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Whole Foods Market appears to be hurting from grocery sticker shock and ambitious expansion plans. The stock took a beating Wednesday after reporting second-quarter results that missed Wall Street expectations - for the third quarter in a row - and after offering guidance that Credit Suisse called “equally disappointing.”

The Austin, Texas-based supermarket chain, which brands itself around its “natural,” local and organic food and merchandise offerings, posted earnings 1 cent a share below the consensus estimate and forecast third- and fourth-quarter earnings to fall from a year ago.

On Wednesday analysts said new stores are continuing to impact returns and that the Wild Oats acquisition is proving challenging: Wild Oats stores added a 6-cent hit to Whole Foods’ second-quarter profit. The company is also seeing margins contract as new stores open, a scenario that’s unlikely to change any time soon, analysts said.

The higher-priced supermarket chain is also losing customers who are hurting from higher prices for the gamut of necessities, from gas to bread. Food inflation shot up to 5.9% in April from 4.7% in March, with every category except meat moving up, and the breadth of the increase suggesting this level of inflation may remain for a while, Goldman Sachs noted Wednesday.

Morgan Stanley said the impact of the ongoing “grocery trade-down” is exacerbated by Whole Foods’ heavy exposure to markets that are feeling the pinch and punch of the real estate bubble. In a note to clients Wednesday, analyst Mark Wiltamuth said more than half of the company’s California locations include “bubble” markets; California makes up around 30% of the total store base for Whole Foods.

“We have consistently cautioned that the [comparisons] could slow with the weaker economy, and the company’s exposure to California… We expect consumer trading down to continue as food inflation drives sticker shock in the grocery aisles throughout the balance of the year,” he wrote.

So what are the prospects for the company’s growth?

Back in February, when it reported first-quarter results, Whole Foods said sales “have been highly resilient during economic downturns,” suggesting the current recessionary period might not hurt the company.

“We attribute our strong sales to many factors, including our loyal core customers and their dedication to a natural and organic lifestyle, our high percentage of perishable product sales, and our extensive selection of high-quality prepared foods that attracts customers trading down from restaurants,” cofounder and chief executive John Mackey said in a statement released with first-quarter results.

But Tuesday’s numbers showed comparable store sales at the supermarket chain dawdling to their slowest growth rate in a year, Think Panmure analyst Suzanne Rice wrote to clients Wednesday.

“This leaves us questioning the company’s ability to accelerate comps in this retail environment,” she said.

Rice maintained an accumulate rating for the stock and said Whole Foods will likely continue to lead the natural foods industry as the sector grows. But her long-term take on the company was somewhat muted. “We believe that margins will begin to improve toward the latter half of 2009 and into 2010, though returns on investment may never get back to the levels they were when Whole Foods was in a higher-growth mode.“