Fig. 5: Longitudinal analysis of microbial diversity and dysbiosis in patients developing AAD.

Microbial diversity and composition in patients developing AAD in the study population (n = 26) was assessed at D1 (green), D6 (blue), S1(purple). a Gradual decrease in Shannon diversity was observed between all timepoints (from D1 to D6: p = 0.018, from D1 to S1: p = 2.74*10⁻⁵, from D6 to S1: p = 0.007). b Similar trends are observed for the Chao1 index (Friedman rank sum: p = 0.054). c Multi-dimensional scaling (MDS) shows distinct clusters for samples collected at each timepoint. d Comparison of the microbiota composition at D1 and S1 conducted using LEfSe (LDA > 2.0) shows large changes in the Firmicutes and Proteobacteria phyla for AAD patients. Proteobacteria are significantly reduced at the occurrence of AAD, and a shift is observed from the Clostridia to Bacilli class at the instance of diarrhea. The cladogram shows distinct taxa of interest. For more details, see Supplementary Fig. 5. Alpha diversity indices were compared using the paired two-sided non-parametric Wilcoxon signed rank test followed by Bonferroni correction of p-values. Box plots indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers) as well as outliers (gray single dots). AAD: patients with non-C. difficile antibiotic-associated diarrhea. D1: rectal swab sample collected upon study enrollment. D6: rectal swab collected ~6 days after initiation and at the end of antibiotic treatment. S1: stool sample collected at the first occurrence of diarrhea (variable time-point). LEfSe: linear discriminant analysis effect size. LDA: Linear discriminant analysis score. *p < 0.05, **p ≤ 0.01, ***p ≤ 0.001.