1. Methods in Lung Microbiome Research
- Author
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Stavros Garantziotis, Leopoldo N. Segal, Robert P. Dickson, Janice M. Leung, Tricia D. LeVan, Georgios D Kitsios, Philip L. Molyneaux, Jose C. Clemente, Yvonne J. Huang, David N O'Dwyer, Sharon M. Carney, Bethany B. Moore, Kirsten M. Kloepfer, and Michael J. Cox
- Subjects
Microbiological Techniques ,0301 basic medicine ,Pulmonary and Respiratory Medicine ,Lung microbiome ,analysis ,Respiratory System ,Clinical Biochemistry ,microbiome ,Health outcomes ,Models, Biological ,Rigour ,Specimen Handling ,lung ,methods ,Translational Research, Biomedical ,03 medical and health sciences ,0302 clinical medicine ,Anti-Infective Agents ,microbiome, lung, reporting, analysis, methods, review ,Animals ,Humans ,Microbiome ,1102 Cardiorespiratory Medicine and Haematology ,Molecular Biology ,reporting ,Host Microbial Interactions ,Whole Genome Sequencing ,Microbiota ,Sputum ,Reproducibility of Results ,Environmental Exposure ,Cell Biology ,Research opportunities ,Data science ,Bacterial Typing Techniques ,Body Fluids ,Translational Review ,030104 developmental biology ,Breath Tests ,030228 respiratory system ,Models, Animal ,Dysbiosis ,Metagenomics ,Epidemiologic Methods ,Psychology - Abstract
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 will hopefully provide the foundation for formulating consensus approaches in lung microbiome research.
- Published
- 2020
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