A honey bee colony is more than just bees. There is a whole ecology from microscopic to fairly large there are many symbiotic plus some benign relationships in the ecology of a bee colony. Even those benign relationships often crowd out pathogenic organisms.
Macro and Microfauna
For instance, there are over 32 kinds of mites that live in harmony with bees. When these are allowed to live (instead of being killed by acaracides) there are insects in the hive that eat them, such as the pseudoscorpion which also eat the malignant mites.
An examination of feral colonies shows just in the macroscopic arena the colony is full of life forms as diverse as mites, beetles, waxworms, ants and roaches.
There are many microflora that live in the bees and in the colony. These vary from fungi to bacteria to yeasts. Many are necessary for the digestion of pollen or the maintenance of a healthy digestive tract by crowding out pathogens that would otherwise take over. Even seemingly benign ones and sometimes even mildly pathogenic ones often serve a beneficial purpose by supplanting otherwise deadly ones.
Many of the Lactobacillus genus are needed to properly digest the pollen and many of the Bifidobacterium and Gluconacetobacter genus are beneficial in the sense that they crowd out Nosema and other pathogens and probably contribute to digestion as well.
Even some seemingly pathogenic organisms such as Aspergillus fumigatus which causes stonebrood, supplants worse pathogens, in this case Nosema. Or Ascosphaera apis which causes Chalkbrood but prevents European Foulbrood.
Upsetting the Balance
How much do we upset the balance of this rich ecosystem when applying anti-bacterials such as tylan or terramycin and anti-fungals such as Fumidil? Even essential oils and organic acids have anti-bacterial and anti-fungal effects. Then we kill off many of the mites and insects with acaracides.
After totally unbalancing this complex society of diverse organisms with no regard for benefit or not and contaminating the wax that we reuse and put in the hives as foundation, we are surprised to find that the bees are failing. Under such circumstances I would be surprised to find them flourishing!
For More Reading
Try an internet search on the following phrases and read some of what comes back:
bees microflora (10,900 hits)
bees "symbiotic mites" (30 hits)
bees symbiotic bacteria (25,100 hits)
Here are a few of the specific strains and groups you might want to research further: