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"The porous structure of wood enables it to absorb and retain bacteria," she wrote, adding that wood aging boards "could be a potential source of pathogenic microorganisms in the finished products."

Callahan said that aging wheels of cheese on wood racks is critical to their craft. The wooden planks help to control moisture and provide an amenable surface for the microbes that add flavor and character to cheese. Switching to metal or plastic shelves would be costly and would change the taste of aged cheeses.

Cheese would "definitely come out differently" on stainless steel or plastic shelving, although the result is hard to predict, Callahan said.

Social media blew up in this week as cheesemakers from California to Vermont took to the Internet. The hashtag #saveourcheese surfaced on Twitter. Chefs and cheese lovers took to Facebook and blogs to rebut the notion that wood was harmful.

Cleanliness is critical to cheesemaking regardless of the material used for aging shelves, said Gabe Luddy, the fourth-generation cheesemaker at Vella Cheese Company in Sonoma.

"We've always prided ourselves on having a very clean plant," he said.

The 82-year-old company's signature product, dry jack cheese, is aged on wood, a practice Luddy said is legal in Canada and Europe.

Callahan, whose 24-year-old company's product line includes three aged cheeses, said there is "conflicting evidence" on whether wood surfaces accommodate bacteria growth, but the same concern applies to plastic if the surface is roughened, for example by knife cuts, he said.

The cheese industry has "zero tolerance" for the presence of bacteria in its products, Callahan said.

In a statement issued Tuesday in response to the growing controversy, the FDA said it had adopted no new rule on the use of wooden shelves in cheesemaking, nor taken "any enforcement action based solely on the use of wooden shelves."

The agency said it "will engage with the artisanal cheese-making community" to determine whether certain cheeses can be safely aged on wood.

The head of the 1,500-member American Cheese Society said the trade group will begin discussions on the matter with the FDA beginning next week.

"We feel that wood is safe and cleanable for aging cheeses," said Nora Weiser, the organization's executive director.

In key cheesemaking states such as California, Wisconsin and Vermont, up to 75 percent of the cheesemaker members of the American Cheese Society use wood to age or ripen some of their products. Half the cheeses imported into the U.S. are aged on wood, the group said.

Artisan cheesemaking is a small industry in the North Bay with an ardent following. The Sonoma Marin Cheese Trail listing 29 cheesemakers in the two counties.

The controversy erupted Monday with numerous media reports that the FDA had adopted a ban on wood aging boards, citing the letter sent by Metz in January to the New York state Agriculture Department.

"FDA may destroy American artisan cheese industry," a Forbes report said.

"It made for a great headline," Luddy said. "The story kind of blew up."

FDA spokeswoman Lauren Sucher said the letter was "correspondence between two regulators — not an agency announcement of new policy."

The FDA's statement Tuesday said the agency was "always open to evidence that shows that wood can be safely used for specific processes, such as aging cheese.

Weiser, head of the cheesemakers' group, said companies can go about business as usual "if they are doing it properly."

The local cheesemakers said they foresee no immediate rule change by the FDA, but the matter is not resolved.

"I'm not sure this has completely gone to rest," Callahan said.

The New York Times contributed to this story.