"I don't think it's fair to say that "modern diets are
the problem"."
Yeah, see, I didn't say that. You edited that to mean something completely different from what I said/meant. My sentence started with "perhaps", had no italics and I went on to ask how that could be tested. So I think this is a not great comment. It feels almost slanderous to me.
But I think it's fair to say that the many benefits of modern diets are accompanied by some serious negative side effects, and that the human microbiome has not yet had enough time to evolve into an optimal state for coping with them.
That's part of my assumption. But, also, it seems to me that the modern diet has chemical impacts that are pretty well-established as promoting disease. Not that we have to eat crap, but a lot of us do, in fact, live on rather crappy food -- microwave meals, food "products", etc. I think it's complicated and that the impact of food chemistry is not well studied or taken all that seriously. People who think relatively small changes may have big impacts tend to dismissed as quacks.