomes have different impacts. The diversity of sputum microbiomes is closely related to the development and mortality of COPD.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2021)

Article Cardiac & Cardiovascular Systems

Lower airway bacterial microbiome may influence recurrence alter resection of early-stage non-small cell lung cancer

Santosh K. Patnaik et al.

Summary: The composition of the lower airway microbiome before surgery may be associated with recurrence in early non-small cell lung cancer (NSCLC). The presence of a specific microbiome signature was linked to shorter recurrence-free survival and increased expression of genes related to cell proliferation and epithelial mesenchymal transition in tumors.

JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY (2021)

Article Oncology

Cancer Statistics, 2021

Rebecca L. Siegel et al.

Summary: Every year, the American Cancer Society projects the numbers of new cancer cases and deaths in the United States, with the latest data showing a significant decline in lung cancer mortality, while prostate cancer mortality has plateaued and breast and colorectal cancer mortality have slowed. Improvements in treatment have accelerated progress against lung cancer, leading to a record drop in overall cancer mortality.

CA-A CANCER JOURNAL FOR CLINICIANS (2021)

Article Respiratory System

Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study

Eleanor Valenzi et al.

Summary: The study revealed the heterogeneity of lung microbiota in patients with IPF, with different bacterial loads and compositions associated with distinct clinical outcomes.

THORAX (2021)

Article Multidisciplinary Sciences

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

Jinuk Jeong et al.

Summary: This study compared sFL16S and V3V4 sequencing methods on human gut microbiota samples and found that sFL16S showed better resolution and identification accuracy at the species level. This indicates that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.

SCIENTIFIC REPORTS (2021)

Article Critical Care Medicine

Lung microbiota predict chronic rejection in healthy lung transplant recipients: a prospective cohort study

Michael P. Combs et al.

Summary: The characteristics of the respiratory microbiome in healthy lung transplant recipients within the first year of transplantation have a significant impact on subsequent CLAD-free survival, with an increased lung bacterial burden predicting chronic rejection and death. The lung microbiome represents an understudied and potentially modifiable risk factor for lung allograft dysfunction.

LANCET RESPIRATORY MEDICINE (2021)

Article Multidisciplinary Sciences

Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures

Shashank Gupta et al.

Summary: The study reveals that different respiratory illnesses have unique microbial features that can be used as diagnostic markers to differentiate among various respiratory illnesses. The lung microbiome of patients with stable COPD is more diverse compared to those with exacerbated COPD and ILD patients.

SCIENTIFIC REPORTS (2021)

Article Biotechnology & Applied Microbiology

Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort

Kristopher Opron et al.

Summary: In a study of 181 participants from the SPIROMICS study, lung microbiota composition was found to be closely associated with clinical features, symptom burden, and functional impairment in COPD patients. Different microbiota compositions were linked to different clinical presentations.

NPJ BIOFILMS AND MICROBIOMES (2021)

Article Critical Care Medicine

Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary T-Helper Cell Type 17 Response that Mitigates Susceptibility to Streptococcus pneumoniae

Benjamin G. Wu et al.

Summary: The study found that aspiration with oral commensals in mice led to short-term lower-airway dysbiosis, but induced a prolonged inflammatory response, including IL-17-producing T cells, lasting at least 14 days. Furthermore, aspiration with oral commensals decreased hosts' susceptibility to respiratory challenge with S. pneumoniae.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2021)

Review Cardiac & Cardiovascular Systems

The lung microbiome in lung transplantation

John E. McGinniss et al.

Summary: Culture-independent study of the lower respiratory tract after lung transplantation has enabled an understanding of the dysbiotic lung microbiome, with specific features possibly linked to host responses and clinical outcomes such as chronic lung allograft dysfunction (CLAD), but many questions remain unanswered.

JOURNAL OF HEART AND LUNG TRANSPLANTATION (2021)

Article Oncology

Lower Airway Dysbiosis Affects Lung Cancer Progression

Jun-Chieh J. Tsay et al.

Summary: In lung cancer patients, dysbiosis of the lower airway microbiota is more prevalent in advanced stages and associated with poor prognosis, upregulation of IL17, PI3K pathways, etc. in the airway transcriptome. The dysbiosis with V. parvula in the lower airway of the KP lung cancer model leads to decreased survival and tumor progression.

CANCER DISCOVERY (2021)

Article Allergy

Risk of childhood wheeze and asthma after respiratory syncytial virus infection in full-term infants

Asuncion Mejias et al.

PEDIATRIC ALLERGY AND IMMUNOLOGY (2020)

Review Biochemistry & Molecular Biology

Methods in Lung Microbiome Research

Sharon M. Carney et al.

AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY (2020)

Article Cardiac & Cardiovascular Systems

Influence of azithromycin and allograft rejection on the post-lung transplant microbiota

Christopher D. Spence et al.

JOURNAL OF HEART AND LUNG TRANSPLANTATION (2020)

Article Critical Care Medicine

Lung Microbiota Predict Clinical Outcomes in Critically Ill Patients

Robert P. Dickson et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2020)

Review Immunology

The Role of Lung and Gut Microbiota in the Pathology of Asthma

Weronika Barcik et al.

IMMUNITY (2020)

Article Critical Care Medicine

Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease

Micheal Mac Aogain et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2020)

Article Multidisciplinary Sciences

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis

Corina N. D'Alessandro-Gabazza et al.

NATURE COMMUNICATIONS (2020)

Article Cardiac & Cardiovascular Systems

Azithromycin prophylaxis after lung transplantation is associated with improved overall survival

David Li et al.

JOURNAL OF HEART AND LUNG TRANSPLANTATION (2020)

Article Cardiac & Cardiovascular Systems

Extracellular DNA in sputum is associated with pulmonary function and hospitalization in patients with cystic fibrosis

Taila Cristina Piva et al.

RESPIRATORY MEDICINE (2020)

Article Allergy

Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma

Chunrong Huang et al.

CLINICAL AND TRANSLATIONAL ALLERGY (2020)

Article Respiratory System

The airway microbiota and exacerbations of COPD

Elise Orvedal Leiten et al.

ERJ OPEN RESEARCH (2020)

Review Critical Care Medicine

The importance of airway and lung microbiome in the critically ill

Ignacio Martin-Loeches et al.

CRITICAL CARE (2020)

Article Respiratory System

Microbial burden and viral exacerbations in a longitudinal multicenter COPD cohort

Jerome Bouquet et al.

RESPIRATORY RESEARCH (2020)

Article Respiratory System

Trends in prevalence and incidence of chronic respiratory diseases from 1990 to 2017

Min Xie et al.

RESPIRATORY RESEARCH (2020)

Article Oncology

The Microbiome in Lung Cancer Tissue and Recurrence-Free Survival

Brandilyn A. Peters et al.

CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION (2019)

Article Biochemistry & Molecular Biology

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells

Chengcheng Jin et al.

Article Biochemistry & Molecular Biology

Laboratory contamination over time during low-biomass sample analysis

Laura S. Weyrich et al.

MOLECULAR ECOLOGY RESOURCES (2019)

Editorial Material Biology

Multiple levels of the unknown in microbiome research

Andrew Maltez Thomas et al.

BMC BIOLOGY (2019)

Article Allergy

Associations between fungal and bacterial microbiota of airways and asthma endotypes

Anukriti Sharma et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2019)

Review Gastroenterology & Hepatology

Gut microbiota in colorectal cancer: mechanisms of action and clinical applications

Sunny H. Wong et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2019)

Article Multidisciplinary Sciences

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Jethro S. Johnson et al.

NATURE COMMUNICATIONS (2019)

Article Physiology

Short-chain fatty acids increase TNF alpha-induced inflammation in primary human lung mesenchymal cells through the activation of p38 MAPK

Sandra Rufting et al.

AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY (2019)

Article Critical Care Medicine

Sputum Microbiome Is Associated with 1-Year Mortality after Chronic Obstructive Pulmonary Disease Hospitalizations

Fernando Sergio Leitao Filho et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2019)

Article Respiratory System

The lung and gut microbiome: what has to be taken into consideration for cystic fibrosis?

Genevieve Hery-Arnaud et al.

JOURNAL OF CYSTIC FIBROSIS (2019)

Article Critical Care Medicine

Lung Microbiota Contribute to Pulmonary Inflammation and Disease Progression in Pulmonary Fibrosis

David N. O'Dwyer et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2019)

Article Respiratory System

Airway host-microbiome interactions in chronic obstructive pulmonary disease

Zhang Wang et al.

RESPIRATORY RESEARCH (2019)

Review Gastroenterology & Hepatology

short chain fatty acids as potential therapeutic agents in human gastrointestinal and inflammatory disorders

P. A. Gill et al.

ALIMENTARY PHARMACOLOGY & THERAPEUTICS (2018)

Article Critical Care Medicine

The Lung Microbiota of Healthy Mice Are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity

Robert P. Dickson et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2018)

Article Critical Care Medicine

Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients

Ariane R. Panzer et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2018)

Article Critical Care Medicine

Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer

Jun-Chieh J. Tsay et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2018)

Article Oncology

Issue Information

CA-A CANCER JOURNAL FOR CLINICIANS (2018)

Article Allergy

Inflammatory phenotypes in patients with severe asthma are associated with distinct airway microbiology

Steven L. Taylor et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2018)

Article Microbiology

Improving saliva shotgun metagenomics by chemical host DNA depletion

Clarisse A. Marotz et al.

