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The usual suspects
The everyday triggers
Intolerance is not allergy
The Merck Veterinary Manual's allergy guidance draws a line worth knowing: an intolerance (this food upsets his stomach) is a digestive problem, while a true food allergy is an immune response - most often to a protein - that typically shows up as skin signs like chronic itching, sometimes with digestive upset alongside. The distinction matters because the fixes differ: intolerances are managed by avoiding the trigger, while suspected allergies are worked up properly.
The elimination trial, briefly
If your vet suspects a food allergy, the standard tool is an elimination-challenge diet: weeks of a strict novel or hydrolyzed protein diet - nothing else passing the lips, no treats, no flavored chews - followed by deliberate reintroduction to see what provokes signs. Merck's allergy guidance stresses the same two rules that make it work: absolute strictness during the trial, and patience, because the schedule runs in weeks - up to about three months - not days. Done casually, it tells you nothing; done properly, it ends the guessing.
A simpler first step
Before any of that: two weeks of boring consistency. One food, minimal plain treats, zero table food, and entries in the stool log. A surprising share of "chronic sensitive stomach" is actually a daily drizzle of rich extras nobody was counting. The log makes that visible - and if the gut stays upset on a truly boring menu, that's meaningful information for your vet too.