Fig. 1. Short-term diet alters the gut microbiota.

Ten subjects were tracked across each diet arm. (A) Fiber intake on the plant-based diet rose from a median baseline value of 9.3±2.1 to 25.6±1.1 g/1,000kcal (p=0.007; two-sided Wilcoxon signed-rank test), but was negligible on the animal-based diet (p=0.005). (B) Daily fat intake doubled on the animal-based diet from a baseline of 32.5±2.2% to 69.5±0.4% kcal (p=0.005), but dropped on the plant-based diet to 22.1±1.7% (p=0.02). (C) Protein intake rose on the animal-based diet to 30.1±0.5% kcal from a baseline level of 16.2±1.3% (p=0.005) and decreased on the plant-based diet to 10.0±0.3% (p=0.005). (D) Within-sample species diversity (α-diversity, Shannon’s Diversity Index), did not significantly change during either diet. (E) The similarity of each individual’s gut microbiota to their baseline communities (β-diversity, Jensen-Shannon distance) decreased on the animal-based diet (dates with q<0.05 identified with asterisks; Bonferroni-corrected, two-sided Mann-Whitney U test). Community differences were apparent one day after a tracing dye showed the animal-based diet reached the gut (blue arrows depict appearance of food dyes added to first and last diet day meals; Extended Data Fig. 3a).