Intestinal microbiota composition of mice following ileitis induction. Main intestinal bacterial groups were quantified by molecular analysis of fecal samples derived from C57BL/6 wildtype (WT; black circles) and TLR-9 deficient (TLR-9-/-; white circles) mice before (N, naïve) and seven days after ileitis induction by peroral T. gondii infection (ILE). Quantitative real time-PCR analyses amplified bacterial 16S rRNA variable regions and 16S rRNA gene numbers/ng DNA from the following bacterial groups: (A) Total eubacterial load, (B) Enterobacteria, (C) Enterococci, (D) Lactobacilli, (E) Bifidobacteria, (F) Bacteroides/Prevotella spp, (G) Clostridium leptum group, (H) Clostridium coccoides group, and (I) Mouse intestinal Bacteroides. Numbers of mice harboring the respective bacterial 16S rRNA out of the total number of analyzed animals are given in parentheses. Medians and significance levels (P-values) determined by Mann–Whitney-U test are indicated. Data shown were pooled from three independent experiments.