Fig. 3

The effect of antibiotics on the porcine gut microbiome. The microbiome of each sample was evaluated by sequencing of the V3V4 region of the rRNA gene. a All samples of the study coloured by sampling time. Weeks marked with * in the legend are not included in the other panels due to under-sampling. b–h Animals were stratified at each time point into untreated (black) and antibiotic treated groups (red). Significance was evaluated by PERMANOVA at each time point adjusting for pen and variance described by treatment status is represented by the R²-value and corresponding p-value. Ellipses represents the 95% standard error of the centroids of each group. All panes are represented by the first and second nMDS-axis. Since the axes of nMDS are arbitrary, they are removed for brevity