Supplementary file 1_Impact of Avibacterium paragallinarum infection on the upper respiratory tract microbiome of chickens.docx

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.</p>