Methods in Lung Microbiome Research

The lung microbiome is associated with host immune response and health outcomes in experimental models and patient cohorts. Lung microbiome research is increasing in volume and scope; however, there are no established guidelines for study design, conduct, and reporting of lung microbiome studies. St...

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Published inAmerican journal of respiratory cell and molecular biology Vol. 62; no. 3; pp. 283 - 299
Main Authors Carney, Sharon M., Clemente, Jose C., Cox, Michael J., Dickson, Robert P., Huang, Yvonne J., Kitsios, Georgios D., Kloepfer, Kirsten M., Leung, Janice M., LeVan, Tricia D., Molyneaux, Philip L., Moore, Bethany B., O’Dwyer, David N., Segal, Leopoldo N., Garantziotis, Stavros
Format Journal Article
LanguageEnglish
Published United States American Thoracic Society 01.03.2020
Subjects
Animals
Anti-Infective Agents - pharmacology
Bacterial Typing Techniques
Body Fluids - microbiology
Breath Tests
Clinical trials
Dysbiosis - microbiology
Environmental Exposure
Epidemiologic Methods
Host Microbial Interactions
Humans
Immune response
Lung - microbiology
Lung cancer
Lungs
Metagenomics - methods
Microbiological Techniques
Microbiomes
Microbiota - drug effects
Models, Animal
Models, Biological
Reproducibility of Results
Research methodology
Respiratory System - microbiology
Specimen Handling - methods
Sputum - microbiology
Translational Research, Biomedical
Translational Review
Whole Genome Sequencing
lung
analysis
microbiome
methods
reporting
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Summary:The lung microbiome is associated with host immune response and health outcomes in experimental models and patient cohorts. Lung microbiome research is increasing in volume and scope; however, there are no established guidelines for study design, conduct, and reporting of lung microbiome studies. Standardized approaches to yield reliable and reproducible data that can be synthesized across studies will ultimately improve the scientific rigor and impact of published work and greatly benefit microbiome research. In this review, we identify and address several key elements of microbiome research: conceptual modeling and hypothesis framing; study design; experimental methodology and pitfalls; data analysis; and reporting considerations. Finally, we explore possible future directions and research opportunities. Our goal is to aid investigators who are interested in this burgeoning research area and hopefully provide the foundation for formulating consensus approaches in lung microbiome research.
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ISSN:1044-1549
1535-4989
1535-4989
DOI:10.1165/rcmb.2019-0273TR