Humans did not change significantly since the stone age, so that's why a paleo diet makes so much sense. But as we increasingly get to know, the human organism is very dependent on the bacteria that live in/on us.
Do you think these bacteria have changed? And how? And how would that affect us?
I think type of food intake drastically alters gut flora. THey also say gut flora is passed on from the mother, via childbirth, milk, and intimate contact. So there is likely a continuing process of what bacteria you get and don't get starting from birth and moving through the generations. You can't get bacteria that you were never exposed to. PLus we are a much cleaner society. Most kids are live in cement environments and do not play in the mud or see much of nature. Even assuming previous gut flora were perfectly evolved to their conditions and did not evolve much in that old environment, since we have drastically changed gut flora's environment via hormones, antibiotics, food intake types, nutrient availability, chemicals, etc, it is basically assured that gut flora have adapted in kind to the new environments.