That is a wonderful vet hospital in Boston.
I really wish I had a new miracle for the IBD but it is a matter or adjusting medications and food and trying to come to that perfect equilibrium. He is on an excellent combination of drugs. Things can certainly be tweaked but I am not sure that we are going to find that one drug that will make all the difference. I agree the major issue is the IBD, primarily because of the discomfort with the loose stool and the now slowly lowering protein levels. My top worry with him doing great for years and suddenly not is if something changed in the GI tract (in some situations IBD can be a precursor to cancer). Some specialists believe if we are certain of our original diagnosis that the immunosuppressive drugs are not always a good thing; so perhaps playing with this and focusing on small intestinal bacterial overgrowth.
Some subtle IBD treatment changes you can always discuss with your veterinarian:
1)A lower fat diet, which seems to help reduce the protein losing problem a bit. Ask if they think the bethanechol could be worsening the IBD since it sounds awfully suspicious it might be and then perhaps trying an alternative.
2) Adding back in metronidazole or another drug for anti diarrhea and anti-inflammatory like sulfasalazine for a bit might be a good trial.
3) Prebiotics to support normal intestinal bacterial (these are different than probiotics)
4) Herbal therapies which primarily prove consistently helpful in small intestinal bacterial overgrowth:
Bu Zhong Yi Qi Tang (Ginseng and Astragalus Combination, Natural Path Herb Company; Boost the Qi, Kan Herb)
Huo Xiang Zheng Qi San (Agastache Combination, Natural Path Herb Company; Protect the Middle, Kan Herb)
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