Fig. 2

A Relative abundance (%) showing the top 10 species per group over time from week 1 up to year 2, where time is in weeks. B Plots show differential abundance analysis using Songbird with VDnoab group as reference run using the formula C(Group, Treatment('VDnoab')). The plot on the left side corresponds to the CSnoab group as treatment while that on the right depicts the CSab group as treatment against the reference group. In both cases, negative values (blue bars) represent the association to the reference group (here VDnoab) while positive values (red bars) represent the association to the treatment group; here CSnoab (on left plot) and CSab (right side plot). C Heatmap representing the association of bacterial abundance with time. Results from Spearman correlation analysis using the relative abundance of species for each group to time-point. P values were adjusted using BH, those < 0.05 were considered significant, and corresponding species and their coefficients were plotted. In the plot, blue bands denote decreasing with time (negative coefficient), red bands denote positive coefficient which means increasing over time, while grey means NA denoting not detected significantly as top 10 in that group