Recent studies of the microbiome propose that resident microbes play a beneficial role in maintaining human health, as they could either stimulate the host immunity or directly complete with invading pathogens. Lower respiratory disease (pneumonia, lung cancer) is a leading cause of sickness and mortality. However, most previous studies on lung microbiome were based on 16S ribosome RNA sequencing; the viability and functionality of the microbiome, as well as its interaction with host immune systems, has not been well-studied.  Recently, Li Mingkun’s group analyzed 34 bronchoalveolar lavage fluid samples using metatranscriptome data and assessed the association between the lung microbiome and microbial gene expression, host gene expression, cytokine concentration and over 20 clinical features. Intriguingly, they found a stratified structure of the lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response and COPD exacerbation frequency. These observations support an active host-microbial interaction in the lung, thus suggest that the microbiome plays a significant role in lung homeostasis. Diversity of the lung microbiome may partially account for the variation in susceptibility to particular diseases as well as different responses to specific treatments. Thus, the lung microbiome could be a potential biomarker for assessing lung health and targets for medical intervention. The results were published in an American Society for Microbiology journal mSystems and recommended as “Editor’s Pick”. Link to the article: https://msystems.asm.org/content/3/5/e00199-18.