Is there a question here?
Not sure exactly what kind of discussion you're attempting to generate.
If your question is, "can you imagine some of the healing items or magic out there to be microorganisms?"
Sure, why not. You could totally imagine that healing magic stimulates microorganisms in the body.
Natural Medicine, Herbalist, and Healing Plaster already cover that to an extent. Streptomyces just produces antibiotics. How would you represent an antibiotic? Probably almost the same as Antiplague. I'm all for more fungal stuff, but this is one area that seems like it's covered well already.