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With what you are describing, I am concerned about primary GI condition such as severe IBD. Another possibility is cancer of the GI tract but this is more common among cats and less common among dogs. IBD (or cancer) is diagnosed definitively with biopsies. These can be taken vis endoscopy or during exploratory laparotomy. The difference between these methods is that the surgical biopsies allow full thickness biopsies to e obtained which can potentially give us more information and they allow more of the GI tract to be biopsied as the scope is limited in how far it can go into the intestines. Typically, endoscopy can reach the stomach and maybe the beginning of the small intestine but not much farther. A colonoscopy is a good compliment to the upper GI endoscopy as this can get some of the lower GI tract but again, the entire GI tract cannot be biopsied this way. Surgery is typically more expensive and certainly more invasive but give us more information. Endoscopy is less invasive but offers smaller biopsies that may miss a bigger problem. Which of these are better for your dog would require discussion with your veterinarian.
There is blood testing that can be performed as well to evaluate the health of the GI tract and this tests for certain vitamins that are produced by the bacteria in the small intestine or the ability of the intestine to absorb certain vitamins. Based on this testing, the location of the GI tract that is diseased can be determined.
These tests are often performed by an internal medicine specialist and I recommend a consult with the internist closest to you. Your family veterinarian can provide a referral for you as well.
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