Supplementary Figure 3.

Engraftment of SER-287 species is dose-dependent and facilitated by vancomycin preconditioning; preconditioned patient microbiome samples become more similar to SER-287 dose composition after rebound from vancomycin. Similarity between a subject’s microbiome and SER-287 dose composition is quantified with a binary Jaccard similarity coefficient of spore-forming species in subject samples and SER-287 doses; the change in similarity for each subject and timepoint is relative to that subjects’ baseline sample (y-axis) across time (x-axis). Black horizontal dashed line indicates the threshold where a subjects’ spore fraction is more (>0) or less (<0) similar to SER-287 post-treatment. Initial preconditioning with vancomycin moves patient samples further from SER-287 dose composition; by day 10 in the vancomycin/SER-287 daily dosing arm, the patient spore-forming microbiome becomes more similar to SER-287 and remains so through the 8-week dosing period (day 56) and the long-term follow-up at day 84 (P < .05, Wilcoxon signed-rank test, all time points); in the vancomycin/SER-287 weekly dosing arm, only the day 56 time point was statistically significant P < .05, consistent with a dose-dependent effect.