Fig. 2

Diversity of the gut microbiota in healthy subjects, in patients with CD, and in patients with UC. (a–c) Comparisons of the alpha-diversity indices among the three patient groups. The intra-individual bacterial diversity within the samples was measured by determining (a) the abundance-based coverage estimator (ACE) for species richness, (b) Shannon’s evenness index for species evenness, and (c) inverse Simpson’s index for community diversity. The alpha-diversity values for each group are presented as box plots. The lines, boxes, and whiskers in the box plots represent the median, 25th and 75th percentiles, and the minimum-to-maximum distributions of replicate values, respectively. (d–e) PCoA, based on the (d) unweighted and (e) weighted UniFrac distance matrix, of the bacterial 16 S rRNA gene sequence data for fecal samples from healthy subjects (n = 117), patients with CD (n = 223), and patients with UC (n = 300). (f–g) Differences in alpha diversity according to disease behavior types (inflammatory, stricturing, and penetrating) in the CD group are presented as (f) richness and (g) evenness. (h) PCoA, based on the weighted UniFrac distance matrix, of the bacterial 16 S rRNA gene sequence data for fecal samples is shown according to the disease behavior types (general vs. advanced types) in patients with CD (n = 223). The data were analysed using the Kruskal-Wallis test (a, b, c, f, and g) and PERMANOVA, with 999 permutations (d–e) to obtain the statistical significance. CD, Crohn’s disease; UC, ulcerative colitis; PCoA, Principal coordinate analysis; CD-Inflammatory, inflammatory type of CD; CD-Stricturing + Penetrating, stricturing and penetrating types of CD.