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Anything--ANYTHING--non-acidic, like soups, vegetables, fruits, meats, gravies, etc., MUST be processed in a pressure canner at 10 lbs pressure for no less time than what the recipe specifies!!! A water bath canner just doesn't get the water & product hot enough for long enough to kill micro-organisms that might kill you! Pressure canning forces the air out of the jar--& everything needs air to grow. I am in the restaurant industry & have taken many courses on food & air-borne illness & am also an avid canner. I know for a fact that sometimes simply boiling a product is not enough to kill bacteria. Did you know that there are bacteria out there that can survive in the freezer?! It's true!!! Be VERY careful when canning your products & go the extra effort to keep from poisoning you & your family & friends. You're one lucky lady. Botulism poisoning can be fatal.
Soup stock should be processed in a pressure canner for 45 minutes under 10 pounds of pressure. A water bath simply will not kill organisms that will grow in it. Thank God it turned acidic, if you ate it, you probably would have gotten really sick.
Are you sure that this soup can be canned safely using the "water bath" method? Most vegetables and all meat should be canned using a Pressure Canner. Check with your local extension office, the library or other canning sites on the web and see what they say. I can chicken stock quite frequently and always use a pressure canner.
I would make sure that when you can, after you pull the jars out of the water bath, to make sure the lids seal after they are removed from the water to set. You'll hear a "pop" if they are sealing correctly. I would also check and make sure of the time you process the jars to be exactly what the recipe calls for as well as the temperature of the water. Is it boiling or just come to a light simmer? Make sure it's boiling, as it can really mess w/the canning if it's not done to the letter of the recipe. Hope this helps you!