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I want to thank everyone for all their support and advice. I have gotten none from my wonderful breeder, so it really means a lot to me. My puppy Max is still having soft stools. He has been treated for Giardia twice, he has been treated for Coccidias, he has been treated with probiotics, and he has been on the ID prescription diet for 3 weeks. He also had $429 worth of blood work that showed some elevation in his white blood cells which they said could mean he still has some form of parasite so next week they are going to treat him for Clostridium P. although they say when dogs have this they have watery stools and cramping, which he does not. After we try the next antibiotic, the next step is some prescription high end food that is supposed to be hypoallergenic and if that doesn't work an intestinal biopsy, which I don't think I will do. Soooo, the saga continues for poor Max, my sweet little boy. I would love to know if any of his litter mates are having this problem, but I was kicked off the breeder's website for positng that my puppy had Giardia.

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Elevated white cell count definitely means something is going on with the immune system. I'd talk with a knowledgeable, holistic vet about a suitable diet but there are LOTS of instances where a good diet provides the proper support for a body so that it can overcome an infection. Even in humans, they stress how important eating healthy is when you are sick. Good food will definitely help with an infection. "Cure" it maybe not, but it would certainly help to strengthen him so his own body can triumph.
I have an immuno-compromised dog who I know would be dead right now if we hadn't switched her to raw when we did. Not every diet is the right one for every dog, but cooked, whole food with probiotics and enzymes would still be an improvement.
I'm sorry if I sound like a jerk. I just got my wisdom teeth removed and I can't sleep. I've been through similar things with my own dogs and client dogs and I just want to help. We lost our lab WAY to early because we never got any second opinions, or tried any sort of holistic approaches. We just listened to the vet we were using at the time and my whole family will always regret that.
I also have an immuno-compromised dog, and I know he would be much sicker, if not dead, if I had listened to the junk science & misinformation on the raw feeding websites and the advice in forums to "change his food." Instead, I approached his disease from a scientific perspective, aided by my own formal education in biology and nutrition, and a board-certified veterinary immunologist. "Holistic" simply means "whole"...an integrated approach to illness, using all means available to treat it, and does NOT mean "natural". An effective "holistic" approach to illness encompasses all aspects of medicine, not just diet, and not just "natural". There are millions of "natural" substances that can kill you. And drugs that save lives...and come from plants, by the way.
This is not the place to debate the nonsensical idea that there is anything the least bit therapeutic about raw food as opposed to cooked food, or the misinformation provided by the raw feeding websites of the relationship between diet and the immune system, let alone the immune system in general. It is important to understand that the immune system involves lots of different kinds of white blood cells that all serve different functions. For example, the antibodies that are formed against disease through innoculation are a different kind of antibody than the ones that cause allergic reactions. The physiological process in each case is entirely different. The immune system is quite complicated. Nutrition is certainly important in maintaining and improving health. But "eating healthy" means obtaining the calories, vitamins and minerals the body requires to function. Your idea of a "good" diet and my idea of a good diet, or "eating healthy" may be very different. In either case, there is absolutely no proof of any kind that food can make any difference at all in cases of bacterial or viral infections, and certainly not against parasites. Animals in "the wild" die from these things...and they all eat raw diets.
Max needs to have his problem reliably diagnosed and treated. Period. I'm sorry you're in pain, and I know you are trying to help, but a dog's life can also be lost by listening to the "holistic" and raw feeding theories of treating illness.
I go with Karen and Lynne. Go for a homecooked simple diet and stick with it for weeks. Give it time to settle the digestive system. Also, I would add some probiotic powder to his food. I would also supplement his food with a spoonful or two of cooked (plain no sugar) pumpkin alternated with plain yogurt. I also would stop treats if you are treating him until all is settled. Hang in there. It will be better.....
I would listen to Karen and Lynne too. Their advice has really helped us through tough times with Timbow in the past. I hope everything gets solved, I would consider getting a second opinion from another vet though?!
I seem to be a little late to this discussion, but by soft stools, what do you mean? Toothpaste like? Completely runny? More than three or four times a day. Some dogs just have "soft stools". Right now Roo has lovely pickable stools all the time. Tigger has "soft stools" - considerably softer than toothpaste, but does hold some form. It is just the way they are. Humans come that way too. In any case, it is always helpful to this kind of dog to pick a really quality dogfood and STICK WITH IT. Add a spoonful of cooked plain pumpkin to every meal. Or hamburger and rice boiled together in a really big pot and fozen in meal size portions. Feed this for six months ( hence the big pot). In the fifth month gradually introduce the kibble you are going to feed. And I mean gradually - take up the whole month. This always helped my colitis prone husky and she lived to the ripe old age of 15+. Checking in with the vet is always wise too.

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