Any reason why an rx diet isn't worth a try?
IMO, diet of vet's choice. If that doesn't work, then more intestinal blood testing and/or diagnostic imaging. If the stool is still loose after and no problem is detected, it would be time to talk about exploratory/biopsy. It's just not healthy long-term, and he is so young still.
There are a few things that could be tried (omegas assuming that there is inflammation present, probiotics if you are convinced that they work, etc.). But really, if dietary management isn't working, IMO he is too young to not find an answer (if possible). Has your vet tried Metro? Tylan?
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