Fiber-packed foods are hitting store shelves. Be careful, doctors say.

But emerging research shows that some fibers used in these products, especially in high doses, could lead to health problems in some people. And a growing number of doctors and nutrition researchers say you should skip them.

“People are kind of overdoing it thinking more is better, but too much of a good thing is too much of a good thing," says Beth Czerwony, a registered dietitian at the Cleveland Clinic Center for Human Nutrition.

Fiber usually leads to reduced inflammation, but in some people it can actually cause it. Some dietitians are hearing patients complain of bloating and pain after eating lots of fiber-enriched packaged food and drinks.

Plants versus processing

There’s a big difference between eating naturally high-fiber foods like fruits, vegetables, beans and whole grains, and fiber-enhanced processed foods and supplements, researchers say.

Fiber is good for us generally, and most people don’t eat enough of it. Fiber is part of plants that our bodies largely can’t digest. It keeps us full, lowers cholesterol and helps stabilize blood sugar. People who eat high-fiber diets have lower risks of obesity, heart disease, cancer and Type 2 diabetes.

Eating a variety of fiber-rich foods means getting a range of different fibers. That’s important for the healthy functioning of the gut microbiome, the collection of microbes that inhabit our digestive tract, says Dr. Purna Kashyap, director of the microbiomics program at Mayo Clinic. Individual fibers feed different bacteria and newer research is finding that fibers have specific—and different—mechanisms for affecting health.

“You can’t just say, ‘I’m going to eat junk all day and then I’m going to have a fiber soda, so there you go, I’ve filled my quota for fiber,’" says Kashyap.

Many snack bars and drinks with added fiber aren’t things we should be having often anyway, says Abigail Johnson, associate director of the Nutrition Coordinating Center at the University of Minnesota School of Public Health. They often contain high amounts of added sugar and include additives such as emulsifiers, which studies have found cause dysfunction in the microbiome.

Many fiber-added snacks and drinks aren’t things we should consume every day anyway, because of added sugar and emulsifiers.

Johnson worries that the added fiber, which is often touted on the label, gives these products a “health halo," making them more appealing to consumers. About 53% of consumers say they plan to buy more high-fiber foods in 2025, according to a 19-country survey by NielsenIQ released in May.

Growing concerns

One of the main fibers used in packaged foods and drinks is inulin, which is usually derived from chicory root.

Research by scientists at Georgia State University, primarily in animals, has found that inulin can alter the immune system in a way that may increase the risk of liver cancer. Other research on inulin in people, by scientists at Stanford University, has found that the substance alters liver enzymes.

Scientists note that studies are small and animal research doesn’t always translate to humans. But the results are causing concern. “The benefits of fiber are pretty hard to reproduce safely by using these supplements and engineered foods," says Andrew Gewirtz, a professor at Georgia State University who led the research there.

“What I worry about is somebody who is eating mostly processed foods, very little fiber and decides they’re going to take a large amount of the supplement to make up for it," Gewirtz says. The occasional soda with inulin is probably fine for someone who has a relatively healthy diet, he says.

Gewirtz’s research on another common fiber, psyllium, hasn’t found an increased cancer risk.

Balancing act

Many fiber-enriched packaged foods contain only one or two types of fiber. Consuming large amounts of some specific fibers could lead to excessive growth of the specific bacteria in the gut that feed on those fibers, throwing off the microbiome’s balance, says Heather Armstrong, a nutrition and microbiome researcher and associate professor at the University of Alberta, in Canada.

In some fiber-added foods, there are only one or two types of fiber, which could throw of the microbiome’s balance, experts say.

“You don’t want one or two microbes that completely overwhelm the whole system," she says.

Armstrong and colleagues have found that when some people consume inulin or another fiber, fructooligosaccharides, they can develop inflammation and symptoms like pain and bloating. Eating large amounts of the fibers may also exacerbate symptoms of multiple sclerosis and GI disorders like inflammatory bowel disease, according to recent studies.

The problem, she says, is that these people’s microbiomes can’t adequately break down the fiber. Armstrong’s lab has been developing a test that aims to assess people’s microbiome and identify which fibers are beneficial for them.

The takeaway from the science now, dietitians and researchers say, is to get your fiber from whole foods.

“Just eating an apple is probably the best fiber supplement you can imagine," says Dr. Sean Spencer, medical director of microbiome diagnostics and therapeutics at Stanford Medicine.

Write to Andrea Petersen at andrea.petersen@wsj.com