GMOs don't really contain any unnatural substances unless they've been deliberately put in, to my knowledge, that's not many, most GMOs that contain additional substances contain natural substances since it's easier to copy an existing gene than making a new one.

To my knowledge, pesticides and glyphosate in the levels present in most food don't really have any effect on our internal microbiome, which is mainly non-plant based and the few plant based single-cellers in that biome aren't that harmed by glyphosate and should quickly develop immunity.