Extended Data Fig. 5: Strain and species-level similarity across relationships.

A) Gut microbiome strain sharing rates and species-level similarity metrics (Aitchison similarity, Bray-Curtis similarity, and Jaccard binary similarity) between individuals in the same household (“within household”) as compared to unrelated non-cohabiting individuals in different villages of the same population (“within population”) and individuals in different populations (“interpopulation”). For comparability with strain sharing rates, species-level comparisons are depicted as similarity indices (1 - distance or dissimilarity). All comparisons are significant (Padj<0.05, Kruskal-Wallis tests with Post-hoc Dunn tests, Table S8). The social-distance based gradient followed by strain sharing rates is notably stronger than that observed by species-level similarity metrics (Table S8). Boxes: lower and upper quartiles, middle line: median; whiskers: 1.5 × IQR. B) Oral microbiome strain sharing rates and species-level similarity metrics (Aitchison, Bray-Curtis, and Jaccard binary similarities) between individuals in the same household (“within household”) as compared to unrelated non-cohabiting individuals in different villages of the same population (“within population”) and individuals in different populations (“interpopulation”). For comparability with strain sharing rates, species-level comparisons are depicted as similarity indices (1 - distance or dissimilarity). All comparisons are significant (Padj<0.05, Kruskal-Wallis tests with Post-hoc Dunn tests, Table S28). Boxes: lower and upper quartiles, middle line: median; whiskers: 1.5 × IQR.