Fig. 4: Longitudinal analysis of the impact of antibiotic therapy on the intestinal microbiota.
From: Microbiota-based markers predictive of development of Clostridioides difficile infection
Microbial diversity was compared prior to broad-spectrum antibiotic treatment at D1 (green) and after treatment at D6 (purple) following treatment with PBLs (n = 194), OBLs (n = 133), and FQNs (n = 63). a A distinct reduction was observed in Shannon diversity in patients treated with all antibiotic classes (p = 8.98*10−6, p = 2.06*10−5, and p = 0.007, respectively). b Similarly, distinct reductions in Chao1 diversity was observed following treatment with all antibiotic classes (p = 0.011, p = 0.001, and p = 9.26 × 10−5, respectively). c Treatment with each antibiotic class resulted in a shift in microbial composition illustrated by the Jaccard distances between the D1 and D6 samples. d The heatmap illustrates distinctly abundant taxa (LDA > 3.0) identified using LEfSe. For more details, see Supplementary Table 10. Alpha diversity indices were compared using the paired two-sided non-parametric Wilcoxon signed rank test. Box plots in indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers) as well as outliers (gray single dots). PBL: penicillin + beta-lactamase inhibitor. OBL: other beta-lactam antibiotics. FQN: fluoroquinolones. LDA: Linear discriminant analysis score. D1: rectal swab sample collected upon study enrollment. D6: rectal swab collected ~6 days after initiation and at the end of antibiotic treatment. LEfSe: linear discriminant analysis effect size. LDA: linear discriminant analysis score. OTU: operational taxonomic unit. *p < 0.05, **p ≤ 0.01, ***p ≤ 0.001.
