I was thinking of sushi wraps and Fruit Roll-Ups when I spoke of food patents but you are right that ingredients on their own would probably not qualify for a patent.
Here to show what is required for recipes to be patented is information from the USPTO on "Can Recipes Be Patented?"
http://www.uspto.gov/custom-page/inventors-eye-advice-1
It is possible to a certain extent to keep an invention confidential, at least during the patent application process, which can keep a trade secret a secret until a patent issues. If a Nonpublication Request is filed with the application, the trade secret can be preserved in case a patent is
not granted. But there is a trade-off for trade-secret holders if a patent IS granted. The secret eventually will no longer be secret.
Generally the best most trade secret holders can do to protect their secrets is rely on non-disclosure/confidentiality agreements - which are often enough to protect the secret because the penalties for disclosing the secret can be harsh. But any agreement is only as good as those entering into them, so a certain amount of trust between parties is necessary.