Figure 3.

Metagenomic analysis of the murine intestinal microbiota upon treatment with neomycin. (A) Quantitative real-time PCR analysis of 16S rDNA copy number from the feces or ileal contents of mice treated with conventional water (CNV, black) or neomycin (NEO, gray). Horizontal lines depict median values. (B) Family-level phylogenetic analyses of fecal bacterial sequences from conventional and neomycin-treated mice. Frequencies of significantly altered bacterial taxa in feces were compared individually at day 21. (C) Family-level phylogenetic analysis of ileal contents taken at day 21, with individual frequency comparisons of significantly altered taxa. All data represent averages from 8 mice in each treatment condition, housed as pairs in 4 separate cages. Box-and-whisker plots depict medians ± interquartile range. Statistical significance for all comparisons was analyzed by Kruskal-Wallis tests with correction for false discovery rate. *P < .05; **P < .01.