First, it's good to see this article, 5 years ago it was considered "alternative medicine", "quackery" and "pseudoscience". People finally read 30 years of clinical reports and told the food and drug companies to STFU.

1) Yes, junk food kills healthy git flora.

2) Worse, excessive carbohydrates (> 30% by calorie) promote the overgrowth of healthy gut flora. They feed yeasts, most notably candia that eat sugar and piss ammonia causing any number of somatic and mental illnesses ranging from mild to severe.

3) Pasteurization is a double edged sword here. While it was a great asset in the fight against food borne disease such as listeria it also kills not only vitamins (which is why scurvy came back in the early 20th century as "infantile scurvy" because heated milk neutralized vitamin C) but the beneficial bacteria.

You don't have to go back to paleolithic times to see how things were different - wine/beer/ale/mead/ginger beer was quaffed with every meal, so not only were we not eating crap that killed good gut flora and promoted bad ones but we were getting a good dose of healthy gut flora in naturally fermented foods 3x a day.

Neurotransmitters are made in the gut. The ancient Greeks wrote that a healthy gut means a healthy brain and now we know it's true and why it's true.