MICROBIOME (2018)

Article Respiratory System

Evaluation of the airway microbiome in nontuberculous mycobacteria disease

Imran Sulaiman et al.

EUROPEAN RESPIRATORY JOURNAL (2018)

Article Respiratory System

Effects of smoking on the lower respiratory tract microbiome in mice

Rui Zhang et al.

RESPIRATORY RESEARCH (2018)

Article Biotechnology & Applied Microbiology

Interaction between the microbiome and TP53 in human lung cancer

K. Leigh Greathouse et al.

GENOME BIOLOGY (2018)

Review Microbiology

Emerging pathogenic links between microbiota and the gut-lung axis

Kurtis F. Budden et al.

NATURE REVIEWS MICROBIOLOGY (2017)

Review Immunology

The lung mycobiome in the next-generation sequencing era

Laura Tipton et al.

VIRULENCE (2017)

Review Immunology

Microbiome-Modulated Metabolites at the Interface of Host Immunity

Eran Blacher et al.

JOURNAL OF IMMUNOLOGY (2017)

Review Medicine, General & Internal

Chronic obstructive pulmonary disease

Klaus F. Rabe et al.

LANCET (2017)

Article Microbiology

Dysbiosis and Its Discontents

Katarzyna B. Hooks et al.

Article Microbiology

Bacterial Topography of the Healthy Human Lower Respiratory Tract

Robert P. Dickson et al.

Article Multidisciplinary Sciences

The microbiota protects against respiratory infection via GM-CSF signaling

Rebecca L. Brown et al.

NATURE COMMUNICATIONS (2017)

Review Microbiology

Optimizing methods and dodging pitfalls in microbiome research

Dorothy Kim et al.

MICROBIOME (2017)

Article Respiratory System

Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients

Solveig Tangedal et al.

RESPIRATORY RESEARCH (2017)

Article Oncology

Risk factors of Lung Cancer in nonsmoker

Nahid Akhtar et al.

CURRENT PROBLEMS IN CANCER (2017)

Article Biotechnology & Applied Microbiology

Microbiota in Exhaled Breath Condensate and the Lung

Laura Glendinning et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2017)

Review Immunology

Dysbiosis and the immune system

Maayan Levy et al.

NATURE REVIEWS IMMUNOLOGY (2017)

Article Respiratory System

Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma

Jodie L. Simpson et al.

EUROPEAN RESPIRATORY JOURNAL (2016)

Review Oncology

COPD, emphysema and the onset of lung cancer. A systematic review

Cecilia Mouronte-Roibas et al.

CANCER LETTERS (2016)

Review Infectious Diseases

Torquetenovirus: the human virome from bench to bedside

D. Focosi et al.

CLINICAL MICROBIOLOGY AND INFECTION (2016)

Editorial Material Respiratory System

The lung microbiome: the perfect culprit for COPD exacerbations?

Carine Gomez et al.

EUROPEAN RESPIRATORY JOURNAL (2016)

Article Cardiac & Cardiovascular Systems

Long-term effects of azithromycin in patients with cystic fibrosis

Clementine Samson et al.

RESPIRATORY MEDICINE (2016)

Article Biochemistry & Molecular Biology

Revised Estimates for the Number of Human and Bacteria Cells in the Body

Ron Sender et al.

PLOS BIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features

Guoqin Yu et al.

GENOME BIOLOGY (2016)

Article Critical Care Medicine

The Role of Short-Chain Fatty Acids, Produced by Anaerobic Bacteria, in the Cystic Fibrosis Airway

Bojana Mirkovic et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2015)

Article Respiratory System

Short-chain fatty acids affect cystic fibrosis airway inflammation and bacterial growth

Peyman Ghorbani et al.

EUROPEAN RESPIRATORY JOURNAL (2015)

Article Medicine, General & Internal

Risk factors for asthma: is prevention possible?

Richard Beasley et al.

LANCET (2015)

Review Urology & Nephrology

The microbiome of the urinary tract-a role beyond infection

Samantha A. Whiteside et al.

NATURE REVIEWS UROLOGY (2015)

Review Otorhinolaryngology

Asthma: definitions and pathophysiology

James W. Mims

INTERNATIONAL FORUM OF ALLERGY & RHINOLOGY (2015)

Article Microbiology

Insights into the Role of Erysipelotrichaceae in the Human Host

Nadeem O. Kaakoush

Frontiers in Cellular and Infection Microbiology (2015)

Article Multidisciplinary Sciences

Functional Metagenomics of the Bronchial Microbiome in COPD

Laura Millares et al.

