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All studies involving human microbiomes, published in the English language, and using the search terms \u201cCOPD\u201d, \u201cChronic Obstructive Pulmonary Disease\u201d, \u201cBronchiectasis\u201d, \u201cBCO\u201d or \u201cBronchiectasis and COPD overlap\u201d, AND \u201cmicrobiome\u201d, \u201cmycobiome\u201d or \u201cmetagenomics\u201d were included.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Despite variability in sampling methods and specimen types used, microbiome composition remains relatively comparable in COPD and bronchiectasis with prominence of Proteobacteria, Firmicutes and Bacteroidetes. Alterations to airway microbiomes occur in association to disease severity and\/or exacerbations in COPD and bronchiectasis. Decreased alpha diversity and <jats:italic>Haemophilus<\/jats:italic>\u2010predominant microbiomes are associated with poorer survival in COPD, while, in bronchiectasis, <jats:italic>Pseudomonas\u2010<\/jats:italic>predominant microbiomes demonstrate high exacerbation frequency and greater symptom burden while <jats:italic>Aspergillus<\/jats:italic>\u2010dominant mycobiome profiles associate with exacerbations. The role of the microbiome in BCO remains understudied.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Use of next\u2010generation sequencing has revolutionised our detection and understanding of the airway microbiome in chronic respiratory diseases such as COPD and bronchiectasis. Targeted amplicon sequencing reveals important associations between the respiratory microbiome and disease outcome while metagenomics may elucidate functional pathways. 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