At least refer to them as "microbes"."Germ" is actually short for "germinate", which means to grow, and which is by and large a good thing (seeds germinate, for example).
Also, reproductive cells (egg, sperm, and their progenitors) are referred to as "germ cells", also good things.
And most microbial organisms are not harmful! In fact, were it not for many of them we would not have survived thus far.
If one wants to talk about nasty microbes, the best term to use is "pathogen", which is short for "pathogenic", meaning to cause disease.
Scientific literacy is about being specific as much as anything else!
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