Excellent questions, Crystal.
It could very well be liver issues...Even if he does have an extrahepatic shunt, he may have blown more shunts by this age if he hasn't been getting proper liver support. It's more likely MVD though. IBD and liver disease are very commonly seen together.
The conversion of protein to a dry matter basis is EXTREMELY important to take into consideration...50% protein is way too high for a liver compromised dogs exhibiting the symptoms you have described.
It is not true that you would see *more severe* symptoms by now if he really had liver issues...There are several dogs that have not been diagnosed until 6 or 7 or even 8 years old who have had a liver shunt.
Different dogs exhibit different symptoms depending on the severity of the liver problem at that time.
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