Colloquially, it can also be used to refer to microbes (micro-organisms). This meaning is discouraged here.
Entymologically, a "bug" is a specific sub-order (Hetereoptera), the so-called "true bugs". This sub-order contains about 40,000 species, in the order Hemiptera of insects. Example Heteroptera include bed bugs, leaf-footed bugs, seed bugs, pond skaters, and stink bugs.