Extended Data Fig. 5: Comparative Analysis of IgA-Bound Bacteria and Microbiome Shifts Post-Dietary Intervention.

A) Boxplots comparing the overall fraction of bacteria bound by IgA in native samples (as assessed by bacterial flow cytometry) in baseline samples versus after dietary intervention of increased consumption of fermented foods (left) or fibre (right). Lines connect samples from the same subjects over time. P-value from Wilcoxon signed-rank test. For fermented and fibre groups, n = 4, 7; p = 0.25, 0.38, respectively. B) Violin plot of weighted UniFrac distance between the same subjects in baseline vs. intervention samples (top) and weighted UniFrac distance between different subjects (bottom; this represents the UniFrac distances between samples taken from unrelated subjects at either timepoint). P-values from comparing the distribution of IgA+ vs native weighted UniFrac distances using two-sided Wilcoxon rank-sum test; n = the number of comparisons considered in each the IgA+ and native fractions. C) Principal component analysis of weighted UniFrac distance between all metagenomes in this study. Lines connect native and IgA+ metagenomes from the same stool sample. D) Violin plot comparing the weighted UniFrac distance between samples from the same subjects (top) and the absolute abundance of the difference in the total fraction of bacteria bound by IgA (bottom). Normalization of differences performed using min-max scaling prior to comparison. P-value from two-sided Wilcoxon signed-rank test. Boxplots show the minimum and maximum (whiskers), median (center line), and interquartile range (box bounds); whiskers extend up to 1.5 times the interquartile range.