Fig. 5

The dynamic changes in the gut microbiota before and after treatment in the capsule group. A Phylum level changes between the healthy donors and patients with CD at various time points. B Alpha diversity indices (Chao1, ACE, Shannon and Simpson) changes between the healthy donors and patients with CD at various time-points. There was a significant reduction in the alpha diversity in patients in the FMT 0W group compared with donors and patients in the FMT 10W group (Kruskal–Wallis H test, P < 0.001, with *P < 0.05, **P < 0.01, ***P < 0.001). C Principal coordinate analysis (PCoA) comparisons of the microbial communities between the healthy donors and patients with CD at various time-points. The FMT 10W and donor samples were significantly clustered together than the FMT 0W samples. D Comparison of the Gut Microbiome Health Indices (GMHIs) in the different groups. The GMHIs of patients in the FMT 0W group were significantly lower than those of the healthy donors and patients in the FMT 10W group (Wilcoxon signed-rank test, P < 0.001). E Comparison of the microbial dysbiosis index (MDI) in the different groups. The MDI of patients in the FMT 0W group was significantly lower than that of the healthy donors and patients in the FMT 10W group (Wilcoxon signed-rank test, P < 0.001). HD: healthy donor; FMT 0W: before treatment; FMT 5W: at week 5 after oral capsule treatment; FMT 10W: at week 10 after oral capsule treatment