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Thank you for your question. My name is***** I have been a small animal veterinarian for 13 years. I do have some questions that will give me a better understanding about what is going on so that I can answer you questions.
First, I understand that he had surgical biopsies done to diagnose the IBD. Were there any other abnormalities on blood work (such as low proteins, etc). Second, what treatments are you doing now? What medications? What diet?
One thing that I don't see in your list of medications is steroids.... IBD often produces massive inflammation in the intestine and steroids can be so helpful in bringing that inflammation down. You have to wait about 10 days after surgery to start them because they slow healing, but you could start that now. I would also start Vitamin B12 injections. Most IBD dogs are vitamine B deficient. And if the medication you are using to prevent vomiting isn't working, try another one. Try one that can be given by injection. I like Cerenia injectable.
Diet can be helpful in managing IBD long term, but in the short term you have to focus on getting the vomiting under control and the vomiting stopped. Ask your veterinarian bout vitamin B12 and some steroids. If they don't help then I might start to lose hope, but at this point you haven't done the most important thing... get the inflammation treated.
Honestly, I have to think there is something more than IBD going on.... IBD responds quickly and completely to prednisone and certain controls the vomiting associated with IBD very effectively. It sounds like you have had a good workup with appropriate treatment, but I would really think something is being missed. You could try taking him to a university hospital if there is one near you for a second opinion. They may pick up on something that your veterinarian is missing.