Micro organisms need three things to proliferate: Moisture, the correct temperature range and something to feed upon, generally some organic material.
Condensate control from cooling coils is required. Make sure your face air velocity is below 550 fpm absolute maximum or preferably less than 500. Otherwise condensate will blow off the cooling coil. Also check for air bypass around the bottom of the coil that could aspirate condensate.
For a draw through air handler make sure that there is a properly configured trap in the condensate drain that allows the condensate to work it's way out against the negative pressure.
Rough surfaces such as fiberglass insulation tend to accumulate dust and dirt which in turn will provide a breeding ground for fungus. Smooth surfaces are much better.
Silver containing alloys are available, the silver kills microorganisms.
There is no substitute for a duct cleaning program that includes cleaning of air handlers.