Applying ecological theories in research: lessons learned from microbial ecology and evolution?

The persisting dogma that the healthy human lung is sterile led to neglect of the lung microbiome for a long time and it is only recently that it has been acknowledged as an issue. Culture-independent methods have shown that a diverse microbial community is present in the lung of healthy individuals and that it harbours important functional traits. However, as in the whole field of human microbiome research, empirical work is lagging far behind the overwhelming amounts of data produced as a result of advances in NGS techniques. Adaptations of classical models and theories from ecology and evolution might help to close this gap and provide the basis for directed, theory-driven (lung) microbiome research in health and disease. In this chapter, we will provide some ecological theories that are widely applied in microbial ecology and discuss their relevance for future lines of research in lung microbiome research.