Any diet that has real food. Quality animal nutrition and plant nutrition will work for the gut and the body.
The Mediterranean diet is also bollocks. Not that I think it’s bad, we know it’s a decent diet. But it’s not what the Mediterranean actually compose their diet of. I say this being the grandson of a language professor, learning cultural and ancestoral diet changes as well as cooking for myself.
I’d also watch about this “biome diversity” and “diet diversity” being beneficial it makes no sense and the evidence is shallow if we’re honest.
Can you link some of the articles you’ve read? I think that might help me better understand where you’re coming from and what to answer. But intuitively (sorry i don’t have a source, just a guess) I’d say that the micro biome balances itself for the most part, assuming you eat a varied diet that composes a lot of whole foods