Rationale: Rhinovirus infection is followed by significantly increased frequencies of positive, potentially pathogenic sputum cultures in chronic obstructive pulmonary disease (COPD). However, it remains unclear whether these represent de novo infections or an increased load of organisms from the complex microbial communities (microbiome) in the lower airways. Objectives: To investigate the effect of rhinovirus infection on the airway bacterial microbiome. Methods: Subjects with COPD (n ¼ 14) and healthy control subjects with normal lung function (n ¼ 17) were infected with rhinovirus. Induced sputum was collected at baseline before rhinovirus inoculation and again on Days 5, 15, and 42 after rhinovirus infection and DNA was extracted. The V3-V5 region of the bacterial 16S ribosomal RNA gene was amplified and pyrosequenced, resulting in 370,849 high-quality reads from 112 of the possible 124 time points. Measurements and Main Results: At 15 days after rhinovirus infection, there was a sixfold increase in 16S copy number (P ¼ 0.007) and a 16% rise in numbers of proteobacterial sequences, most notably in potentially pathogenic Haemophilus influenzae (P ¼ 2.7 3 10 -20 ), from a preexisting community. These changes occurred only in the sputum microbiome of subjects with COPD and were still evident 42 days after infection. This was in contrast to the temporal stability demonstrated in the microbiome of healthy smokers and nonsmokers. Conclusions: After rhinovirus infection, there is a rise in bacterial burden and a significant outgrowth of Haemophilus influenzae from the existing microbiota of subjects with COPD. This is not observed in healthy individuals. Our findings suggest that rhinovirus infection in COPD alters the respiratory microbiome and may precipitate secondary bacterial infections.Keywords: rhinovirus; chronic obstructive pulmonary disease; bacteria; microbiome Chronic obstructive pulmonary disease (COPD) is a growing global health epidemic, predicted to be the fourth leading cause of mortality worldwide by 2030 (1). Despite the chronic nature of COPD, acute exacerbations are the major cause of mortality, accounting for almost 70% of health care costs and accelerating the progressive decline in lung function (2). The great majority of exacerbations are caused by respiratory infections with bacteria and viruses, each of which has been detected in about 50% of cases, with coinfection common (3). The concurrent presence of bacteria and viruses during exacerbations of COPD has been shown to be associated with a greater decline in lung function and prolonged hospital stay (3, 4).Current understanding of the interactions between viruses and bacteria in exacerbations of obstructive airway disease is based predominantly upon classical microbial culture techniques. These have suggested that the lower airways are sterile , has therefore supplied the information regarding J.F.'s contribution to the manuscript and his competing interests, and it is correct to the best of her knowledge.The funders had no role in stu...