Impact of Avibacterium paragallinarum infection on the upper respiratory tract microbiome of chickens

Abstract

Avibacterium paragallinarum, the causative agent of infectious coryza, causes infection in the upper respiratory tract (URT) of chickens, leading to substantial economic losses. While respiratory pathogens are known to disrupt host-associated microbiomes, A. paragallinarum’s impact on the chicken URT microbiome remains poorly understood. This study characterized microbiome changes in chicken URT following A. paragallinarum infection and examined whether different field strains induced distinct alterations. Four field strains were used to challenge separate groups of four-week-old specific-pathogen-free chickens, with one uninfected control group. Choanal swabs were collected at multiple time points post-challenge, pooled by group, and subjected to 16S rRNA V3-V4 amplicon sequencing. Microbial composition and diversity were characterized and compared among groups. Because of the limited biological replicates, statistical analyses and associated p-values were interpreted as exploratory. The URT microbiome was initially dominated by Firmicutes, followed by Proteobacteria, with the latter showing an increasing trend during infection. Infected group exhibited lower microbial richness compared to the noninfected based on the Chao1 index (p = 0.03175) and observed ASVs (p = 0.03372), with richness reaching the lowest level at 4 days post-inoculation (dpi) and returning to baseline by 9 dpi. Microbial community composition differed between infected and noninfected groups based on unweighted UniFrac distances (p = 0.027, PERMDISP ns). No differences in microbial diversity measures were observed among the individual strain groups. The findings suggest that A. paragallinarum infection is associated with transient yet notable alterations in microbial richness and community composition in URT, even in absence of overt clinical signs.