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You are quite correct that a smaller tube size can work better to siphon out small size water containers.

A straight piece of rigid tubing from the LFS attached to some flexible vinyl tubing works fine. I have been sucking on siphon tubes for years and haven't gotten sick from it yet. I do not go out of my way to suck up mouthfuls of tank water but it has happened. Disgusting though it is; it is not the end of the world. I keep various sizes for different purposes.
 
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