I don't want to sound like I am a qualified expert in the field. But I have been at the research level for so long now, that I have reached the place where many experts will confess, there is still so much we do not know about the world of microbiology.
And like medicine, the the scope of knowledge (we do have) is so vast, that one person could not possibly have a global understanding sufficient enough to grasp everything.
Right now, for example, I have just discovered something very significant from stool culture (multiple phases in) that has me thinking.
The original experiment was to coax the growth of a type of plasmodium species, that is known to exist in specimen. The idea was to find the "fungal" components for identification and data storage.
What I found was a almost complete absence of bacterial growth (very unusual), but a high content of L-form bacteria (something of a significant observation).
These L-forms are very stealth, have been used in bioweapons research, have Antibiotic resistance, and are suspected of being at the core of many unexplained diseases, including cancer.
I should post images for those who are curious.
Anyway, the point I was making, we are still in frontier territory with regard to microbiology.