Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in analog hosts

Infection with influenza can be exacerbated by bacterial co-infections, which often results in disease exacerbation because of host responses and cellular damage. The native microbiome likely plays a role, yet the effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. We performed a longitudinal study to assess temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes had stable heathy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibited large changes in bacterial community composition over time and between individuals. Non-healthy ecostates of infected individuals progressed towards the healthy ecostate over time, coinciding with viral clearance. Blooms of Pseudomonas were a statistically associated constant in the disturbed microbiomes. The dynamic and resilient nature of the microbiome during influenza virus infection in multiple hosts provides a potential therapeutic target.