What would a bad diet or bad habit look like from the perspective of the human "biome"? Sugars and simple starches would have been absorbed higher up in the digestive tract, so I don't think they'd have much of an effect. According to some of the writing on resistant starch, low carb diets fail to provide enough food for the biome to thrive.

I haven't lost faith in low carb because I feel much better on it, but it looks like some low carb advocates are turning toward "safe starches" because they've shifted their focus from the hormonal effects of food to the importance of maintaining a population of good gut bacteria.