Cloacal swab sample from waterfowl Raw sequence reads. Cloacal swab samples from waterfowl

Waterfowl, especially ducks of the genus Anas, are natural reservoir species for Influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAV subtypes and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. In this study, we investigate those and additional mallards plus four more species of Anas ducks to ask whether all the duck species have similar IAV positive and IAV negative cloacal microbiomes or if the relationship between a host, influenza and the microbiome is species specific.