Abstract
Influenza A viruses (IAV) are highly contagious respiratory pathogens responsible for several global pandemics. Typically classified into subtypes by its envelope proteins hemagglutinin (HA) and neuraminidase (NA), individual IAV HA and NA subtypes are often aggregated into two larger groups per protein based on phylogeny, used to predict the pathogenicity of a particular virus. Importantly, mallard ducks are major IAV reservoirs, contributing to zoonotic transmission to humans. Research has observed IAV-induced changes in cloacal microbiome composition within mallards; however, the effects of viral subtypes remain largely uncharacterized. This research seeks to characterize these HA and NA phylogenetic subgroup effects, evaluate how they differ from one another, and predict phylogenetic subgroups of infections. 16S rRNA sequencing data from cloacal microbiomes of uninfected and IAV-infected mallards were used to explore this. Alpha- and beta-diversity, differential abundance, indicator taxa, and predicted functional potential analyses supported previous findings of IAV-induced changes to cloacal microbiome composition and function respectively, but showed no significant differences among either HA or NA phylogenetic subgroups. Consequently, RandomForest predictive models–trained to predict HA or NA subgroup of infection using samples’ genera abundances–exhibited weak predictive power. Altogether, these findings suggested that the effects of IAV infection on the cloacal microbiomes of mallards were independent of HA and NA phylogenetic subgroups. With a persisting lack of understanding of different IAV HA and NA proteins’ effects on host microbiomes, this research highlights the importance of further examining IAV viral proteins and their effects on host microbiomes.