Your speculation about veggie bits getting in there makes some sense. Good thing guppies are omnivores. Though if a fish, which is largely vegetarian, is really hungry and gets a chance to suck down a baby guppy - it will. And keepers when returning from vacation, have found the plants in a tank of carnivores have been pretty chewed up.

I think that tiny bits of flake food also get pulled all over until a fine mesh stops them. Additionally there are all sorts of microscopic critters (rotifers, protists and the like) on gravel, especially on plants, occasionally in the water column and quite likely under the gravel and within the filters. If beneficial bacteria can live there, why not creatures a little higher up the ladder? :)