U.S. dietary guidelines have long recommended that people steer clear of whole milk, and for decades, Americans have obeyed. Whole milk sales shrunk. It was banned from school lunch programs. Purchases of low-fat dairy climbed.

“Replace whole milk and full-fat milk products with fat-free or low-fat choices,” says the “Dietary Guidelines for Americans,” the federal government’s influential advice book.

Whether this massive shift in eating habits has made anyone healthier is an open question among scientists, however. In fact, research published in recent years indicates that the opposite might be true: millions might have been better off had they stuck with whole milk.

By warning people against full-fat dairy foods, the United States is “losing a huge opportunity for the prevention of disease,” said Marcia Otto, an assistant professor of epidemiology at the University of Texas and the lead author of large studies published in 2012 and 2013, which were funded by government and academic institutions, not the industry. “What we have learned over the last decade is that certain foods that are high in fat seem to be beneficial.”

This year, as the “Dietary Guidelines for Americans” undergoes one of its periodic updates, the federal bureaucrats writing them must confront what may be the most controversial and weighty question in all of nutrition: Does the consumption of so-called saturated fats — the ones characteristic of meat and dairy products — contribute to heart disease?

It is an important question. Heart disease is the leading cause of mortality in the United States.

But the idea that spurning saturated fat will, by itself, make people healthier has never been fully proven, and in recent years repeated clinical trials and large-scale observational studies have produced evidence to the contrary.

After all the decades of research, it is possible that the key lesson on fats is twofold. Cutting saturated fats from diets, and replacing them with carbohydrates, as is often done, likely will not reduce heart disease risk. But cutting saturated fats and replacing them with unsaturated fats — the type of fats characteristic of fish, nuts and vegetable oils — might.

This shift in understanding has led to accusations that the Dietary Guidelines harmed those people who for years avoided fats and loaded up on the carbohydrates in foods that were marketed as “low fat.”

It also has raised questions about the scientific foundations of the government’s diet advice: To what extent did the federal government, and the diet scientists they relied upon, go wrong? When the evidence is incomplete on a dietary question, should the government refrain from making recommendations?

The dietary science has drawn the skepticism of some on Capitol Hill. This month, a House committee aired concerns regarding the evidence for the guidelines with Agriculture Secretary Tom Vilsack and Health and Human Services Secretary Sylvia Burwell. Lawmakers from both parties expressed frustration about how the government recommendations have shifted.

“People may be losing confidence in the guidelines,” said Minnesota Rep. Collin Peterson, the top Democrat on the House Agriculture Committee.

The Dietary Guidelines have stepped back slightly from their blanket advice to reduce saturated fats, adding the caveat that saturated fats ought to be replaced with unsaturated fats. But Dariush Mozaffarian, a cardiologist, epidemiologist, and dean of the Friedman School of Nutrition Science & Policy at Tufts University, said that in his view the Dietary Guidelines have yet to retreat far enough from the idea that saturated fat is a dietary evil.

It certainly seemed at times that there was strong evidence against saturated fats.

The history of the fat warning is usually traced to the work of Ancel Keys, a scientist at the University of Minnesota, who examined fat consumption and rates of heart disease in various countries. In places where people eat lots of fat, he found high levels of heart disease. One of his famous charts, from 1953, showed that in the United States, where close to 40 percent of the diet came from fat, people suffered a disproportionate number of heart disease deaths. People in Japan and Italy, by contrast, consumed less fat and died of heart disease less often.

To Keys, the data offered proof that Americans could improve their health by reducing the fats in their diets.

Public health authorities were soon recommending that people reduce their consumption of saturated fats as a means of lowering heart disease risks.

But the subsequent years of science have shown that by itself, cutting saturated fats appears to do little to reduce heart disease.

So what about whole milk?

While nutrition advice is often presented in terms of “macronutrients” — fats, proteins, carbohydrates — foods may be more than the sum of their scientific parts. Milk is a good example. Repeated research on milk, funded by public institutions, has provided evidence that the fats in milk are, for some reason, different.