PLOS ONE (2015)

Article Respiratory System

Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography

Robert P. Dickson et al.

ANNALS OF THE AMERICAN THORACIC SOCIETY (2015)

Article Respiratory System

Assessment of Airway Microbiota and Inflammation in Cystic Fibrosis Using Multiple Sampling Methods

Edith T. Zemanick et al.

ANNALS OF THE AMERICAN THORACIC SOCIETY (2015)

Article Critical Care Medicine

The Role of Bacteria in the Pathogenesis and Progression of Idiopathic Pulmonary Fibrosis

Phillip L. Molyneaux et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2014)

Review Biochemistry & Molecular Biology

Role of the Microbiota in Immunity and Inflammation

Yasmine Belkaid et al.

Article Environmental Sciences

The Potential Role of Lung Microbiota in Lung Cancer Attributed to Household Coal Burning Exposures

H. Dean Hosgood et al.

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS (2014)

Article Biochemistry & Molecular Biology

Lung microbiota promotes tolerance to allergens in neonates via PD-L1

Eva S. Gollwitzer et al.

NATURE MEDICINE (2014)

Article Multidisciplinary Sciences

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition

Pamela V. Chang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Critical Care Medicine

Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study

MeiLan K. Han et al.

LANCET RESPIRATORY MEDICINE (2014)

Article Microbiology

Cell-associated bacteria in the human lung microbiome

Robert P. Dickson et al.

MICROBIOME (2014)

Article Critical Care Medicine

Widespread Colonization of the Lung by Tropheryma whipplei in HIV Infection

Catherine Lozupone et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2013)

Article Critical Care Medicine

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

Alison Morris et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2013)

Article Allergy

Asthma-associated differences in microbial composition of induced sputum

Pradeep Reddy Marri et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2013)

Article Respiratory System

Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities

Yan Wei Lim et al.

JOURNAL OF CYSTIC FIBROSIS (2013)

Review Public, Environmental & Occupational Health

Previous Lung Diseases and Lung Cancer Risk: A Pooled Analysis From the International Lung Cancer Consortium

Darren R. Brenner et al.

AMERICAN JOURNAL OF EPIDEMIOLOGY (2012)

Article Critical Care Medicine

Lung-enriched Organisms and Aberrant Bacterial and Fungal Respiratory Microbiota after Lung Transplant

Emily S. Charlson et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2012)

Article Critical Care Medicine

The Lung Tissue Microbiome in Chronic Obstructive Pulmonary Disease

Marc A. Sze et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2012)

Article Medicine, General & Internal

Chronic obstructive pulmonary disease

Marc Decramer et al.

LANCET (2012)

Review Multidisciplinary Sciences

Interactions Between the Microbiota and the Immune System

Lora V. Hooper et al.

SCIENCE (2012)

Article Critical Care Medicine

Dysregulation of Allergic Airway Inflammation in the Absence of Microbial Colonization

Tina Herbst et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2011)

Article Critical Care Medicine

Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

Emily S. Charlson et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2011)

Article Critical Care Medicine

Viral Infection in Acute Exacerbation of Idiopathic Pulmonary Fibrosis

Sharon Chao Wootton et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2011)

Article Medicine, General & Internal

Azithromycin for Prevention of Exacerbations of COPD

Richard K. Albert et al.

NEW ENGLAND JOURNAL OF MEDICINE (2011)

Article Multidisciplinary Sciences

Analysis of the Lung Microbiome in the Healthy Smoker and in COPD

John R. Erb-Downward et al.

PLOS ONE (2011)

Article Infectious Diseases

The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples

G. B. Rogers et al.

CLINICAL MICROBIOLOGY AND INFECTION (2010)

Article Multidisciplinary Sciences

Disordered Microbial Communities in Asthmatic Airways

Markus Hilty et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers

Emily S. Charlson et al.

PLOS ONE (2010)

Article Cell Biology

Airway PI3K Pathway Activation Is an Early and Reversible Event in Lung Cancer Development

Adam M. Gustafson et al.

SCIENCE TRANSLATIONAL MEDICINE (2010)

Article Biochemistry & Molecular Biology

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Ivaylo I. Ivanov et al.

Article Biochemistry & Molecular Biology

Effects of short chain fatty acids on effector mechanisms of neutrophils

Marco A. R. Vinolo et al.

CELL BIOCHEMISTRY AND FUNCTION (2009)

Article Critical Care Medicine

Infections and airway inflammation in chronic obstructive pulmonary disease severe exacerbations

Alberto Papi et al.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2006)

Article Medicine, General & Internal

New strains of bacteria and exacerbations of chronic obstructive pulmonary disease

S Sethi et al.

NEW ENGLAND JOURNAL OF MEDICINE (2002)