Fig. 3: Diet-induced changes in alpha and beta diversity across the three diet groups.

Alpha and beta diversity of the microbiota (A), ARGs (B), VGs (C), and MGEs (D) were accessed before and after switching from a normal diet to a high-fat or high-fiber diet. Data are presented as median with IQR in box plots; horizontal lines within the boxes represent the firstquartile, median, and third quartile, respectively. Whiskers represent the range of values within the first quartile—1.5× the interquartile range and the third quartile + 1.5× the interquartile range. The Wilcoxon rank sum test was used to detect significance in Shannon index differences, with ^*p < 0.05, ^**p < 0.01, ^***p < 0.001, and NS no significance. Circles represent the 95% confidential interval for the corresponding group in beta diversity, with significant differences detected using PERMANOVA (permutations = 999).