I went to a panel that discussed gut microbes at Chicon, and had a few ideas for making use of them:
1) Microbes as sensors. Take existing gut bacteria, electroporate in a reporter plasmid, reintroduce orally. The reporter can be a sensor protein hooked up to GFP or an enzyme that acts on a microbial product to make a derivative not found normally in bacteria, and easily detectable and distinguished from normal chemicals in the gut.
1a) Detection can be by examining poop. A souped up Japanese toilet would be the least obtrusive solution.
1b) if the product is fluorescent, detection can be by direct gut imaging, as is done for mice.
2) Introduce GFP producing bacterial into the gut, and use them like barium is used for gut imaging. Imaging would be done using transilluminated epifluorescence microscope or a fluorescence light box
and thermoelectrically cooled CCD camera. By moving the detector and light source around, enough images can be made for low resolution computed tomographic imaging.
3) Introduce gut bacteria that absorb methane. Natural methane absorbing bacteria, normally present in low numbers can be introduced to increase total gut methane absorbtion, or if methane absorbtion happens at low levels, bacteria could be selected to find strains that do it at a higher level. A third option is to engineer normal gut bacteria to have this capability.