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  My Maddie has been on Flagyl off and on for IBD.  I give it to her whenever she has a flare up.  My vet gave me little clear capsules that I take apart, put the pill inside and close it back together.  When I asked my vet why it needs to be in a capsule, he said because the taste is so horrid.  Maybe you could give your vet a call and ask for some of those empty capsules.  Then, you could still put the pill in something, but your puppy wouldn't get the awful taste.  
 Good luck and I hope your little one improves!
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