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Advice for Chipotle from someone who's been there

As Chipotle undergoes an investigation for yet another E. coli outbreak, the stock is now down 22% since early November, when the first case of E. coli was reported.

Chipotle's latest move is announcing it's changing its supply chain to "reduce the risk of contamination to a level near zero."

On a smaller scale, Jim Thornton knows something about what Chipotle's leadership is going through. Thornton served as president & CEO of Botanical Laboratories and in 2012, the natural supplements company began a voluntary recall of its products after reports of some salmonella or E. coli contamination.

"You have to have a very solid recall plan. You look at all the microbial testing and look at where all the ingredients come from," Thornton told CNBC.

"It's a very tedious process. It's painstaking."

A person walks past a Chipotle Mexican Grill store location in downtown Portland on November 3, 2015 in Portland, Oregon.
Steve Dykes | Getty Images
A person walks past a Chipotle Mexican Grill store location in downtown Portland on November 3, 2015 in Portland, Oregon.

Thornton believes the tremendous growth in organic farming is to blame for outbreaks and correlates to a steady increase in food borne illness, with over 43 million individuals in the U.S. contracting some form of it per year.

"We've had enormous growth in the organic farms," Thornton said. "I think it's really great Chipotle is using small farms, but regulation has to catch up with water systems, soil systems, verification systems and oversight and compliance."