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Nutrition labels aren’t enough to predict diet’s effects on gut microbes

To predict how diet shapes a person’s gut microbiome, researchers came up with a new way to categorize foods.

ByKatherine J. WuNOVA NextNOVA Next

Humans spend a lot of our time poring over nutrition labels. But a quick gut check shows that the trillions of bacterial cells in our bodies couldn’t care less. Image Credit: Ridofranz, iStock

When it comes to nutrition, human and microbe don’t quite see eye to eye.

According to new research published today in the journal Cell Host & Microbe, nutrition labels aren’t enough to predict diet’s effects on the gut microbiome, the bustling population of friendly microbes that colonize the human colon. A food’s influence on our resident microbes seems to have more to do with where it falls in subgroups of categories like dairy, meats, and vegetables, than what its overall carbohydrate or fat content is.

On the whole, the study, which closely tracked dietary records and stool samples from 34 individuals over a period of two weeks, also shows that food isn’t the only thing that governs how the gut microbiome changes over time. Although diet helps predict the composition of these communities from day to day in an individual, microbes generally don’t respond to foods in the same way from person to person.

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The findings reinforce the idea that there’s no one-size-fits-all protocol for establishing and maintaining a healthy microbiome—and suggest that dietary interventions targeted at gut microbes may need to be tailored to individual patients.

“For a long time, we’ve been trying to move toward prescribing diets for the microbiome,” says Courtney Robinson, a microbiologist at Howard University who was not involved in the study. “We still don’t really know how to make a ‘healthy’ microbiome...but [this study] offers a more granular assessment on this process that we haven’t had before.”

Researchers have long known that diet can shape and reshape the gut microbiome, which plays a role in essential functions from synthesizing vitamins to guarding against infection. But the ways in which specific foods and nutrients affect the hundreds or thousands of microbial species that colonize the human digestive tract remain mostly mysterious. Both diet and microbiome vary enormously from person to person, and tend to change from day to day, even within the same individual.


Just like there's not one healthy diet, there's not one healthy microbiome—and different sets of gut microbes can react differently to identical foods. Image Credit: Lisovskaya, iStock

To disentangle some of this complexity, a team of researchers led by Abigail Johnson and Dan Knights at the University of Minnesota put 34 humans and their microbes under the figurative microscope.

For the duration of the 17-day study, participants recorded everything they ate and provided daily fecal samples. But when the researchers tried to match shifts in diet to changes in the gut, they realized they needed a new way to categorize foods. Broadly speaking, most of the people enrolled in the study were eating nutritionally similar diets, with about the same proportions of carbohydrates, fats, and proteins, making these categories too vague to yield much insight. Going food item by food item, however, was a pointless extreme at the other end of the spectrum. “That was one of the biggest limitations we hit,” Johnson says. “Nobody eats the same things.”

Instead, Johnson, who is both a microbiologist and registered dietician, and her team decided to sort the dietary data in a manner based loosely on USDA nutrition guidelines. The approach, Johnson explains, is comparable to an extremely detailed version of the food groups most American kids are taught in school. For instance, a category like dairy might be further broken down into milks, creams, milk desserts, and cheeses. In this new system, nutritionally similar foods like rice and potatoes—which are known to be interpreted differently by gut microbes—ended up in different subgroups.

Using these patterns, the researchers were then able to predict what a person’s gut microbiome might look like based on what they’d eaten over the past several days. Diet, however, is just one of a constellation of factors that influence which microbes will and won’t thrive in a given individual’s gut. These food-based forecasts also required prior knowledge about what each individual’s microbiome looked like at baseline. As a result, the predictions were completely personalized, and couldn’t be generalized among participants.

But a lack of uniformity isn’t cause for concern: Just like there isn’t one healthy diet, there isn’t one healthy microbiome. Even though the study’s participants were eating different foods, and harbored substantially different communities in their guts, all were in relatively good health, Johnson says. (Two of the participants subsisted almost entirely on the dietary replacement beverage Soylent for the duration of the study, and their microbiomes didn’t seem to suffer.)

“There’s a tendency to want to categorize things as good or bad,” says Amy Jacobson, a microbiologist at Stanford University who was not involved in the study. “But those types of black and white categorizations are difficult to make [for the gut microbiome]. What could be ‘good’ for one person may not be good for another.”

With that in mind, a personalized medicine approach makes sense, says Gilberto Flores, a microbial ecologist at California State University, Northridge who was not involved in the study. More work is needed to figure out if these predictions pan out long term, and with a larger, more diverse population of individuals. As research like this continues, however, similar models “could be a powerful tool in the future,” he says.

For now, these results underscore the fact that people still have a lot to learn about the food on their plates, Knights says. The nutrients human cells extract and absorb from the things we eat are the same ones that end up on labels, but a good portion of food matter is accessible only to the microbes in our colon. Deep in the large intestine, one organism’s trash can quickly become another’s treasure—and it’s here that this undigested “junk” starts to make a difference. Microbes simply don’t interpret foods in the same ways we do, and it may be time to start acknowledging their point of view.


Nutrition Facts labels track broad categories like carbohydrates and protein. But within these groups are a variety of chemicals, compounds, and molecules that are all interpreted differently by the microbes that live in our guts. Image Credit: zoranm, iStock

What’s not yet clear is what exactly comprises the dietary dark matter that nutrition labels leave off. One likely culprit is fiber, which is a single word that actually encompasses many, many different subtypes. “Microbes care intensely about the exact chemical structures of fibers, which can be different even between two different types of rice,” Knights says. “It’s going to take a long time for humans to build that knowledge base.” And the intricacies of fiber are likely just the tip of the nutritional iceberg, he adds. There are probably many more molecular nuances to food that humans haven’t even begun to uncover.

If all this sounds frustratingly complicated, that’s because it is. How, and to what extent, diet alters the microbiome are still open questions, says Gabriela Fragiadakis, a microbiologist and immunologist at Stanford University who was not involved in the study.

That being said, years of research have shown that the foods thought to be beneficial for the gut microbiome tend to overlap with dietary recommendations for people, she says. For all our differences, humans and microbes still have plenty in common. Stick to that rule of thumb, she says, “and at worst, you’ll still be consuming a healthy diet.”

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