Feces and phylogeny

A couple of weeks ago I wondered aloud about the question of whether diet-related changes in the nature of gut bacteria could have significant effects in evolution.  The paper I was writing about at the time showed that flies fed different diets quickly began to prefer mates who had been fed the same diet, and this preference appeared to be due to a change in the composition of gut bacteria.  But is the composition of gut bacteria maintained over evolutionary timescales? A recent paper (Ochman et al. 2010.  Evolutionary relationships of wild hominids recapitulated by gut microbial communities.  PLoS Biology doi:10.1371/journal.pbio.1000546) suggests that it is; but the role of diet remains unclear.