FIGURE 3.

The effect of recovery treatments on the gut microbiome after vancomycin. Vancomycin administration was followed by either natural recovery (NR), Bifidobacterium bifidum (PR), or fecal transplants (FT), and changes to the gut microbiome were observed over time. Alpha diversity measured by (A) Shannon Index and (B) Chao1 Index for each treatment over time ± standard error. (C) Bray-Curtis Index of Dissimilarity vs baseline for each treatment over time ± standard error. The Bray-Curtis Index was used to quantify the amount of microbial shift from the first day of the experiment (baseline) for each individual. Colored asterisks indicate significance vs control for NR, PR, and FT groups based on Two-Way rm-ANOVA and Tukey’s HSD post hoc test (*p < 0.05, **p < 0.01, ***p < 0.001). Data for the control samples are indicated as the black dotted line, with NR (V) groups in red, PR (VB) groups in green, and FT (VF) groups in blue. (D) The microbial community at each time point at the phylum level for (a) control, (b) V, (c) VB, and (d) VF. (E) Heat map of taxa that significantly changed after antibiotic administration. Significant taxa were identified using factor analysis (factor loading >0.4). The lowest taxonomic rank for which information was available is indicated in square brackets (F: family, G: genus). Weeks shaded in blue indicate weeks in which antibiotics were administered, and weeks shaded in yellow indicate weeks in which a recovery treatment (natural recovery, probiotics, or fecal transplants) were administered.