Fig. 2: Microbiota profiles differ across Tanzanians living in rural and urban regions.

ASV-level (a) and genus-level (b) Shannon diversity between study groups. Box plots represent the 25th and 75th percentiles (lower and upper boundaries of boxes, respectively), the median (middle horizontal line), and measurements that fall within 1.5 times the interquartile range (IQR; distance between 25th and 75th percentiles; whiskers). Density plots were used to visualize the distribution of data points. Statistical significance between groups was assessed using linear models with observed richness or Shannon diversity as an outcome, adjusting for vaccination status, age, sex, and sequencing depth. c Principal component analysis (PCA) biplot using CLR-transformed genus-level microbiota features across day 56 samples. Percentages in square brackets denote the total variance explained by the first two principal coordinates. Each data point indicates a stool microbiota sample colored by group (rural/urban living). Ellipses reflect the data spread at a 95% confidence level. Density plots show the distribution of MDS1 (x-axis) and MDS2 (y-axis) scores. The 15 highest ranking genera across all day 56 samples were simultaneously visualized (squares). R² and statistical significance of the association between the group and the overall microbiota composition was assessed using PERMANOVA-test (1,000 permutations), while adjusting for vaccination status, age, and sex. d Bar plots indicating the effect size (R²) of the association between demographic, technical, lifestyle, or food-related variables (or derived scores based on these variables; see Supplementary Fig. 3 and Supplementary Fig. 4) and the overall microbiota composition. Statistical significance was assessed using PERMANOVA-tests. Each variable was tested separately. All analyses were adjusted for living location (except when assessing the impact of lifestyle/food-related variables, helminth infection status or sex), vaccination status, age, and sex.