The fruit flies you’ve seen eating fresh fruit are probably Drosophila suzukii (spotted wing fruit fly). Most (all?) other Drosophila species (including the model organism Drosophila melanogaster) only feed on rotting fruit. Though they’ll consume the sugars too, not just the microorganisms.

There are also some more distantly related flies that feed on fresh fruit and are commonly called fruit flies (eg the Mediterranean fruit fly Ceratitis capitata)