Thank you for taking the time to explain the situational context of each of the studies. That helps with understanding far more than the dumbed-down headlines that are designed to shock and intrigue, rather than inform. Even if journalists are trying to be unbiased and informative, they lack your background knowledge. (I doubt any of them were in a class where one of the scientists was discussing his research.)

It's amazing how delicate the microbiome can be, but also how resilient. I was recently on a course of antibiotics, and the ER doctor warned that I needed to stay off all sugar, white bread, etc. while on them. I ended up unable to digest milk/cheese, but within about a week, taking probiotics and prebiotic foods, including fiber, the bacteria recovered, and I had no further problem with dairy. If I'd been eating sugar while on the antibiotics, the bad actor bacteria you mentioned could have taken over.