Fig 3. Ethnicity-associated variation in metagenomic communities and functions.

The gradient of colors denotes variation explained by the variables, and asterisk symbol indicates p-value of PERMANOVA with Bray–Curtis distance that was performed at all combined dietary stages for taxonomy at the strain level, COGs, ARGs, and CAZymes [peptidoglycanase for virome]. adonis2(data ~ Ethnicity + Antibiotic Use + Hormonal Contraceptive, permutations = perm, method = “bray”, by = “margin”), where perm = with (data, how(nperm = 999, blocks = Day)). See S2 Fig for details of functional categories used for assembly-based PERMANOVA. Data underlying this figure can be found at S1 Data. ARG, antibiotic-resistant gene; CAZymes, carbohydrate active enzymes; COG, cluster of orthologous groups; PERMANOVA, permutational multivariate analysis of variance.