Fig. 2

In vivo study plan and findings. a In vivo study plan of the monoinoculation experiment. b E. coli counts in the feces between M8 mice and GF mice feces at the end of the experiment. Bars indicate mean and error bars indicate standard deviation around the mean. c FISH analysis of GF ileum slices. No bacteria were observed in the GF cross section. Bar = 50 µm. d FISH analysis of M8 mice ileum slices. Bar = 50 µm. E. coli was observed in deeper tissue layers including the lamina propria of the mucosa, submucosal spaces and intestinal crypts. e Cecal bile acids comparison between GF and M8 mice. Bars indicate mean and error bars indicate standard deviation around the mean. GF germ-free, M8 GF mice monoinoculated with M8 strain of E. coli, DAPI 4′,6-diamidino-2-phenylindole, CY3 cyanine 3, bMCA β-muricholic acid, TaMCA tauro-α-muricholic acid, TbMCA tauro-β-muricholic acid, TCA taurocholic acid, TCDCA taurochenodeoxycholic acid, TUDCA tauroursodeoxycholic acid