In science, a hypothesis is a proposed explanation for a phenomenon. That would be what you in everyday language likely call a theory.

A Scientific theory is to quote the beginning of https://en.wikipedia.org/wiki/Scientific_theory

>A scientific theory is an explanation of an aspect of the natural world and universe that has been repeatedly tested and corroborated in accordance with the scientific method, using accepted protocols of observation, measurement, and evaluation of results.

So in the 19th century, what caused diseases was not really known. That bacteria is what causes infection was not known, So you might have the hypothesis that bacteria is what caused the infection. After expiration and test like what https://en.wikipedia.org/wiki/Robert_Koch did that shows that bacteria it the cause of many diseases.

The result is what is called https://en.wikipedia.org/wiki/Germ_theory_of_disease that germs can cause diseases. It is not just bacteria and another living thing like fungi( for example mold), protists (for example amoebas) etc. It can alos be no loving thing like viruses, prions, viroids etc.

So everything about how germs cause disease is a theory. The hypothesis was the idea before it was tested and shown to match reality.

That do not mean that all diseases are because of germ, it can be your own cells that do not work as they should. Autoimmune disease is for example your own immune system attaching your own tissue.

Before that https://en.wikipedia.org/wiki/Miasma_theory obsolete medical theory, that bad air causes disease, so it was the smell that could cause it. It was proposed as early as 4th century BC by Hippocrates. If you look at https://en.wikipedia.org/wiki/Plague_doctor with masks with beaks that contain dried flowers, herbs, and other things to keep the smells away. It likely helped because it keep droplets with bacteria away just like the facemask that is used today but the smell was not the cause.

The name malaria if from Italia where "mal" is bad and "aria" is air, so the literary means bad air. It was believed that the smell in for example wetlands caused it, the real explanation is that is a parasite that is transferred by mosquitos. So it did not smell but the existence of mosquitos in some areas caused it.

So both are explanations of a phenomenon Miasma theory was believed in for centuries even if it was not correct. But getting rid of smells can also reduce exposure to germs, so in a way it worked but why it works was not correct.