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Cramer: Wall Street having a crisis of faith on this stock

Wall Street seems to have lost faith in what was once the growth darling of organic and all-natural food stocks, CNBC's Jim Cramer said on Wednesday.

Just before shares of Whole Foods Market tanked more than 20 percent when trading opened Wednesday morning, Cramer said analysts that cover the organic grocer appeared to have turned on the company, expressing "rebellion" on Tuesday evening's conference call. Whole Foods reported quarterly earnings Tuesday that fell short of Wall Street's expectations.

"This was one of those conference calls where the analysts actually outright questioned whether the company is being serious about the competition," Cramer said on "Squawk on the Street."

"I think what people are going to say is I'd rather shop there than own the stock. The problem is there's a loss of faith here," he said.

Five analysts lowered their ratings on the grocery chain after Whole Foods' earnings. The company also cut its 2014 forecasts for same-store sales and earnings as competition increases in its sector.

Read MoreWhole Foods earnings, revenue miss; shares plunge

In an interview with CNBC on Tuesday, Whole Foods co-CEO Walter Robb chalked up the disappointing quarter to "short-term headwinds," such as investments the company has made in new stores, frigid winter weather and price adjustments.

Walter Robb, co-chief executive officer of Whole Foods Market Inc.
Bryan Mitchell | Bloomberg | Getty Images
Walter Robb, co-chief executive officer of Whole Foods Market Inc.

"The analyst community has a job to do," Robb told CNBC. "They have to report it as we see it. Our job is to execute and perform. These numbers are a little softer than what we like to see for sure. But if you look within those numbers there's lots of good points in there. It really comes down to we have to execute."

Robb said the increased competition from the likes of Wal-Mart and The Fresh Market won't affect the long-term vitality of Whole Foods. When the dust settles in the organic grocery market sector, Robb said, his company's quality standards should win out.

Disclosure: Cramer's charitable trust does not own shares of Whole Foods.

—By CNBC's Jeff Morganteen. The Associated Press contributed to this report.