Extended Data Fig. 9: Mutation rates and mutated gene profiles binned by sub-cohort and period relative to weaning.

(A-C) Breadth-and genome-size adjusted popSNP counts by years since seeding (A) for all persisting RGs (n = 255 breastfed-origin persisting MAGs, 359 formula-origin persisting MAGs; P = 0.912, two-tailed Mann-Whitney test), (B) for persisting RGs seeded pre-weaning (n = 125 breastfed-origin persisting MAGs, 192 formula-origin persisting MAGs; P = 0.754, two-tailed Mann-Whitney test), or (C) for persisting RGs seeded post-weaning (n = 130 breastfed-origin persisting MAGs, 167 formula-origin persisting MAGs; P = 0.965, two-tailed Mann-Whitney test), each binned by pre-weaning diet. (D) Mutation rates per persisting RG, binned by seeding in respect to weaning. Non-mutating RGs from each cohort are excluded prior to statistical analysis (n = 225 pre-weaning persisting MAGs, 221 post-weaning persisting MAGs; P < 0.0001, two-tailed Mann-Whitney test). (E) For each RG that persists through weaning, mutation rate calculated from seeding to the last timepoint (TP) before weaning, and mutation rate calculated between the immediate timepoints flanking weaning. RGs that did not accrue any mutations pre-weaning are excluded prior to statistical analysis (n = 45 persisting MAGs, P = 0.0292, two-tailed Wilcoxon matched-pairs test). (F) Pairwise Bray-Curtis dissimilarity between pre-weaning and post-weaning distributions relative to that of each mother, binned by intra- vs. inter-family comparisons (n = 4 infants, 4 mothers; P = 0.63 same vs. different family, pre-weaning, P = 0.72 same vs. different family, post-weaning, two-tailed Kruskal-Wallis test). Boxes represent IQR with median line, and whiskers extend to 1.5xIQR.