Figure 3.
Depletion of E. coli induced dynamic changes in gut microbiota
Gut microbiota were profiled using absolute quantification of 16S rRNA amplicon sequencing at baseline (day 0) and 4, 8, and 14 days after a gavage of killed (control group) or T7 phage (T7H).
(A–C) Shannon, Simpson, and Chao1 indices of alpha diversity of gut microbiota calculated by amplicon sequence variant at four time points in each group of mice (n = 12 for each group; data displayed as mean ± SD). p values for the comparisons of alpha diversity between two groups of mice at same time point or between different time points within same mice group are calculated via repeated-measures ANOVA.
(D) Principal-coordinate analysis (PCoA) based on Bray-Curtis metrics was conducted at four time points in each group of mice (n = 12 for each group). p values for the comparisons of overall microbial community composition between two groups of mice at same time point are calculated by permutational multivariate ANOVA using distance matrices.
(E) The abundance changes of 24 bacterial genera that are regulated by T7 phage and significantly change over time are shown in two heatmaps: left for control group, and right for T7 group (n = 12 for each group). Four blocks for each bacterium indicate four time points. The color represents the change fold of absolute abundance in contrast to that at baseline.