It can also simply be that it is an irritant not an allergy. For instance, when I had acid reflux (had it when I was very overweight - went away completely when I lost), certain foods would increase the acid content not due to allergies but they were irritants. If I avoided them, I would eliminate or reduce. With reduced weight, I can eat those irritants and although I get slightly gassy - I don't have a bad case.
I brought this up to Guelph when I was dealing with a dog's sensitive tummy and found that stress also plays a part in the shape of your stomach. Therefore weight, sensitivity, allergies or stress or any combo can throw everything off kilter. For each dog it would be different but watch a dog that gets stressed and then listen to their tummies. Their stress level shows up in their tummies very fast usually - in grumbling to soft stools to diarrhea to even vomiting or any combo.
When we go into a vet, we often do not talk about stress but stress is very real in dogs and those dogs need their self esteem built up - their confidence. Or they need slow conditioning to whatever is stressing them out. That's not to say that is the case in any dog but it *CAN* be a factor that is over looked. It is something I overlooked and usually I just assume it is the food or some parasite -they are sick etc but if it is longterm no matter what food - one has to consider stress. That doesn't mean there is anything WRONG with your dog. It just means he/she is a sensitive soul and when you boost their confidence, it usually all comes together.
All dogs have fears just like us but some have better coping skills and some need to learn coping skills with our help.
It is also why it is VERY important not to get a puppy too early as the last few weeks they learn critical coping skills from their canine mom. Shoshi took a long time to become assertive and this year I can tell you she has found her voice and backbone completely but even with my help - well the pack helped her the most. I mean she is even lifting her leg to do her business like the other females. Time -it is a good thing.
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