Figure 5.

Alpha and Beta diversity, and taxonomy results of the intestinal microbiome (mice experiment). (A) Alpha diversity (OTUs level) of the intestinal microbiome from the 4 groups: Control-day 1, SC-day 10, FSS-day 10 and FMS-day 10. Three indices were considered: Fisher alpha (a parametric index that models species’ abundance as logseries distribution), richness (number of species) and Shannon index (a widely used index that considers species’ abundance and evenness). Pair-wise ANOVA was calculated between the groups and if significant, stars are shown on top (* p < 0.05, ** p < 0.01 and *** p < 0.001). (B) Beta diversity results; (B1) Principal Co-ordinate Analysis (PCOA) showing clustering of samples. The chart was produced using unweighted UniFrac (UniFrac) at OTUs level. Ellipses are 95% confidence interval of standard error. The table in (B2) summarises PERMANOVA results for all the distances, Bray-Curtis, unweighted UniFrac (U. UniFrac) and weighted (W. UniFrac). R2 refers to the percentage of variability among samples’ microbiome that can be explained by that factor/metadata. (C) Taxonomy summary for stool at phylum level. (D) Taxa differential analysis at phylum, order and genus levels are presented through bar charts; these show Log2 fold change between the groups compared, (y axis on the left and dark grey bar) and the mean abundance across all the samples (y axis on the right and light grey bar), details of the comparisons per chart are in the right bottom of the chart. Detail of taxa differential analysis results, including p values and adjusted p values, is in Supplementary Table S3. FS = ferrous sulphate and FM = ferric maltol.