Fig. 5

Changes over Time. Changes in relative abundances over time of the genera Haemophilus, Neisseria, Staphylococus and the bacterial species H. parainfluenzae, Neisseria subflava and Staphylococcus aureus. Strong trends towards increases in the relative abundance of the bacterial genera Haemophilus (raw p-value = 0.0041, false discovery rate (FDR) 0.178) and Neisseria (raw p-value = 0.0049, FDR 0.178) were observed, as well as a weaker trend towards increases of the bacterial genus Staphylococcus (raw p = value 0.0749, FRD 0.518). Analysis on species level revealed trends toward increases of Haemophilus parainfluenzae (raw p-value = 0.0098 FDR = 0.12), Neisseria subflava (raw p-value = 0.012 FDR = 0.12), Staphylococcus aureus (raw p-value = 0.0856 FDR = 0.245) during infection. Plots represent mean ± SEM