Whenever a biopsy detected a bacteria or fungal infection, it was usually concluded that the infection was secondary.
In other words, inflammation often triggered by foreign proteins kills the outer layer of skin on your lips.
The dead layer, without protection from blood, is breeding ground for both bacteria and fungi, but just finding bacteria and fungi inside the dead layer in no way proves that you EC is caused or triggered by those bacteria, though that possibility can not be excluded either.
Bacteria in your mouth or on your lips may as well play a very important role in triggering your EC, but I doubt any biopsy can be used to prove it, because those bacteria live naturally there anyway ...