Fig. 3: Characterization of microbial diversity in baseline (D1) samples.
From: Microbiota-based markers predictive of development of Clostridioides difficile infection
a CDI patients (n = 14, brown) display distinctly lower alpha diversity expressed by the Shannon index compared to AAD (n = 64, blue, p = 0.037) and ND patients (n = 669, green, p = 0.005) at D1. AAD patients similarly display lower Shannon diversity compared to ND patients, however not sufficient to be statistically significant (p = 0.087). b Both CDI and AAD patients display lower diversity expressed by the Chao1 index compared to ND patients (p = 0.001 and 0.017, respectively) at D1. Compared to patients who develop AAD, CDI patients display lower Chao1 indices (p = 0.049). c Cladogram generated by LEfSe demonstrating significantly higher abundances of Actinobacteria, Alphaproteobacteria, and Enterococcus spp. in the gut microbiota of CDI patients at baseline (D1) compared to AAD and ND patients. The cladogram shows distinctly abundant taxa of interest. For more details, see Supplementary Fig. 4. Alpha diversity indices were compared using the non-parametric two-sided Wilcoxon rank sum 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. CDI: patients with confirmed C. difficile infection. ND: non-diarrheic patients. LEfSe: Linear discriminant analysis effect size. LDA: linear discriminant analysis score. *p < 0.05. **p ≤ 0.01. ***p ≤ 0.001.
