I was at the gym and they have these bottles of disinfectant to clean after
you've used the equipment, I started thinking about the kanji's and started
wondering why the 2nd kanji used is 「毒」 (poison).

Why the kanji for poison? Why not use something like 「消」 and 「菌」? Curious...

(I do know there's also 殺菌.)
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kanji etymology
Etymology of 「消毒」
It is a good question.  
I thought about your question sincerely. And I led the following answer. This
may have nothing to do with studying Japanese language (lol).  
You know all germs or bacteria may not necessarily have a bad influence on
human beings. I think that among bacteria or germs, there are some ones that
have substance having poisonous influence on human beings but others have not.  
The old clever person would think that it was more effective to put out the
poisonous substance of bacteria or germs to protect human beings than to put
out or kill all kinds of bacteria or germs. So they would coin the word
"消毒{しょうどく}" rather than "消菌{しょうきん}" and named the disinfectant
"消毒{しょうどく}"剤{ざい}.
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* 消毒 = _disinfection_
  * 殺菌 ≈ _sterilization_ (more accurate term for it is 滅菌)

> [**Disinfect vs.
> Sterilize**](http://www.diffen.com/difference/Disinfect_vs_Sterilize)
>
> Disinfection and sterilization are both decontamination processes. While
> **disinfection** is the process of eliminating or reducing _harmful_
> microorganisms from inanimate objects and surfaces, **sterilization** is the
> process of killing _all_ microorganisms. That is the main **difference
> between sterilizing and disinfecting**.

毒 in 消毒 should be understood as "harm". It doesn't refer to chemical
substances here.

消菌 sounds quite funny to me. Since 消 chiefly means "make vanish", it reminds
me of some kind of tile-matching game where germs of same color suddenly pop
when adjacent to others.

[![enter image description
here](https://i.stack.imgur.com/mb8sS.jpg)](https://i.stack.imgur.com/mb8sS.jpg)
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