In OoT, Ganondorf made Jabu develop all of those enemies inside. An old thread said it was Ganondorf who put the message in the bottle:

"Help me, I am waiting for you in Jabu Jabu's Belly
-Ruto"

The argument was he did this to lure Link into getting that Spiritual Stone. I believe in the other side, that it was really Ruto who wrote the message and sent it out of Jabu (think where, ewww).

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