For years scientists have believed that when it comes to weight gain, all calories are created equal.

But an intriguing new study, published in the journal Nature Communications, suggests that’s not true. The body appears to react differently to calories ingested from high-fiber whole foods vs. ultra-processed junk foods.

The reason? Cheap processed foods are more quickly absorbed in your upper gastrointestinal tract, which means more calories for your body and fewer for your gut microbiome, which is located near the end of your digestive tract. But when we eat high-fiber foods, they aren’t absorbed as easily, so they make the full journey down your digestive tract to your large intestine, where the trillions of bacteria that make up your gut microbiome are waiting.

By eating a fiber-rich diet, you are not just feeding yourself, but also your intestinal microbes, which, the new research shows, effectively reduces your calorie intake.

The study reveals that inside all of us, our gut microbes are in a tug of war with our bodies for calories, said Karen D. Corbin, an investigator at the AdventHealth Translational Research Institute of Metabolism and Diabetes in Orlando and the lead author of the study.

“On a Western diet that doesn’t feed the microbes very much, almost all the energy goes to us and very little goes to the microbes,” Corbin said. “We don’t give the microbes any opportunity to utilize the calories we ate because we use them all. We pull the rope all the way to one end.”

Corbin and her colleagues wanted to understand how the gut microbiome might be involved in regulating weight and metabolic health, so they designed a clinical trial that was small but rigorous.

They recruited 17 healthy men and women and compared what happened when they were fed a fiber-rich diet vs. a diet of highly processed foods. The researchers provided the participants all of their meals and had them follow each diet for 22 days.

For half of their time on each diet, the participants lived in a metabolic ward, where researchers tracked every calorie they ate and controlled their physical activity levels. They also spent six days during each diet phase in a tiny, airtight room called a metabolic chamber. This allowed the scientists to determine exactly how many calories the participants burned. The researchers collected bowel movements and used special techniques to analyze things like the amount of energy and bacteria in their feces.

The two diets were polar opposites. One, called the Western diet, contained many highly processed foods typical of what the average American eats – foods like crispy puffed rice cereal, white bread, American cheese, ground beef, cheese puffs, vanilla wafers, cold cuts and other processed meats, and sugary snacks and fruit juices.

The other diet was called the “microbiome enhancer diet,” and it was designed so as much nourishing food as possible would reach the gut microbiota. When we eat fiber, our gut microbes thrive on it and break it down through a process called fermentation. This produces a lot of healthy byproducts, such as short-chain fatty acids, which are good for our metabolic health.

In the study, the microbiome enhancer diet contained many foods that have a special type of fiber called resistant starch, found in things like oats, beans, lentils, chickpeas, brown rice, quinoa and other whole grains. The diet also includes many nuts, fruits and vegetables.

To prevent food from being absorbed too quickly and to maximize the amount of food that would reach the microbes in the large intestine, the researchers avoided foods that were processed, ground or refined. The participants were given whole nuts, for example, instead of nut butter, and fed chunks of steak instead of ground beef. The meals were designed to minimize highly processed foods.

The two diets provided each participant with the same amount of calories and similar amounts of protein, fat and carbohydrates.

“They had the same calories, but one would go down to the colon and feed the microbes, and the other one is completely digested and given to us,” said Steven R. Smith, a co-senior author of the study and the chief scientific officer at AdventHealth. “The microbiome enhancer diet was really designed to make your gut microbiota happy.”

The scientists found that the participants absorbed significantly fewer calories on the fiber-rich diet compared to the processed diet. On average, they lost 217 calories a day on the fiber-rich diet, about 116 more calories than they lost on the processed-food diet.

But there was a wide range: Some participants lost nearly 400 calories a day on the fiber-rich diet. These lost calories showed up in their stool in several ways. The participants had more undigested food in their feces for instance. But they also had significantly more bacterial “biomass” and short-chain fatty acids in their stool – a sign that their gut microbes were busy multiplying and fermenting.

“It takes energy to make bacteria,” Corbin said. “So, instead of the energy going to us, it’s going to expand this community, and we know that because in their poop the biomass went up by about eight and a half times.”

This created a lot of benefits for the participants. On the fiber-rich diet, they had higher circulating levels of short-chain fatty acids and increased levels of hormones such as GLP-1, which promotes satiety. (The new popular diabetes and weight loss drugs, Ozempic and Wegovy, work by mimicking the action of GLP-1.)

The participants lost slightly more weight and body fat on the fiber-rich diet. Yet despite absorbing fewer daily calories, they did not show any signs of increased hunger.

Daniel Drucker, an endocrinologist and professor of medicine at the University of Toronto, called the study “very rigorous, careful and well done.” He said the finding that a high-fiber diet is good for you was not surprising, but that the study sheds light on some of the mechanisms that explain why.

He called the research an interesting “proof of concept,” but he said more research was needed to see whether the findings might apply not just to healthy young adults but to older adults and people with metabolic diseases.

“These were healthy people studied in a controlled environment,” he said. “Would we see the same quantitative and favorable changes in a population of people in the real world with obesity and heart disease and diabetes? That’s a difficult study to do.”

Many studies have suggested the gut microbiome plays a role in our weight and body composition. Scientists have found that people with obesity, for example, have less bacterial diversity in their guts and other differences in their microbiomes compared to lean people.

Sean Gibbons, a microbiome specialist and assistant professor at the Institute for Systems Biology in Seattle, said the new study was striking because it indicates that people could lose weight and body fat simply by switching to a diet that targets their gut microbiomes, even without exercising more or cutting back on calories.

Gibbons, who was not involved in the new study, said it confirms what he has seen in his own research: That a diet that increases the growth and activity of your gut microbes “is a net positive for being metabolically healthy and losing weight.”

“Globally, a lot of people are transitioning more and more to processed foods,” he said. “That’s not great for our microbiomes or for our metabolic health.”

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