Figure 4

Alpha diversity of pig fecal samples. Comparison of Shannon diversity index scores were shown for weeks 3, 8 and 12 in panels A, B and C respectively. The alpha diversity metrics were calculated using the entire amplicon sequence variant dataset. The lines inside boxes represent the mean and superscripts with different letters are significantly different from each other (p <  0.05). Comparison of Shannon diversity indices among piglets from different litters (Black: L0, orange: L1, blue: L2, red: L3, maroon: L4, yellow: L5) were performed using one-way ANOVA and Tukey’s test was used to perform post hoc comparisons. Litters were represented in sequential numbers 0–5. L0 included uninoculated control piglets. Litters 1–5 included all M. hyopneumoniae experimentally inoculated piglets. Piglets from L3 and L5 showed the least LS, whereas those from L2 and L4 showed the highest LS.