Changing your diet disrupts the gut biome. When I started eating bran flakes it massively disrupted my gut biome. Should I be alarmed? Or are you slipping a double standard in there, perhaps from the naturalistic fallacy?
Maybe you should see if you adjust to the bran flakes, cut them out if you don't improve, and see if there's a difference? All sorts of things can disrupt gut biomes, and I think ancestral diets are an interesting area of study. Gut inflammation is absolutely rampant.