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A toxin generally refers to a naturally occurring substance that is poisonous (toxic) to your body in some way1. Toxins can be secreted by bacteria (examples: food poisoning, bacterial gastroenteritis, toxic shock syndrome, scarlet fever or scarletina), diphtheria, or perhaps be found in a plant (example: poisonous mushrooms) or food (example: aflatoxin, a toxin in peanuts).
1As opposed to a poison, which would imply a chemical, for example arsenic or lead.