He mostly just said that are mice are designed to run on a grain based diet. The study is clearly motivated by the natural diet of a particular organism. From the intro: "The Western diet contributes to many chronic, diet-related illnesses in the United States, including the obesity epidemic (Cordain et al., 2005). Western diets are typically high in fat and simple carbohydrates (CHOs) (Cordain et al., 2005). Higher intake of fats and refined sugars are associated with deficits in cognitive flexibility and hippocampal-dependent memory in humans (Kalmijn, 2000 and Francis and Stevenson, 2011) and an increase in the incidence of Alzheimer’s disease (Pasinetti, 2002)." When that diet is altered, things will change, including gut bacteria. Will there be other important changes? The study doesn't address that, but the sensible working hypothesis should be: yes, radical dietary changes affect more than gut bacteria. Let's look at the end of the discussion to see if this makes a difference: " Interestingly, mice fed 33% fat, in the form of lean ground beef, showed better long- and short-term memory than those on 12% fat (Li et al., 2009)." Maybe all the stuff in the diet besides the current macronutrients of interest actually matter??