In general, eating the same diet as thin/healthy people will cause your microbiome to shift toward the microbiome of thin/healthy people. This is because your microbial population is largely determined by resource availability and resource type, and adaptation happens quite quickly (ie speeds not unlike those shown in http://www.youtube.com/watch?v=Pb272zsixSQ)

However, I believe it's wrong to conclude that thin/healthy people have the kind of microbiome you should be aiming for.

The microbiome you want (or rather I want) is the one my ancestor's had, just like I want the food I eat to be similar to the food my ancestor's ate. Unfortunately this is basically impossible given modern farming techniques, which remove most of the food-borne microbes found on natural crops.

See http://humanfoodproject.com/rebecoming-human-happened-day-re... for more on this from the founder of the American Gut Project.