- how thick is the intestinal lining (i.e. is it greater than 1mm?)
- how easy it is to do surgery on the mouse to get to the intestine?
- how easy is it to sew the mouse back up and have sorta a ready-access flap into the intestine like Svoboda does with the mouse neurons?
- how much will it alter the physiology of the mouse to have an open wound near the intestine?
Update Dec 2, 2007
Jost Enninga, Philippe Sansonetti and Regis Tournebize wrote an excellent review that covers this idea and much more (as is always the case, this idea has already be worked on to some extent, though never in the context of an intestine as far as I know).
Roundtrip explorations of bacterial infection: from single cells to the entire host and back.
Trends in Microbiology, Nov 2007