Fig. 2

Chicken colon microbiota alpha diversity indices and simple linear regression plots comparing H9N2 infected and uninfected RIR chickens. SPF RIR chickens were challenged with H9N2 AIV A/chicken/Pakistan/UDL01/08. Colon samples were collected at day 0 (pre-challenge), day two, day four and day ten post challenge from H9N2 infected group and non-infected control groups. a The number of observed bacteria taxa (OTUs) in different experimental groups. b Faith's phylogenetic diversity in different experimental groups. c Shannon indices in the different groups. Kruskal Wallis pairwise statistics were used to assess differences in community richness; *p ≤ 0.05. Only statistical differences between the groups at each time point are marked on the graph. The bottom row of linear regression plots shows the change in relative abundance (d), phylogenetic diversity (e), Shannon index (f) from time t to time t + 1 (y-axis) in H9N2 AIV A/chicken/Pakistan/UDL01/08 infected and control groups