It happens as soon as the dough balls are in the oven on their way to becoming cookies. The mixing bowl, spoon and batter beckon. Just a taste. It’s a tradition.

Food experts have long warned that that moment can lead to a bout of salmonella poisoning because of uncooked eggs in batter. But a whole new reason to just wash out the bowl emerged in May when batches of raw flour were linked to E. coli for the first time.

The maker of the flour, General Mills, recalled 45 million pounds of it, about 2 percent of its annual output. Producers of bread mixes and other products containing General Mills flour pulled them off shelves, too.

Now, the Golden Valley-based company is at the center of a fast-moving discussion among scientists and regulators about how serious the development is and what should be done about it.

“Pathogens, or bad bacteria, evolve. They can become more virulent or they can show up in products we didn’t expect, and that’s what’s happened with flour,” said Sandra Eskin, director of food safety at the Pew Charitable Trusts.

The Food and Drug Administration and Centers for Disease Control are still trying to pinpoint how the E. coli bacteria, which originate in feces and usually reach humans through raw or undercooked meat, entered a General Mills plant in Kansas City. Perhaps an animal’s waste in a wheat field made it through the harvest and milling process. Perhaps there was contaminated groundwater.

Though the risk is low, food makers and scientists have long known flour can carry some illness. That’s because it’s a raw good that goes from the field to mill to kitchens with no step for killing unseen bacteria. Usually, dangerous bacteria is killed when flour is baked or cooked as an ingredient in other foods, from breads to cookies to the coating on fried chicken.

“Flour is made from wheat that is grown outdoors where bacteria are often present. There is very little research that has been done regarding the prevalence of the naturally occurring environmental contaminant E. coli in flour,” General Mills said in a statement.

“It is known that the milling process does not remove these contaminants,” the company said, adding that its flour products were never meant to be consumed raw.

But for many consumers, this was their first time hearing that flour can pose risk. Government agencies have been largely silent on flour safety., a website managed by the U.S. Health Department that provide consumers with tips for avoiding foodborne pitfalls, fails to mention any risks associated with flour. On a page that warns against eating raw cookie dough, it specifically lists eggs and salmonella as the reason but says nothing about flour.

In the past decade, flour has been the suspected culprit in several foodborne illness outbreaks. One came in 2009, when more than 70 people were sickened from consuming uncooked prepackaged Nestlé Toll House cookie dough products. But investigators could never definitively trace it back to the flour. Nestlé has since implemented an extra kill step but still advises against eating its products uncooked.

The contamination of General Mills flour, traced to a period from last November to this February, is a turning point.

At least three of the 46 people known to have gotten sick from General Mills’ flour still had the original flour sack packaging that allowed the FDA and CDC to test and verify the exact source of the E. coli.

“This was the smoking gun. They actually isolated it from a patient’s flour bag,” said Mike Doyle, a food safety expert at the University of Georgia. “That more definitive connection has not been made before.”

For food and ingredient makers like General Mills, the discovery raises new questions about production, costs and liability. There are ways food companies can kill bacteria in flour during the milling and production process, but will they be worth it? The leading “kill step” is heat treatment, which General Mills says “would impact its baking performance such as rising properties.”

Jon Faubion, a Kansas State University professor and specialist in baking science and flour functionality, said, “If it’s done correctly, and people are doing it now, it doesn’t have to have a significant effect on the product. But it holds the possibility of having an adverse effect. The most likely impact would be changes in the protein, the gluten. It would lower the breadmaking quality of the flour.”

The outbreak is also likely to create more regulatory scrutiny of General Mills. A federal food safety law taking effect next month gives regulators more oversight of products with a history of problems. As a result, General Mills could face more inspections “because they have a product that is now deemed troublesome and that could have implications for other flour millers,” said Richard Wegener, an attorney at Faegre Baker Daniels who often represents food manufacturers.

A spokesman for General Mills said it has recommended to the FDA that it convene experts focused on identifying long-term solutions, like whole genome sequencing, for food intended to be cooked and not eaten raw. Whole genome sequencing allows investigators to more precisely match bacteria DNA, strengthening the connection between a source and sickness.

“The science and testing is so mature now that you’re going to find more [cases of] contamination,” Wegener said.

The FDA and CDC are still investigating the E. coli contamination at General Mills. A flour sample tested during an inspection in April at the Kansas City facility showed no evidence of E. coli, according the documents requested by the Star Tribune. The FDA has not yet responded to a public records request for any inspections conducted after the recall was announced in June.

The agency has yet to release evidence that it has pinpointed a field or supplier where the E. coli originated.