Fig. 3: Comparison between the donors.

a Negative correlation between donor microbiota engraftment and pre-FMT alpha diversity as measured by Shannon’s index. The correlation coefficient and P value (0.0001) are from a Spearman’s correlation test. b Donor microbiota engraftment at the species level, defined as the percentage of post-FMT species that were shared exclusively between the post-FMT sample and FMT product. These species were absent in pre-FMT and baseline patient samples. The P value is from a Kruskal–Wallis test. Data from 5, 6, and 6 patients treated with FMT from donors 1, 2, and 3 are included, respectively. c Donor microbiota engraftment at the species level, adjusted for pre-FMT microbiota diversity and FMT donor/patient sex match status. The results are from a linear regression model, where engraftment was the outcome variable, donor number was the main predictor, and pre-FMT microbiota diversity (measured by Shannon’s index) and FMT donor/recipient sex concordance (yes vs. no) were the covariates. Donor-specific regression residuals are plotted. The P values are from the regression model; they are two-sided, correspond to the donor term (comparing donor 3 to donors 1 and 2), and indicate the unadjusted significance of pairwise comparisons between donors. Data from 5, 6, and 6 patients treated with FMT from donors 1, 2, and 3 are included, respectively. d Post-FMT microbiota alpha diversity as measured by Shannon’s index. The P value is from a Kruskal–Wallis test. Data from 5, 6, and 6 patients treated with FMT from donors 1, 2, and 3 are included, respectively. e Relative reduction in patient-donor Aitchison’s distance from pre- to post-FMT. The P value is from a Kruskal–Wallis test. Data from 5, 6, and 6 patients treated with FMT from donors 1, 2, and 3 are included, respectively. f Donor microbiota engraftment at the strain level, defined as the percentage of post-FMT strains that were shared exclusively between the post-FMT sample and FMT product. These strains were absent in pre-FMT and baseline patient samples. The P value is from a Kruskal–Wallis test. Data from 5, 6, and 6 patients treated with FMT from donors 1, 2, and 3 are included, respectively. g Negative correlation between donor microbiota engraftment and compositional similarity between post-FMT and donor microbiota. The correlation coefficient and P value are from a Spearman’s correlation test. h Per-species strain-level donor microbiota engraftment. Species present in at least 25% of post-FMT samples were included. Species that were not present in the donor used for the patient were not included because engraftment could not occur (by definition). The results for all species irrespective of the 25% prevalence threshold are provided in Supplementary Data 1. Numbers in the right column (“Total”) indicate how many times the species was detected in post-FMT samples. Each box in (b–f) shows the median (middle line) and interquartile range. Black circles indicate means. Whisker lines indicate non-outlier maximum and minimum values. A small jitter is included for better visualization. Patient IDs are shown in (a–g) and can be linked to their corresponding donors using data in Fig. 1. FMT fecal microbiota transplantation.