For infected birds, relative abundances of bacterial phyla at the two sampling time points carried out post infection are represented in Figure S1B, Tables S4A–D. Figure 1 shows that the phylum Proteobacteria decreased while Firmicutes increased at either 21 (7 dpi) or 28 days of age (14 dpi). There was a significant decrease in Actinobacteria and Proteobacteria in the jejunal mucosa at 14 dpi (P = 0.006; q = 0.100 and P = 0.005; q = 0.100), while Firmicutes and Bacteroidetes were more abundant in the infected birds compared to the controls (P = 0.005; q = 0.100 and P = 0.023; q = 0.217, Table S4A). However, in the cecal content and cecal mucosa, Bacteroidetes (P = 0.001; q = 0.019) increased at 7 dpi, but decreased (P = 0.002; q = 0.026 and P = 0.005; q = 0.048) at 14 dpi in the infected birds compared with the controls, indicating that the Campylobacter infection modulates the jejunal and cecal phylum abundances in different ways.