Credit: National Cancer Institute
Credit: National Cancer Institute

You Are What You Eat, All 100 Trillion Of You

The old adage that “you are what you eat” is especially true when you bring your gut microbes into the picture.

Your guts are home to trillions of bacteria and other microbes, which outnumber your own cells by ten to one. This microbiome—the collective term for the microbes and their genes—helps to break down the food you eat, among many other important roles. It’s like one of your organs, albeit one made of legions of swarming cells, none of which are human.

It can also change… and fast.

By setting ten volunteers on either a vegetarian menu or a carnivorous one, Lawrence David from Duke University and Harvard University’s Peter Turnbaugh have shown that when our diet changes, our gut bacteria react very quickly. Within days, some species step into the limelight, while others fade into the background. They activate different genes, pull off different metabolic tricks, and secrete different substances. Our microbiome, it seems, can rapidly switch between plant-eating and meat-eating modes.

“There are interesting evolutionary implications to such a rapid response,” says David. Our menus are fairly stable now, but our ancestors faced steady supplies of plants punctuated by volatile gluts of meat. “The ability for the gut microbiome to quickly react to changes in diet may have conferred an extra layer of nutritional buffering, and provided ancient humans with increased dietary flexibility.”

“They show convincingly, with very elegant, conclusive experiments, that diet has a dominant role in determining the microbiome,” says Carlotta De Filippo from the Edmund Mach Foundation in Italy.

But Oluf Pedersen from the University of Copenhagen has “major concerns about whether the findings are robust and whether they can be generalized”. Everyone who studies the gut microbiome knows that it varies a lot from person to person, says Pedersen, so it’s not clear if these results will generalize to other people beyond the small number in the study. “It will be important run comparable studies in larger samples.”

This isn’t the first time that scientists have looked at how diet affects our gut microbiome. Other studies have shown that as we grow up, bacteria that specialise on digesting milk give way to those that digest the more complex nutrients in solid food. If we eat mainly plants, like African hunter-gatherers, our guts are filled with plant-digesting specialists that break down fibre. If we’re raised on a Western diet, high in animal protein, sugar and fat, we end up with a microbiome that’s less diverse, better at harvesting this energy-rich flood. And as people eat a low-calorie diet, and lose weight, their gut communities shift towards bacteria that are associated with leanness rather than obesity.

But all of these studies all looked at long-term trends that play out over weeks, months, or lifetimes. David’s team wanted to see what happens over days. If you flood your gut with different food, how long does it take for your microbiome to react?


They did this by recruiting ten volunteers who were willing to collect daily faecal samples. They each ate two different diets for five straight days —a plant-based one that was rich in grains, legumes, fruit and vegetables, and an animal-based one composed of meat, eggs and cheese.

In general, the animal diet led to more dramatic changes than the plant one. It fostered a more diverse gut microbiome and it made 22 species more abundant (compared to just 3 for the plant diet). Some of these ascents were easily explained. When we eat fatty food, we produce more bile—a bitter fluid that helps to break down fats. Bile stunts the growth of many gut bacteria, so it’s no surprise that the species that became most common during the animal diet are those that can resist bile.

One of the bile-resistant bugs—Bilophila wadsworthia—can cause inflammatory bowel disease in mice. Other produce substances like deoxycholic acid (DCA) that (again, in mice) can increase the risk of liver cancer. It’s not clear if these risks apply to people but the results do suggest that the microbiome could react to dietary changes in potentially harmful ways.

David and Turnbaugh’s team also found that the altered gut communities did different things. During the plant diet, they became better at breaking down carbohydrates; during the animal diet, protein digestion was their forte. On the meat-heavy days, they activated more genes for breaking down harmful chemicals found in charred meat, and for making vitamins.

And these changes happened very quickly. Some were obvious by day one. By day four, you could pick up a stool sample, list the active genes within it, and predict with total accuracy which diet the owners had been on.

In fact, when the recruits ate the plant-based diets, the active genes in their gut bacteria quickly resembled those in plant-eating mammals. When the recruits ate meaty fare, their gut microbiome became more like that of carnivores. “This refines an idea in the field that gut microbiomes in animals reflect millions of years of co-evolution,” says David. His results suggest that diet can lead to similar differences in mere days.

Just two days after the volunteers stopped their diets, things were back to normal. The gut microbiome, it seems, is a fickle beast—easily changed, but not permanently so.

The team also found that our food doesn’t just change the microbes that already exist in the gut—they also add some new ones. The animal diet brought in a wave of immigrant bacteria that are found in (or used to make) yoghurts, cheese, and cured meats. The plant diet also introduced a virus that infects spinach.** “This surprised us as we thought the acids in the digestive tract would kill a lot of food-borne microbes,” says David. “This supports the notion that probiotics could affect the gut microbiome, as orally ingested microbes may survive and be active in the gut.”


The diets in the experiments are meant to be extremes, and the results don’t necessarily tell us that one is better than the other, especially with such a small sample. The point is that our gut microbiomes are more flexible than we previously thought. A recent study showed that most of the strains in our guts stay there for decades or more. But while the roster is clearly stable, their relative numbers fluctuate a lot, and food-borne newcomers can gain a foothold.

Think about the implications of that. You could view yourself as an individual human with some microbes inside you. Alternatively, you could view yourself as a super-organism—a cooperating colony of cells, some of which are human but most of which are microbial.

And if that’s the case, David and Turnbaugh’s study shows that you become a very different you when you change what you eat.

* Nine of the volunteers were omnivores, but one was a lifelong vegetarian.  “That did matter quite a bit,” says David, “as his gut microbiome was quite distinct from the other subjects’. We think it would be an interesting follow-up study to perform a larger, more targeted analysis of a cohort of vegetarians.”

** If viruses like this can replicate in the gut, it means that the guts of plant-eaters like cows could be huge melting pots, where viruses from different plants could meet and swap their genes.

Reference: David, Maurice, Carmody, Gootenberg, Button, Wolfe, Ling, Devlin, Varma, Fischbach, Biddinger, Dutton & Turnbaugh. 2013. Diet rapidly and reproducibly alters the human gut microbiome. Nature

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