The glyphosate–microbiome argument rests on the shikimate pathway: plants and many bacteria have it, humans don't. That makes the mechanism plausible and the dose question decisive.

Where I think both sides overreach: "mechanism exists" is not "effect at environmental exposure," and "no effect at environmental exposure" is not established either. This is a genuinely open question and it is being argued as if it were closed.

The dose question is the whole question, and it is the one that never gets funded. Who would pay for that study?

That is the honest answer: nobody with an interest in the outcome being null, and nobody with an interest in it being positive either. Which is why the literature we have is mostly mechanism papers and residue surveys that talk past each other.