Mutations, gene passing, and the evolution of gut microbes

The gut is a particularly interesting niche for evolution because things change there so rapidly. You eat a undercooked hamburger from a poorly butchered cow and all of a sudden your intestine is full of E. coli O157:H7, you've got the worst stomach ache of your life, and you have bloody diarrhea. But this doesn't just create an difficult life for you, this also causes a great deal of confusion for the bacteria that were happily living in your intestine. Before the O157:H7 invaders arrived, your normal intestine residents (i.e. your normal flora) were grabbing the food you didn't eat and passing on the some of the benefits to you. Now all of a sudden the flow rate through your intestine is much faster. Perhaps the normal flora are having trouble staying attached to your intestinal lining? A new food source, blood, has arrived from the E. coli O157:H7 that so rudely invaded your intestine. And most of your intestines normal residents are probably not optimized to eat blood.

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?

1. 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
   
2. 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

Point 1 above deals with mutations and selective pressure. Point 2, the gene-exchanging idea, deals with a phenomenon called horizontal gene transfer. However, it's not clear how often any of these things happen, or if they occur more often in some situations than others (e.g. is there more horizontal gene transfer when there is a strong selecting force like an antibiotic). Mutations and selective pressure has been studied for quite a while in the lab (see the NY Times article "Fast-Reproducing Microbes Provide a Window on Natural Selection") with pretty interesting results. But I think its time we moved these evolution studies into more complicated environments like the gut. We also need to further explore the extent to which horizontal gene transfer plays a role in these organisms' survival and adaptation, because previous studies (as far as I know) have focused more on the mutations in cultures of a single bacteria put under some sort of selective pressure.

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.