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I am sorry to hear about your cat's issues. Please allow me a few minutes to read the question thoroughly and prepare a complete answer. I will be back with you shortly.
GI problems in cats often fall into 2 categories. Cancer (or neoplasia) is one cause and inflammatory or infiltrative disease is another. A biopsy is required to determine the difference between these two conditions and there are 2 ways of obtaining tissue for a biopsy. One is with a scope placed into the mouth and down into the stomach and small intestine and then again placed into the colon. Small pieces of tissue are grabbed with a biopsy instrument and the tissue is then sent to the lab for a pathologist to look at the cells and structure of the tissue and make a diagnosis. The other way to obtain tissue for examination is to perform abdominal surgery to cut pieces out of the intestine ("full thickness") and submit these pieces of tissue for the pathologist to look at.
Endoscopy is performed by an internal medicine specialist as this requires expertise and spacial equipment. Most general practitioners do not have the ability to perform this diagnostic test. The biopsy report also needs to be interpreted by a specialist as there are nuances to it. Its not just a matter of what the pathology report says- this has to be interpreted in light of the clinical presentation and making sure it makes sense with what we are seeing clinically on physical exam and in the history.
There is other testing that can be performed to determine what other treatments need to be implemented including vitamin supplementation, steroids or other immune suppressants, antibiotics, etc. Blood tests can look for vitamin deficiencies that are common among cats with GI disease and assess pancreatic function which can also contribute to diarrhea or digestive issues.
If you are unwilling or unable to have the appropriate testing performed to determine the exact nature of your cat's issue you can talk to the specialist about empiric treatment which is the treatment of a medical condition without any diagnostic testing. The upside of this is that if you get a response you don't have to go through the testing recommended and the cat improves. If he does not respond, however it may be difficult to determine why and sometimes you have to treat by trial and error and try something to see if it works or not and then try something else if that fails. Additionally, should you decide to go forward with the recommended testing in the future (biopsies, function testing, etc) the empiric treatment may affect the results sea prevent you from getting a definitive answer as there may have been a partial response but not a complete one. Does this make sense? Please let me know if I need to clarify anything for you.