Extended Data Fig. 3: Maternal postpartum microbiome dynamics.

(A) Bray-Curtis dissimilarities between stool samples from different mother (“Between”) and stool samples from the same mother over time (“Within”) (n = 87 maternal stool metagenomes, P = 2.2e-16, two-tailed Wilcoxon test). Boxes represent IQR with median line, whiskers extend to 1.5xIQR. (B) Principal coordinate analysis of maternal samples plotted by Bray-Curtis dissimilarity. Samples are colored by months postpartum. Samples from the same mother are connected. (C) Bray-Curtis dissimilarity between mother-infant dyads over time. Distance of child metagenomes to either the average microbiome pro-file for the respective mother (solid orange), the most recent stool sample from the same mother captured before it (dashed orange), and unrelated mothers at the same timepoint (solid navy blue), plotted over time. Measures of center are a smoothed conditional mean (local polynomial regression), with 95% CI shown in gray.