You haven't raised a flag! You've observed (and cited a paper that shows in mouse models under relatively high human dosages) that glyphosate can impact certain gut bacteria species. That's plausible! But all sorts of things do that, and you haven't presented evidence that connects that to an adverse human health outcome. In particular: you haven't cited a source showing glyphosate is causative of gut inflammation.

"It impacts the gut biome" isn't a get-out-of-jail-free card for these arguments; if it were, you could knock down all sorts of things, including specific diets (and most abrupt changes in diet).