Alteration of the chicken upper respiratory microbiota following H9N2 avian influenza virus infection

Several studies have highlighted the importance of the gut microbiota in developing immunity against viral infections in chickens. We have previously shown that H9N2 avian influenza A virus (AIV) infection retards the diversity of the natural colon associated microbiota, which may further influence chicken health following recovery from infection. The effects of influenza infection on the upper respiratory tract (URT) microbiota are largely unknown. Here we showed that H9N2 AIV infection lowers alpha diversity indices in the acute phase of infection in URT, largely due to the family Lactobacillaceae being highly enriched during this time in the respiratory microbiota. Interestingly, microbiota diversity did not return to levels similar to control chickens in the recovery phase after viral shedding has ceased. Beta diversity followed similar trend following challenge. Lactobacillus associate statistically with the disturbed microbiota of infected chickens at acute and recovery phase of infection. Additionally, we study age-related changes in the respiratory microbiota during maturation in chickens. From 7 to 28 days of age, species richness and evenness were observed to advance over time as the microbial composition evolved. Maintaining microbiota homeostasis might be considered as a potential therapeutic target to prevent or aid recovery from H9N2 AIV infection.