Aims : To summarize what is currently known on the microbiome and its influence on health and disease with special attention to lung diseases, from infancy, priming into malfunction of the microbiome in diseases such as allergic diseases, asthma, cystic fibrosis (CF) and later into COPD exacerbations; to highlight studies of early colonisation and microbiome formation into assessing possible intervention strategies to reach a healthy balance of microbial colonization, also important for allergy prevention; to take a critical view on current treatment strategies and stressing the influence of microbial dysbiosis as a feature of some exacerbations in chronic airway diseases such as asthma, CF and COPD.