I'd have to find it, but I recently read an article on how diet affects the flora of the gut. It specifically dealt with how vegans' intestinal landscapes change, but there was also evidence that other more specialized diets likewise affect your "bugs."
If that's what's causing the bloat, it'll probably settle down fairly quickly as carb-loving bug-towns flourish in your intestines while the protein-loving ones deal with declining property values and a dwindling job market.
Edited to add: the more I read about gut flora, the more interesting the subject gets! Google is awesome.