This book comprehensively covers the microbiome in respiratory disease, from the initial research study to the disease-specific implications and related applications. Research on the respiratory microbiome is increasing in volume and scope. This reflects rapidly growing interest in the study of respiratory disease to understand how microbiota shape mechanisms of disease pathogenesis. The respiratory tract spans the nasal passages, sinus cavities, oropharynx, and the tracheobronchial tree of the lungs. In these compartments of the upper and lower respiratory tract, the microbiota have now been studied in the context of several chronic respiratory conditions. These include chronic sinusitis, allergic rhinitis, asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and pulmonary fibrosis, to name a few. The potential impact of ecological interactions (i.e., between microbes and between microbiota and host) within and across respiratory compartments is increasingly recognized.
The book is organized into two main sections. Part I, Principles and Tools, covers conceptual modeling of the respiratory microbiome, experimental methodology with a focus on a priori considerations in study design and sampling, laboratory and computational methods for analysis of respiratory microbiome data, and minimizing interpretive pitfalls. Part II, Applications, discusses the evidence from specific studies that have shed novel insights into the influence of respiratory microbiota on mechanisms or outcomes in specific diseases. Based on current best evidence, disease-specific chapters include chronic rhinosinusitis, asthma (pediatric and adult studies), chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), bronchiectasis not due to CF, idiopathic pulmonary fibrosis, and lung transplant.
This is an ideal reference for forward-thinking practitioners with interest in novel developments in precision medicine applications in lung disease, as well as translational scientists in the field of microbiology, immunology and lung biology.
Author(s): Yvonne J. Huang, Stavros Garantziotis
Series: Respiratory Medicine
Publisher: Humana
Year: 2021
Language: English
Pages: 316
City: New York
Preface
Contents
List of Contributors
Part I: Principles and Tools of Respiratory Microbiome Investigation
Chapter 1: Approaches to Sampling the Respiratory Microbiome
Introduction
Our Evolving Understanding of the Bacterial Topography of the Respiratory Tract
Sources of “Noise” in Sampling the Respiratory Microbiome
Commonly Used Approaches to Sampling the Respiratory Microbiome
Bronchoalveolar Lavage
Protected Specimen Brushing
Sputum
Tracheal Aspirate
Upper Respiratory Tract Swabs
Surgically Resected and Explanted Lung Tissue
Uncommonly Used Noninvasive Sampling Approaches
Sampling the Respiratory Microbiome in Animal Experiments
Summary
References
Chapter 2: Concepts, Tools, and Methodologic Considerations for Lung Microbiome Research
Culture-Independent Microbiology and the New Microbial Tree of Life
Clinical Microbiology Labs
Community Characterization with the 16S rRNA Gene
Identity Methods: Sequencing
Moving Beyond the Myth of the Sterile Lung
Bibliography
Chapter 3: The Rest Is Noise: Finding Signals in Lung Microbiome Data Analysis
Introduction
Data Types in Lung Microbiome Studies
Amplicon-Based Approaches
Shotgun Metagenomics Sequencing and Metatranscriptomics
Single-Cell Microbiome Characterization
Challenges in Lung Microbiome Characterization and Analysis
Fungal and Viral Data in the Lung Microbiome
Analysis of Low Biomass Samples
Identifying and Removing Contaminants
Compositional Data Analysis
Conclusions
References
Part II: Applications: Role of the Microbiome in Respiratory Disease
Chapter 4: Allergic Rhinitis and Chronic Rhinosinusitis
Introduction
The Upper Airway Microbiome
Allergic Rhinitis
Pathophysiology of Allergic Rhinitis
Dysbiosis in Allergic Rhinitis
Local Airway Microbiome vs. Gut Microbiota
Existing Study Designs for Microbiome Role in Causality or as a Disease Modifier
Strength of Associations in Human Studies
