<i>T. gondii</i> infection and high dose indomethacin trigger severe ileitis, dysbiosis and mucosal <i>E. coli</i> invasion in C57BL/6 mice.

<p>(a) Histopathology. Normal ileal histology (inflammation score median = 0, range 0–0) in control mice. Moderate to severe ileitis (4, 3–6) develops in <i>T. gondii</i> mice at 8 days post-infection (T8). <i>G. muris</i>-infected mice develop minimal inflammation (1, 1–1) and mucosal hyperplasia 14 days (G14). High dose indomethacin (HDI) induces severe ileitis (5, 5–7) (H&E 40x). (b) Pyrosequencing reveals a Gram− shift associated with ileitis. Gram+ bacteria predominate in control mice and mice with mild inflammation (G7, G14: Giardia 7 and 14 days p.i., T4: <i>T. gondii</i> 4 days p.i.; LDI: low-dose indomethacin). A shift to >95% Gram− bacteria dominated by the phyla <i>Proteobacteria</i> and <i>Bacteroidetes</i> (p<0.0001) is associated with moderate to severe ileitis in T8 and HDI mice. (c) Association plots of the number of sequences obtained by pyrosequencing corresponding to bacterial families. The area of each rectangle is proportional to the difference in observed and expected frequencies on chi square analysis. The observed frequency of a rectangle is indicated by position relative to baseline, increased (shaded red) or decreased (shaded green) highlighting the ileitis-associated shifts from <i>Firmicutes (Lactobacillaceae, Clostridiales)</i> to <i>Enterobacteriaceae</i> (T8, HDI) and <i>Erysipelotrichaceae</i> (G7, G14, T4). (d) Eubacterial FISH reveals scant luminal and mucosa-associated flora in control mice (EUB338-Cy3, non-EUB338-6FAM with DAPI counterstaining, 40x). Ileitis in T8 and HDI is associated with increased mucosal bacteria and invasive <i>E. coli</i> (<i>E</i>. <i>coli</i>-Cy3, EUB338-6FAM, 40x).