Anything that reaches the gut intact disrupts (ie: manipulates, interacts with, alters, stimulates or suppresses, selects) the gut biome. I'm not pushing back on you except to say that as a mechanistic axiomatic claim of harm, it's missing most of the evidence. You could be right, but you could also be wrong; what you've said so far can't possibly be dispositive.
The mechanism of action of glyphosate inhibits several important amino acid production processes in the gut. I'm simplifying here, but not having glyphosate in the food supply would be a good thing for the gut, and the science agrees on this.
Glyphosate for field prep also doesn't really come through in food, it's much worse with the pre-harvest desiccation.