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Cooking changed human history. Did it change our microbes too?

Gut microbes react differently to raw and cooked versions of the same foods.

ByKatherine J. WuNOVA NextNOVA Next

Mice put on monodiets of raw sweet potatoes can't absorb as many of the tubers' calories, shunting undigested starch to the microbes in their colon. Image Credit: piyaset, iStock

At least 250,000 years ago—perhaps much earlier—an early human ancestor held a morsel of food to a flame and watched it burn.

Sweltering under the heat, chemical bonds broke apart and rearranged, liberating nutrients and neutralizing toxins. What had been a barely-edible hunk of raw material turned soft and palatable, and nutritious. The era of cooked meals had begun.

Though the when and where are still debated, the advent of cooking was inarguably a turning point in our evolution. To date, we’re the only known species that intentionally heat-treats its meals—and doing so fundamentally alters the way the human body experiences its food.

But the human body isn’t just, well, human. For every Homo sapiens cell we’ve got, there’s at least one microbe to match—including the trillions of bacteria that inhabit the colon.

This so-called gut microbiome plays a big role in how humans digest and metabolize food. And if cooking changes how a human body eats, there’s no reason the same shouldn’t be true of the microbes that inhabit it, says Rachel Carmody, a microbial ecologist at Harvard University.

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New research from Carmody and her colleagues suggests that’s exactly the case. She and her team have found that raw and cooked versions of the same foods have distinct effects on the gut microbiomes of both humans and mice, exposing their cells to different nutrients, as well as compounds that can curb bacterial growth. Their study, published today in the journal Nature Microbiology, spotlights a little-explored aspect of the diet-microbiome relationship—and hints that, as humans evolved around the culture of cooking, the living contents of their guts did, too.

“This is a really exciting paper…[answering] a crucial question,” says Alexandra Rosati, an anthropologist at the University of Michigan who was not involved in the study. “The shift to a cooked diet was a foundational transition in human evolution. This helps test how cooking transformed how our bodies work.”


Exposing food to heat changes its flavor, texture, and digestibility. Image Credit: FotografiaBasica, iStock

Carmody, who spent graduate school investigating how food processing affected early human evolution, didn’t originally set out to study microbes. Years of research had clearly shown that heating ingredients can increase their caloric payoff. That’s partly because cooking gives food a head start in the digestive process, upping the number of available nutrients while reducing the amount of energy the body expends on breaking down material.

But even both these factors together couldn’t fully account for the effects of cooking. There was something else, Carmody says, that made heated foods a different dietary experience.

That’s when gut microbes came into the picture. As tenants of the colon, these bacteria encounter whatever foods escape the small intestine, where most nutrients are absorbed—which means their dietary fates are directly tied to ours. But no one had really taken a close look at how gut microbes reacted to the same foods in raw and cooked forms.

To fill in some of these gaps, a team led by Carmody and Peter Turnbaugh, a microbiome researcher at the University of California, San Francisco, put mice on five-day monodiets, feeding them only lean beef or sweet potato—stand-ins for the foods our ancestors probably ate—that was either roasted or left in its natural state.

Heated up or served raw, the meat produced similar results. But even though mice noshing on raw sweet potatoes ate more than their cooked tuber counterparts, they weighed less at the end of the five-day trial. An analysis of their feces also showed that their microbial communities had become less diverse and less populous.

Some of this, Carmody explains, goes back to nutrient availability. The bulk of the calories in tubers come in the form of starch, which breaks down when exposed to heat, becoming more digestible. When limited to raw sweet potatoes, the small intestine absorbs fewer nutrients, shunting more food to the colon, where certain species can feast on a smorgasbord of starch. Other bacteria that lack the machinery to metabolize these molecules, however, might end up starved out.

But the researchers were surprised to find that uncooked tubers weren’t just changing up gut microbes’ daily menu: They seemed to be directly killing off some strains, too.

When the team sifted through the feces of mice subsisting only on raw sweet potatoes, they found the pellets were full of damaged bacterial cells, resembling those from rodents dosed with antibiotics. The find came as a bit of a shock. “We were like, ‘Good grief, what’s happening in our sweet potato?’” Carmody says.

An in-depth chemical analysis of the tubers revealed a clear culprit: bacteria-killing chemicals, produced by the plant to ward off infections. In the raw diets, these heat-sensitive compounds had made it to the gut intact, while mice and microbes eating roasted sweet potatoes had been spared their ill effects.


In their experiment, the researchers fed some mice diets of raw or roasted cuts of beef (eye round roast). Image Credit: Plateresca, iStock

These findings may raise new questions about raw foods, which are often touted as a universally healthy alternative to “bad” processed foods, Turnbaugh says. Raw foods certainly have their nutritional perks, he says. But “in reality, there’s a tradeoff.”

Still, heat doesn’t have uniform effects on all plants, which come in many forms. For instance, similar experiments with less starchy crops, like beets and carrots, produced fewer differences between raw- and cooked-fed microbiomes.

To cap off the project, the team fed a small group of human subjects raw or cooked versions of a more varied diet that included fruits, salads, nuts, and seeds. The interventions were brief—just three days—and didn’t have any obvious effects on weight or wellbeing. But each diet still produced its own noticeable shifts in participants’ bacterial communities.

“This is a cool paper,” says Gilberto Flores, a microbial ecologist and microbiome researcher at California State University, Northridge who was not involved in the study. “I hadn’t given it much thought before, but it makes sense. Cooking is like predigestion...and it’s fascinating to think about how it’s allowed the microbiome to diversify.”

Though the study didn’t dig directly into evolutionary history, it hints that similar effects may have played out in the predecessors of modern humans, whose microbiomes underwent drastic changes after our lineage split off from chimpanzees, Rosati says. This rapid evolution was likely spurred by many cultural and ecological factors, she says, but it’s not hard to see how cooking could have been one of them.


Modern humans have a hard time subsisting healthfully on raw diets, but whole, unprocessed foods still bring important diversity to the human body and its microbes, researchers say. Image Credit: AlexRaths, iStock

The repercussions of this microbial renaissance might then have fed back into us—literally. Many researchers believe that the simple act of adding cooked foods to our diet ushered in a whole set of changes to the human body, perhaps even providing the extra energy our brains needed to outpace those of other primates. Nourished by an expanded set of nutrients, the gut microbes of our predecessors might have played a far bigger role in this metabolic metamorphosis than once thought, the researchers suggest.

If cooking made us human, we could have our microbes to thank.

Of course, a lot has changed since our ancestors first started firing up tubers on the regular. While other primates can still lead healthy lives on completely raw diets, it seems the same is no longer true of humans, Carmody says. But whole foods, which are nutrient-rich and help key members of the gut microbiome thrive, still have their place in the modern world, she adds, especially in industrialized countries where ultra-processed ingredients have become the norm.

“A legacy of cooking has shaped our biology,” Carmody says. “We know the human body has changed in response to cooking. The results we show here tell us the microbial community has as well.”

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