

You can also just expose someone to a pathogen and predict the outcome based on the pathogen. Like the doctor who proved that Helicobacter pylori causes stomach ulcers and cancer by taking a shot of broth laced with the bacteria and, predictably, got stomach ulcers, which he successfully treated with antibiotics.
The idea is that theories have considerable evidence and are consistent with all testing done up to that point. (Warning: I AM NOT SUGGESTING THE FOLLOWING IS TRUE. IT IS A HYPOTHETICAL ONLY) But what if we found out tomorrow that if you put bacteria in an environment with a specific magnetic field, they no longer caused disease and they end up finding out that bacteria poop has magnetize structures of the cell and cause diseases. That antibiotics have the magnetized structures with the opposite polarity that counteract the bacteria poop. Or some shit like that. This would contradict our current understanding of germ theory and it would be proven to be wrong or at least incomplete.
That is why theories are not “proven” because they are ALWAYS open to better explanation if one can be provided. That being said, it is highly unlikely that any well established, defined and tested theory will ever be “disproven” wholecloth, becuase it has always been consistent with observations. Germs are real, disease is clearly related to them in some way, specific germs cause specific reactions in our bodies, etc. But we could always be partially wrong about something, or have an incomplete explanation.