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it could be popeye, ive heard of it ending up with the eyes actually coming out of the socket before. are the eyes looking swollen at all on any of the fry? im wondering if maybe when the fry are resting on the bottom at night if the loach could perhaps be nipping at them...only a possibility though.

zebra loaches like to have company of their own kind too by the way, maybe consider getting the little guy a friend or 2.
 
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