Fig. 3. Auto-FMT improves gut microbiota diversity and composition in allo-HSCT patients.

(A) t-SNE plot provides visualization of gut microbiota composition during allo-HSCT. t-SNE plots were constructed from 3237 fecal samples collected from allo-HSCT patients since 2010; the patients were randomized in the auto-FMT trial. The plot shows a large region of high diversity (IS > 4) and clusters of low diversity corresponding to domination by specific bacterial species, for example, Enterococcus and Klebsiella. (B) Each patient followed a unique trajectory in the t-SNE space. The control patients (C) and those receiving auto-FMT treatment (T) were ranked by post-randomization gut microbiota recovery. The patient’s number and the percentage similarity of the gut microbiota to the initial fecal sample are shown. Patients started with a diverse gut microbiota composition, but then many progressed to domination states with loss of diversity due to the impact of antibiotic and chemotherapy administration. The microbiota composition in patients after auto-FMT (patients T1 to T14) moved closer to the initial composition than it did for control patients (patients C1 to C11). (C) Effect sizes of clinical parameters quantified by a mixed-effects model (along with a 95% CI) show that auto-FMT for allo-HSCT patients improved gut microbiota diversity (left-hand plot; P = 5 × 10⁻⁶) and recovery of the original gut microbiota composition (right-hand plot; P = 5 × 10⁻⁶).