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You could look at...

SIBO or antibiotic responsive diarrhea
SIBO - EPI * Exocrine Pancreatic Insufficiency and do the GI bloodwork through Texas A/M

Giardia treated with Panacur:
Giardia

Look at the food she is being fed and how much. I like to limit ingredients with puppies at first - something simple like some of the Pinnacle or California Natural varieties.

I am sure there are other things but those are the first that come to mind with puppies.
 
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