Methods in lung microbiome research

Research output: Contribution to journalReview articlepeer-review


  • Sharon M. Carney
  • Jose C. Clemente
  • Robert P. Dickson
  • Yvonne J. Huang
  • Georgios D. Kitsios
  • Kirsten M. Kloepfer
  • Janice M. Leung
  • Tricia D. LeVan
  • Philip L. Molyneaux
  • Bethany B. Moore
  • David N. O'Dwyer
  • Leopoldo N. Segal
  • Stavros Garantziotis

Colleges, School and Institutes

External organisations

  • National Heart and Lung Institute
  • Icahn School of Medicine at Mount Sinai
  • Genomic Medicine
  • University of Michigan Medical School
  • University of Pittsburgh Medical Center
  • Indiana University-Purdue University Indianapolis
  • University of British Columbia
  • University of Nebraska Medical Center
  • Royal Brompton and Harefield NHS Trust
  • New York University
  • National Institute of Environmental Health Sciences (NIEHS)


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.


Original languageEnglish
Pages (from-to)283-299
Number of pages17
JournalAmerican Journal of Respiratory Cell and Molecular Biology
Issue number3
Publication statusPublished - 1 Mar 2020


  • Analysis, Lung, Methods, Microbiome, Reporting