Several studies have linked the byproduct, known as distillers grain, to elevated rates of E. coli in cattle. And now, distillers grain is facing further scrutiny because the Food and Drug Administration has found that it often contains antibiotics left over from making ethanol.
Ethanol production relies on enzymes, yeast and sugar to convert corn into fuel. And just as the wrong bacteria in the body can sicken people, it can also cause a variety of ailments in a batch of ethanol.
Marc von Keitz with the University of Minnesota's Biotechnology Institute said in ethanol production, the main enemy is a bacterial bug that makes lactic acid.
"What these organisms do is they also compete with the yeast for the sugar," said von Keitz. "But instead of making alcohol, they make primarily lactic acid."
If [ethanol producers] didn't have distillers grain as a revenue, many more of them wouldn't be able to operate.
If enough of the bacteria are present, von Keitz said fermentation can be ruined.
"It gets acidified to the point that the yeast is no longer able to properly produce ethanol, and then you're stuck with a big batch of corn mash," said von Keitz.
If that happens, there's no ethanol and no profit. To prevent the problem, producers rely on medicine.
"What people operating these plants are trying to do is to keep these lactic acid bacteria in check," said von Keitz. "And one way of doing that is with the help of antibiotics."
Ethanol producers use penicillin and a popular antibiotic called virginiamycin to kill bacteria. And that raises two potential concerns.
One is that these treatments might promote the growth of bacteria that are resistant to antibiotics. The development of these "superbugs" is a major concern in health care because they reduce the effectiveness of medicines.
Marc von Keitz found some bacteria that were, in fact, resistant when he sampled bacteria at four Midwest ethanol plants several years ago.
The second concern is that the antibiotics could find their way to humans through the food chain.
The U.S. Food and Drug Administration has taken a mostly hands-off approach to the use of antibiotics in the ethanol industry. But amid increasing concerns over food safety in recent years, the agency is taking a closer look.
"A year ago we put a survey out to the FDA field people to collect samples of those distillers grains, and start analyzing for antibiotic residues," said Linda Benjamin, a chemist with the FDA's Center of Veterinary Medicine.
Samples were requested from 60 ethanol plants, including some in Minnesota. She said testing showed that many contained antibiotics, mainly four types.
"Penicillin, virginiamycin, erythromycin and tylosin," said Benjamin.
At this point the story gets murky. Benjamin won't say if any of the antibiotics exceeded federal guidelines.
Those guidelines are part of the problem; they're a patchwork and far from definitive on what levels of antibiotics in distillers grain are safe.
If the FDA decides to restrict antibiotics in the ethanol industry, it could have far-reaching consequences.
Distillers grain is a major source of low-cost livestock feed. Any restrictions on its sale and use as feed will hurt the profit-scarce ethanol industry and the livestock farmers who rely on it.
Charlie Staff, executive director of the Distillers Grain Technology Council, said distillers grain is one of the few dependable moneymakers left for the ethanol industry.
"If they didn't have distillers grain as a revenue, many more of them wouldn't be able to operate," said Staff.
Meanwhile the regulatory process continues to play out. The FDA will test more distillers grain samples, and expects to issue a final report this summer.
The maker of virginiamycin declined to comment, but the company is expected to ask the FDA to approve the antibiotic as a human food additive.
Depending on how this regulatory battle winds up, it could change the way Minnesota's 18 ethanol plants distill their product.