Community ecology: the framework for next steps in microbiome research in chronic airway disease

<title>Extract</title> Publications on the human respiratory microbiome have increased exponentially over the last decade, encompassing studies of the upper and lower airways in both children and adults. Collectively, these investigations have established a crucial knowledge base of microbes detectable by culture-independent methods across different airway niches. Given the intricacies of the upper respiratory tract and conducting airways before they terminate in the lungs, this knowledge largely reflects what has been most accessible to sample and study at scale. While important knowledge gaps remain, including the underexplored role of fungi (the mycobiome) and viruses (virome), we now have a general sense of what disease-associated airway microbiota “look like”. Compositionally, these communities often feature increased prevalence of members from taxonomic groups with pathogenic potential (<italic>e.g.</italic> the genera <italic>Pseudomonas, Haemophilus, Moraxella, Streptococcus,</italic> and <italic>Staphylococcus</italic>) [1–6]. In some studies, species-level identification has been possible depending on methodology. However, most studies focus on participants with already established or advanced lung disease, leaving much to be learned about how airway microbial ecology shifts and contributes to disease in its earlier stages.