Figure 4.

Antibiotic exposure alters intestinal microbiota composition

(A–F) Intestinal tract samples were collected from mice at sacrifice at P35, and fecal samples were collected after weaning at P25. DNA was extracted from the intestinal and fecal samples and subjected to 16S rRNA sequencing. Shannon diversity, an alpha-diversity metric, was calculated for samples from (A) ileum, (B) colon, and (C) feces. Unweighted UniFrac, a beta diversity metric is plotted for (D) ileum, (E) colon, and (F) the feces. Statistical significance for Shannon diversity was determined using a non-parametric t test. Histogram shows 95% confidence interval with a line at the mean; ∗ indicates p < 0.05. Comparisons of community structures from control and antibiotic-exposed mice were determined using an Adonis test in R using the Phyloseq and Vegan packages. For each sampling site, the percent sample variation explained by antibiotic treatment was 23.6% (ileum); 37.8% (colon); and 46.4% (fecal). Ellipses show 95% confidence interval for the sample group. p values indicating statistical significance are shown on the corresponding principal component plots.