The vast majority of changes made by humans to food plants, mostly through selective breeding, but also through gene editing, do not infer a selective advantage (except toward more human breeding). Big red fat juicy tomatoes are a disadvantage in the wild, where hundreds of thousands of years of natural selection pre-humans produced small, hardy, efficient, easy to maintain fruits.

Just like with pure-bred dogs, if humans suddenly disappeared it would probably only take a few decades for many species to return to muttier wildtypes.

Sure, some gene-editing is to make the plants hardier. Some of those genes would likely remain.

We're getting rather off-topic, though, which is about whether the bacteria in your mouth would be likely to mutate and/or swap genes with other bacteria in your mouth.