Now let's assume you were misdiagnosed and the doctor gave you antibiotics to get rid of the new E. coli O157:H7 residents in your intestine (unfortunately, the current best treatment for O157:H7 is to wait a week or two for it to go away). Now, the bacteria in your intestine are being bombarded by these antibiotic chemicals that kill off most of them.
So how do bacteria survive, and often thrive, in such a complicated environment?
- they are tiny so lots of them can live in a small space; their large number allows for diversity; and diversity is largely why they survive drastic changes in their environment - only a few diverse individuals of a particular species need to survive each in order for the species to remain a resident of the normal flora
- the different species trade DNA in the gut; this means that if one type of bacteria in the gut develops resistance to a particular antibiotic, another type of bacteria can develop resistance more easily, because they can just obtain the important piece of DNA from the bacteria that already figured out how to survive
Here's what I propose:
Inoculate a gnotobiotic mouse with N species of bacteria (probably make N = low = 2-4; also make the species diverse: one Firmicute, one Bacteroidetes, and one Archaea). You should probably place things under selective pressure to push the organisms in different directions. For example, give the mouse diets that have few of the nutrients necessary for the gut residents, or add one antibiotic resistant strain of bacteria and give the mouse a weak but constant dose of the antibiotic (to see how long / if the bacteria horizontally pass on the gene).
Now pass on the microbial residents to new mice (either the children of the inoculated mouse or another germ-free mouse; both would be interesting). This passing could be done by mixing a little feces in their food, but it would probably just happen naturally if you put them in the same cage for a few days. Now at set times in each mouse's life take a feces sample to be sequenced at a later date (might as well delay sequencing as long as possible, since the stuff gets so much cheaper with time). Then sequence the frozen samples to see the extent of the mutations and gene transfers over time and in different selective environments and genetic backgrounds of mice. The sequencing will also show how the proportions of the normal flora change over time.
The problem with this experiment is that it would take several years of work, and you'd always need to be careful to pass on the flora before the mouse died. But according to that NYTimes article I linked to above, most of the action in the single-species studies occurred at the beginning, so even the early results might yield some interesting insights into gut ecology and evolution.