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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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  • 消毒 = disinfection
  • 殺菌 ≈ sterilization (more accurate term for it is 滅菌)

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.

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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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