Baseline gut microbiome diversity and dissimilarity. (A) Shannon Diversity Index of fecal samples at baseline. Violin plots show the distribution of the Shannon diversity index. The dot with line represents the estimated marginal mean of the linear regression analysis. (B) Beta diversity depicted using principal coordinates of Aitchison distance for species and (C) for functional pathways. Individual data points are represented by light blue dots for the patients not needing therapy intensification and dark blue dots for the patients needing therapy intensification. The large dot represents the centroid, which represents the mean composition of each group.