The dangerous things are the germs themselves, the toxins they make and the spores which can germinate into new germs. Toxins can be hard to destroy, and spores are very very hard to destroy.
Also, not all germs are dangerous to you. Some are not dangerous when they go into your mouth and stomach, but only if they end up in a wound. For example, the spore forming family Clostridium. Clostridium tetani is destroyed by stomach acid, but spores can come back to life in a wound and produce a toxin which kills you (tetanus). Clostridium botulinum is destroyed in adult stomach acid, but not baby stomach acid, so babies under one year old need to be kept away from it.
That spoon is basically fine because you removed surface dirt which could have been harboring germs or spores. But a large part of the reason why it’s fine is that you are a healthy adult with a functioning immune system and acid in your stomach. Your innate defences kill off thousands of threats every day.
Interestingly, once you have put that spoon in your mouth and then into some food you can have introduced mouth germs into the food, which then can grow and produce toxins which are not killed by boiling the food. So yeah, sometimes there are worse germs in a healthy mouth than in a cow shit.
(Using germ to cover all fungi, bacteria, viruses and others)
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