Respiratory syncytial virus subtype influences pediatric airway microbiome independent of viral burden

Background Respiratory syncytial virus (RSV) is the main cause of severe lower respiratory tract infections in infants and young children. Multiple studies have demonstrated that respiratory microbiome composition is strongly associated with susceptibility to viral infection, disease severity, and subsequent respiratory outcomes. However, it is still unclear how different RSV subtypes affect the respiratory microbiome. Results In this study, we examined the airway microbiome in children infected with RSV-A (n = 18) or RSV-B (n = 12) and compared them with recovered individuals (n = 7) using full-length 16S rRNA gene sequencing. We found 598 bacterial genera across 39 phyla in 37 samples, with Bacillota , Pseudomonadota , and Actinomycetota being the most common. While overall microbial diversity stayed stable during infection, RSV changed the makeup of the microbial communities, suggesting that infection mainly reorganizes ecological relationships rather than reducing the number of bacterial types. Our analyses showed that the microbiome differed by RSV subtype (PERMANOVA R² = 0.249, P  = 0.016), with RSV-A samples showing more variation than RSV-B. Differential abundance analysis revealed that RSV-A caused greater changes in the microbiome, with 81 affected genera compared to 31 in RSV-B. Viral load did not have a noticeable effect on microbiome structure, as C _t values explained only 1.8% of the variation (R² = 0.018, P  = 0.776). Despite these changes, a core group of 45 bacterial genera was found in all groups, including RSV-A, RSV-B, and recovered individuals. Conclusions Our results indicate that RSV subtype is a key factor shaping the respiratory microbiome, more so than viral load, and leads to distinct microbial patterns in the pediatric airway. These findings highlight a previously unrecognized aspect of RSV infection and suggest that differences between subtypes may affect disease progression, immune response, and clinical outcomes.