[zaphar]

    microorganisms aren't really part of the food chain

That is not strictly speaking true. Microbes in the soil have a lot to do with the healthy/unhealthy growth of many plants. Microbes in our gut have a drastic effects on our ability to digest food. Just because we don't see them doesn't mean they don't have an effect.

I do believe however that the sheer variety speed of mutation in that portion of the food change insulates it from a lot of damage. Perhaps the same could be said for Insects as well I don't know.