Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

The impact of viral infections, on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections. In this study, we show dynamic changes in respiratory and intestinal microbiota over the course of a sublethal IAV infection in a mouse model. Using a combination of 16S rRNA gene specific next generation sequencing and qPCR as well as culturing of bacterial organ content, we found body site specific and transient microbiota responses to influenza infection. In the lower respiratory tract, we observed only minor qualitative changes in microbiota composition. In the small intestine, IAV induced robust depletion of bacterial content, disruption of mucus layer integrity and higher levels of antimicrobial peptides in Paneth cells. By RNAseq approach, we tried to analyze changes in transcriptomics of lung, and small intestine on the day of maximum changes to dissect possible causal players leading to the phentype observed. mock treated (n=3) or influenza A virus infected (n=4) animals are weighted daily, and sacrifised to collect corresponding tissues on 7 days post infection.