The use of next generation sequencing has revolutionised our detection and understanding of the airway microbiome in chronic respiratory disease including Chronic Obstructive Pulmonary Disease (COPD) and bronchiectasis. Targeted amplicon sequencing reveals important associations between the respiratory microbiome and disease outcome while metagenomics can elucidate functionality. How best to apply this information into patient care, monitoring and potentially treatment however remains challenging, and this talk summarizes how host and environmental microbiomes may be leveraged for clinical application in the era of precision medicine.