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I use a product from Top Performance, it is an Animal Quarters Disenfectant, detergent and deodorant. You can but it from PetEdge.com for around $20 for a gallon which is a very strong concentrate that you dilute with water. It will make about 250 gallons. It is what many vets and groomers use because it also kills parvo virus as well as others. I got an attachment for my garden hose, that I put the disenfectant in and it automatically mixes the solution as I spray. I have raised shelties for about 15 years and I have used this almost as long and love the results.
I knew a guy who use to raise dogs. And he would get the tobacco at a local cigarette factory. It was the stuff that was left over so he got it free. He used it for the dogs bedding and the fleas don't like it. Or I know that you can use cedar chips for the bedding. I use Odo Ban to eliminate the odors they use it in hospitals, nursing and homes for bed pans and etc. cher
Use one part bleach to ten parts water. You will not be able to smell the bleach, and it will sanitize the kennel as your pup needs. Of course if you don't, the urine and fecal residues that filter down through it will make happy maggots and flies galore. There's nothing good about that being a 'natural' situation, it will stress the pup to smithereens. In fact the very confinement that causes the situation will be the unnatural, since in the wild dog species leave urine very widely distributed. Good for you for wanting better for your dog. Real love seeks to meet the needs of the loved one!
Dogs (and animals) are designed with a certain amount of natural resistance to germs. Don't be overly worried like the advertisers (who would like us to buy their products and sanitize everything in sight) want us to be. Daily pick-up of solid waste and changing the location of the run from time to time should suffice. I hope it is large enough to give the dog a chance to relieve itself away from its shade/shelter.
Ask a vet for a recommendation for a pet-safe insecticide to spray the area with, if you like, and follow label directions carefully. "Homemade remedies" are often fuzzy-sounding, but a waste of money when it comes to effectiveness in true scientific studies. We use Frontline to keep fleas/ticks/skeeters from biting. It is wonderful and worth the money. If you can buy in quantity, it is less $.
Plenty of time out of the run for relief and exercise (when you're home) will also limit soiling in the run.
Best Wishes & Happy Pup!