Microbiome Modulation Opportunities
Chronic Rhinosinusitis
Pathophysiology of Chronic Rhinosinusitis
Dysbiosis in Chronic Rhinosinusitis
Existing Study Designs for Microbiome Role in Causality or as a Disease Modifier
Strength of Associations in Human Studies
Microbiome Modulation Opportunities
Conclusion
References
Chapter 5: The Role of the Microbiome in Asthma Inception and Phenotype
Introduction
The Microbiome of the Airways in Asthma
Overview
Defining the Airway Microbiome in Asthma
How to Study the Airway Microbiome in Asthma
Considering Environmental Influences on Asthma and the Human Microbiome
The Airway Microbiome in Health
Early-Life Asthma and the Microbiome
The Microbiome in Adult Asthma
Asthma Phenotypes and the Airway Microbiome
Fungal Microbiome in Asthma
Effects of Asthma Medications on the Airway Microbiome
Effects of Asthma Exacerbations on the Airway Microbiome
Future Directions
References
Chapter 6: Microbiome in Cystic Fibrosis
Introduction
Respiratory Microbiome
Respiratory Tract Anatomy and Respiratory Samples
Contamination of Respiratory Samples
Microbial Profiling Techniques
Recent Developments in CF Respiratory Microbiome Research Approaches
Variability Across Samples
Airway Microbiome Across Age and Disease Status
Pulmonary Exacerbations
CF Respiratory Virome and Mycobiome
CFTR Modulators and Impact on Microbiome
Antibiotic Susceptibility and Microbiome
GI Microbiome
The CF Gastrointestinal Microbiome
GI Microbiome Analytical Methods
CF Fecal Dysbioses in Adults, Children, and Animals with CF
New Clinical Correlations with the CF Fecal Microbiome
The Effects of CF Treatment on Fecal Microbiomes
Remaining Challenges in CF Microbiome Studies
Conclusions
References
Chapter 7: Bronchiectasis
Introduction
Aetiopathogenesis
The Role of Infection
The Case for Microbiome Research in Bronchiectasis
The Airway Microbiology in Bronchiectasis
The Bacteriome in Bronchiectasis
Non-tuberculous Mycobacteria
The Mycobiome in Bronchiectasis
The Virome in Bronchiectasis
Microbial Networks and the ‘Multi-Biome’
Clinical Applications
Future Directions
References
Chapter 8: COPD
Introduction
Bacteriome in Stable COPD
Virome in Stable COPD
Lower Airway Microbiota and the Inflammatory Process in Stable COPD
Resistome in Stable COPD
Effects of Inhaled Medications on the Lower Airway Microbiota
Acute Exacerbations of COPD (AECOPD)
Research Needs in this Area
References
Chapter 9: Idiopathic Pulmonary Fibrosis and Other Interstitial Lung Diseases
Introduction
Idiopathic Pulmonary Fibrosis
Hypersensitivity Pneumonitis
Other Interstitial Lung Diseases
Conclusions and Future Work
References
Chapter 10: Immune Suppression in Lung Disease: Lung Transplantation and HIV
Introduction
The Lung Microbiome in Lung Transplantation and HIV
Composition of the Post-Lung Transplantation Microbiome
HIV Respiratory Tract Microbiome
Oral-Lung and Gut-Lung Axes
Lung Transplant, Aspiration, and Gut Dysbiosis
The Relation Between the Oral and Gastrointestinal Tract with the Lung in HIV
Mucosal Defenses
Tolerance, Immunity, and the Microbiome After Lung Transplantation
HIV and Epithelial Function, T-Cell Exhaustion, and Trained Immunity
Immunometabolism
Lung Metabolome After Transplantation
HIV Lung Metabolome
Microbiota-Mediated Diseases: PGD, CLAD, Lung Infection, and Emphysema
Primary Graft Dysfunction (PGD)
CLAD
Pneumonia and TB
COPD and HIV
Inflammation and Aging
Conclusion
References
Chapter 11: The Microbiome in Acute Lung Injury and ARDS
Acute Lung Injury and the Clinical Syndrome of ARDS
The Microbiome Hypothesis in ARDS
Sampling Lung and Gut Microbiota in ARDS
Respiratory Tract Microbiota in Patients with ARDS
Studies Exclusively in Patients with ARDS or Examining ARDS as an Outcome
Studies in Mechanically Ventilated Patients with or at-Risk for ARDS
The Gut Microbiome in Patients with ARDS
Animal Model Studies for the Role of Microbiota in Acute Lung Injury
Putting Everything Together: The Microbiome Matters in ARDS
Unanswered Questions and Future Research
References
The Future: Knowledge Gaps and Priorities
References
Index
