That reporting shows that the center’s drive to make livestock bigger, leaner, more prolific and more profitable can be punishing, creating harmful complications that require more intensive experiments to solve. The leaner pigs that the center helped develop, for example, are so low in fat that one in five females cannot reproduce; center scientists have been operating on pigs’ ovaries and brains in an attempt to make the sows more fertile.

Even routine care has fallen short. Of the 580,000 animals the center has housed since 1985, when its most ambitious projects got underway, at least 6,500 have starved. A single, treatable malady — mastitis, a painful infection of the udder — has killed more than 625.

The experiments have not always helped the meat business. Industrywide, about 10 million piglets are crushed by their mothers each year, according to pig-production experts, and studies have pointed to bigger litters as a major contributor. Not only do they generate more and weaker piglets, but the mothers have grown larger because they are kept alive longer to reproduce.

Certainly, the production of meat is a rough enterprise. Yet even against that reality — raising animals to be killed, for profit — the center stands out. Some of its trials have continued long after meat producers balked at the harm they caused animals.

The center’s director, E. John Pollak, declined to be interviewed, but in written responses, Agriculture Department officials said the center abides by federal rules on animal welfare. Many current and former employees vigorously defended the center’s work, saying it has helped improve the lives of animals, and people, around the world.

“We’re just as concerned about the humane treatment of animals as anyone else,” said Sherrill E. Echternkamp, a scientist who retired from the center in 2013. Still, he added: “It’s not a perfect world. We are trying to feed a population that is expanding very rapidly, to nine billion by 2050, and if we are going to feed that population, there are some trade-offs.”

The center, in fact, is used as a classroom for teaching animal care. For about 25 years, the University of Nebraska-Lincoln has sent veterinary students into the center from an adjacent building for on-the-job training. Until recently, the university owned all of the animals. But decisions about their use and treatment are made by the center.