Taken together, our data indicate that, despite secondary bile acid production by a healthy microbiota being a useful biomarker for colonization resistance against C. difficile [12,26,31], secondary bile acid production and downstream FXR-FGF19 signaling does not appear to be the primary mechanism by which the microbiota protect the host against C. difficile colonization and infection. Here, NR1H4 is linked to infection.