Fig. 4: Strain-level FMT outcomes vary between species but are predictable ex ante.

a, Strain-level outcomes for selected species are shown for conspecific FMT triads—that is, time series where the focal species was present in both donor and recipient pre FMT. Outcomes are scored as recipient strain persistence (dominance by recipient strains, yellow), donor takeover (blue), donor–recipient coexistence (orange) or influx of novel or previously undetected strains (purple), as indicated in the schematic on the left. Each dot corresponds to one scored FMT. b, Stacked bars representing outcomes for each species across scorable FMTs, scaled to the number of FMTs where the species was observed in the recipient following the intervention. Dashed lines indicate averages for recipient strain persistence within taxonomic groups (x axis). Outcome frequencies across all species are summarized on the left. c, Frequency of colonization by donor or novel (previously undetected) strains per species, as subsets of the data in b. Averages per taxonomic group are represented by dotted lines. d, Prediction accuracies of LASSO models for different binarized FMT outcomes (indicated on the left; Methods) as AUROC, averaged across cross-validation folds per species.