The bunkers are remnants of a Naval ammunition depot that produced bombs during World War II. The depot is now an animal research center where government scientists are working to unlock secrets contained in the genetic makeup of the cattle.
Their focus: the E. coli 0157:H7 bacteria, which can kill if it reaches the dinner table.
"Our purpose is to save little kids' lives," said Mohammad Koohmaraie, director of the center.
The scientists at the Roman L. Hruska U.S. Meat Animal Research Center say they still don't know why the number of beef recalls soared in 2007 or why E. coli contamination appeared to be rising.
"What we try to do is increase our understanding as much as possible about the bug," Koohmaraie said.
The lab has its own feedlot and a herd of about 6,500 cows that are used for genetic research.
In 2007, more than 30 million pounds of ground beef were pulled off the market in 20 recalls because of possible E. coli contamination. That included the second-largest recall in U.S. history, which put Topps Meat Co. out of business.
At least 67 sicknesses were linked to last year's beef recalls. No deaths were reported. In 2006, there were just eight beef recalls and no reported illnesses.
The federal Centers for Disease Control and Prevention estimates that E. coli sickens about 73,000 people and kills 61 each year in the United States. Most of the deaths are people with weak immune systems such as the elderly or very young.
The bacteria was discovered in the late 1970s and is present in the intestines of most cattle. It also can be found in deer, goats and sheep. It doesn't cause problems for the livestock, but the E. coli 0157:H7 variant can cause severe illness in humans.
Symptoms of E. coli infection include stomach cramps and diarrhea that may turn bloody within one to three days.
The large scope of the research being conducted at the Meat Animal Research Center sets its work apart from research at universities and other labs in the USDA's Agricultural Research Service.
"The uniqueness of what we do is in the sample size," Koohmaraie said. "We really don't speak unless we have confidence in the data. A bug like E. coli 0157:h7 is really problematic if you don't design the experiment properly."
One of the lab's current projects will test whether feeding cattle distiller's grain - a byproduct of making the gasoline additive ethanol - has any effect on the level of E. coli and the quality of meat produced.
The Nebraska Corn Board suggested the distiller's grain research last spring, and the lab agreed because more and more feedlots are using the ethanol byproduct, Koohmaraie said.
The research involves 600 cattle. Half are being fed a traditional grain feed and half are being fed distiller's grain. The research will wrap up in June after the cattle have been sold for slaughter and samples of their carcasses have been collected.
Smaller studies already suggest a link between distillers grain and high levels of the bacteria. For instance, researchers at Kansas State University said last fall they found that cattle fed distiller's grain are twice as likely to carry E. coli 0157:H7.
The meat industry significantly increased its efforts to control E. coli after the 1993 outbreak in which four children died and hundreds of people became ill after eating undercooked hamburgers from Jack in the Box restaurants.
The Clay Center lab, which is about 120 miles southwest of Omaha, didn't really have much of a food safety research program until the Jack in the Box outbreak, Koohmaraie said. After that, Congress and the USDA made it a priority to learn more about E. coli and other pathogens.
A great deal of research had already been done on E. coli by then, but the Clay Center lab made an important discovery: E. coli was getting into meat processing plants on the hides of cattle as well as inside the animals' intestines.
That work contributed to the development of systems to wash the hides of cattle and the carcasses with either hot water or chemical solutions as they enter the processing plants.
The lab determined which solutions work best and how washing systems should be designed.
Warren Mirtsching, who oversees food safety for JBS Swift & Co, said the lab showed how valuable a hide washing system can be and that meat packing plants didn't have to spend millions to install an effective system.
"I think they perform a very special niche," Mirtsching said. "They are the validator."