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Medical science had noted that many diseases seemed to be clustered around a common source, and that such diseases often thrived in non-ideal conditions, such as near sewage and swamps. It was theorized that decaying flesh and organic matter gave off some sort of invisible deadly gas that caused the contagion.
However, as epidemiology and experimentation improved, the miasma theory was found wanting. For example, cholera, which was thought to be caused by bad air, was found to affect well off areas and miss some slums. Moreover, the disease was traced to the use of certain wells rather than proximity to sewage.
Koch's work definitively showed that certain micro-organisms caused certain diseases, and miasma theory fell out of favor.