a, Bubble plots show a similar pattern in fecal (n = 8 mice in healthy group, n = 9 mice in CMA group, with fecal samples collected at 2 and 3 weeks post-colonization, same as in Fig. 2a) and ileal samples (n = 22 mice in healthy group, n = 25 mice in CMA group) from healthy- and CMA-colonized mice; 58 OTUs significantly differentially abundant between CMA and healthy donors are shown in the same order as in Fig. 2a. The size of the circle indicates the magnitude of relative abundance enrichment towards either CMA or healthy. Color intensity indicates the statistical significance computed using the DS-FDR permutation test (see Online Methods). b,c, The healthy versus CMA OTU abundance ratio is significantly correlated between mouse fecal and ileal samples. Each dot represents one individual OTU. For b, for each OTU, its average abundance was calculated at the group level among 8 healthy-colonized and 9 CMA-colonized mice for the fecal samples, and among 22 healthy-colonized and 25 CMA-colonized mice for the ileal samples. The ratios of OTU abundance in the feces are plotted on the x axis with the ratio of OTU abundance in the ileum on the y axis. For c, n = 35 (15 healthy-colonized and 20 CMA-colonized) mice collected from at least 2 independent experiments were used for the calculation of both the fecal and ileal OTU abundance ratio, where fecal and ileal samples were collected from the same individual mice. For further details, see the Online Methods.