The early life microbiome: key to respiratory health?

Microbial colonisation of mucosal surfaces starts at birth and diversifies within the first months of life. This process is driven mainly by niche specificity but also by early environmental exposures, ultimately shaping the composition of the microbiome. The early-life microbiota probably performs important functions, including respiratory tract morphogenesis, pathogen resistance and immune-system development. Microbial dysbiosis or imbalance, instigated by altered exposure to lifestyle factors including antimicrobial treatment, is coupled to a dysregulated immune response, possibly leading to microbial overgrowth, infection and inflammation. Shifts in microbial communities have been associated with the early stages of (respiratory) diseases including acute infection, chronic wheeze and asthma, causing a paradigm shift in our current understanding of disease pathogenesis. Mechanistic insights obtained from animal, in vitro and computational models are slowly starting to highlight key host–microbiome–environment interactions contributing to disease. In the future, a systems science approach integrating microbiome data with host and environment characteristics may contribute to novel interventions to better prevent, diagnose and treat respiratory diseases.