Before Antonie van Leeuwenhoek made the first real microscope in the 17th century, people didn't know that bacteria and microorganisms existed. They thought that tiny mites were the smallest creatures their were. Leeuwenhoek basically discovered protists and bacteria.
There was no clue about 'anamicules'. Disease came from gods, devils, and unknown forces. Malaria, for example, literally means 'bad air'
Hi, you may be interested in a couple of recent posts
What did ancient people believe fevers were? featuring /u/cleopatra_philopater on the "four humours" of the Ancient Greeks, and /u/dasher11 on "miasma theory"
With all the major scientific advances from 1200 - 1850 , why did no one figure out that boiling water prevented disease ? featuring /u/queerbees, /u/deadjawa, /u/Aethereus, and others