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Extract contamination: am I OK to use it?

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I'd just pick out the yucky bits and use it. You're correct the boiling will kill off the offending organisms. There's lots of microbial and macro contamination in malted grains, but that doesn't stop anyone from using them or making great beer.

Brew on :mug:
 
It will only be on the surface, sugar is too concentrated for bacteria to survive. Try and get rid of as much of it as you can, then boil what you use.
 
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