While I'm fairly convinced that a lot of dysfunction gets a helping hand from microbiota imbalance, including such faraway targets as pulmonary, cardiac, and even neurodegenerative disorders [1], I think there's a simpler culprit: sugar. Metabolism of simple sugars changes biochemical gears, and we as a culture and society are heavy on its use.
Sugar definitely seems bad, but doesn't explain why simple fecal transplants are able to replicate many of the health effects of a low-carb diet without the actual diet, at least in some obese mice [1]. (PS I am definitely not an expert in this area, just someone who is tired of eating low-carb to maintain weight, and wondering why other people can just eat normal food.)
The whole thing about fecal transplants is that the resulting changes in your microbiome make it so your pull to sugar is weakened. Your diet changes because your cravings change. Imagine how easy it would be if you craved food that was "good for you", or that your cravings for bad food were severely weakened. That's kinda what having a healthy microbiome is like
[1] https://news.ycombinator.com/item?id=29882347