In reference to the patent: US 2006/0235071 A1
Looking in the USPTO Public Pair database, this patent application was abandoned on August 31, 2010, which means the claims and specification are now in the Public Domain and you are free to use their method (in the United States). Keep in mind that there was also a WIPO patent application filed. I have not investigated that application, but it does not look like any grants have issued from that one either.
Even if the grant had issued, I believe you would have had Freedom to Operate as long as you weren't using the isolated and purified substance. To answer that question would likely require professional assistance, as it would depend on your exact formula and the (hypothetical) granted claims.
For what its worth, you will probably see far fewer patent applications such as the one you referenced, due to the unanimous Supreme Court decision from 2013, which made it much more difficult to patent natural products, based solely on isolation and purification:
Association for Molecular Pathology v. Myriad Genetics, 569 U.S. 12 (2013)
See also the Wikipedia Article on 569 U.S. 12.