Fig. 2: Global gut microbiome profiling and engraftment after FMT.

a–h, Species-level Shannon diversity of donor samples (n = 20) at the time of donation and longitudinal patient samples (n = 93) from 20 patients with and without grade 3 irAEs (a) and 18 responder (R) and non-responder (NR) patients (b). One-way ANOVA was used to compare diversity across clinical subgroups at each timepoint, followed by Tukey’s HSD test for pair-wise comparisons. Adjusted P < 0.05 values for multiple testing are shown. Variability is normalized to baseline Bray−Curtis dissimilarity to their respective donor between patients with (n = 10) and without (n = 10) grade 3 irAEs (c) and between R (n = 9) and NR (n = 9) patients (d). Each line represents one patient. Mean and s.e.m. are represented. Statistically significant within-group comparisons from baseline to later timepoints, as well as between groups at T4 and T5, are shown. P values were calculated using the paired t-test or Wilcoxon rank-sum test (based on Shapiro−Wilk test) with FDR correction for within-group comparisons and between-group comparisons. Variability of strain engraftment rate (the number of engrafted strains after FMT divided by the number of strains that could engraft from the donor) over time between patients with (n = 10) and without (n = 10) grade 3 irAEs (e) and between R (n = 9) and NR(n = 9) patients (f). Each dotted line represents one patient. Mean and s.e.m. are represented. Statistically significant within-group comparisons from baseline to later timepoints, as well as between groups, are shown. Two-sided P values were calculated using the Wilcoxon rank-sum test with FDR correction.***P < 0.001. PCoA representing Bray−Curtis β-diversity of baseline (g) and 10 weeks after FMT samples in patients with and without grade 3 irAEs (h). Two-sided P values were calculated using the PERMANOVA test. Box plot bounds represent the 25th and 75th percentiles, with the central line representing the median and the whiskers representing the maximum or minimum values within 1.5× interquartile range. Points outside this range are shown as outliers.