Acute asthma exacerbations cause significant morbidity and healthcare burden. Up to 60% of acute exacerbations are associated respiratory viruses, particularly human rhinoviruses. The role of bacteria in acute exacerbations is unclear yet antibiotics are frequently prescribed. Recent studies revealed a greater abundance of potentially pathogenic bacteria (e.g. Haemophilus spp.) within the airway microbiota in asthma, whilst a greater abundance of commensals (e.g. Prevotella spp.) were observed in health. The current project examined the dynamics of the airway microbiota in the context of a virus-induced asthma exacerbation. The airway microbiota was assessed in a cohort of mild/ moderate asthmatic subjects. Sputum samples were obtained at baseline and following naturally-occurring cold and underwent 16S rRNA gene sequencing. During acute cold, increased relative abundance of Neisseria sp. (Neisseria_2974) significantly correlated with greater peak flow (PEF) decline and IL-1b level. In contrast, Prevotella and Veillonella sp. (Veillonella_10839) relative abundances correlated with reduced PEF decline and lower IL-1b and IL-8 levels respectively. To validate these findings and evaluate the impact of human rhinovirus on the airway microbiota, a cohort of moderate asthmatic and healthy subjects were experimentally infected with rhinovirus-16. Bronchoalveolar lavage was obtained at baseline and at two time-points post infection. The microbiota community between asthmatic and healthy subjects did not differ significantly at baseline or post rhinovirus-16 infection. Following rhinovirus-16 infection, increased Neisseria_2074 relative abundance again correlated with greater PEF decline whilst increased Prevotella relative abundance correlated with reduced clinical symptoms. Furthermore, rhinovirus-16 viral load exhibited a significant linear relationship with the extent of microbiota community change, suggesting that severity of rhinovirus-16 infection may directly impact on the microbiota. In conclusion, an imbalanced airway microbiota was associated with greater PEF decline and pro-inflammatory cytokine levels during a virus-induced asthma exacerbation, though the precise role of the microbiota remains to be determined.