Recent evidence suggests microbial composition of the respiratory tract can influence respiratory health and disease. We sought to further elucidate the role of microbial communities in the upper respiratory tract during acute respiratory viral infections and exacerbations of asthma in a pediatric population. We recruited 155 children, ages 4-18 years, during asthma exacerbations (AE) (n=97) or during cold symptoms (CS) without history of asthma (n=58) from the emergency department over 4 years. A nasopharyngeal swab was obtained to provide both RNA for virus identification by viral genome sequencing and DNA for microbial composition by 16S rRNA gene sequencing. LEfSe analysis was performed to determine differences in relative contribution between microbial communities within and between groups. Subjects with AE and viral infection were found to have more abundant communities of Pseudomonadales (Moraxellaceae) (LDA score 5; p<0.05), while those AE without virus were found to have more Bifidobacteriacea (LDA 3; p<0.05). Heat maps of bacterial communities clustered by weighted UniFrac suggest microbial composition initially separates between AE and CS cohorts. However, viral detection noticeably alters the microbial composition and further separates each cohort into those with and without infection. In our pediatric population, the bacterial family Moraxellaceae was most related to AE during viral infections. Furthermore, viral infection was associated with compositional shifts of the microbiota within each cohort (AE and CS). Taken together, our data suggests AEs are increased during a viral infection that happens concurrently with an upper-respiratory tract that is composed of specific bacterial communities, such as Moraxellaceae.