The Microbiome Diet: Evolving Past Paleo

There is no "one size fits all" when it comes to the microbiome. You could be a vegetarian who eats all those grains and legumes that the Paleo people demonize -- and be extremely healthy. The key is to keep supporting your little friends inside -- your microbiome.
01/14/2015 12:56pm ET | Updated March 16, 2015
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Five fresh fruits and vegetables, part of the daily recommended healthy diet, held on the prongs of forks, on a white background.

For the past several years, the biggest buzzword in diet has been Paleo. This approach to food supposedly re-creates the way our ancestors ate during the Paleolithic period, before the invention of agriculture. Although there are many different incarnations of Paleo, they all agree on one thing: Human genes evolved when our ancestors were still hunters and gatherers. Therefore, according to the Paleo perspective, our genes have simply not had time to catch up to a diet of grains and legumes.

But our bodies are far more flexible than the Paleo people would lead you to believe. That's because Paleo leaves out a crucial factor in the equation: the microbiome.

It's Your Bacteria's Genes That Matter
The microbiome is the community of trillions of bacteria that live in your digestive tract and elsewhere throughout your body. Collectively weighing about three pounds -- the same weight as our brain -- these bacteria outnumber our human cells by a factor of about 9 to 1. I jokingly tell my patients that I might look like a human, but I am really just "bacteria in a suit." Each of us is literally more bacteria than human.

Not only do our bacteria outnumber us, their genes outnumber our genes -- by a factor of 150 to 1. In many ways, their genes have more of an influence over our day-to-day life than our own genes do.

When your microbiome is balanced, you have a terrific ally that keeps your body healthy, promoting good digestion, clear thinking, balanced mood, and glowing overall health. When your microbiome goes out of balance, however, you risk such symptoms as brain fog, depression, anxiety, bad skin and insomnia -- and, down the road, obesity, diabetes, and cancer.

Now, what does this have to do with Paleo? Well, the Paleo view is that human genes evolve with glacial slowness, and that humans haven't yet caught up to the dietary changes brought on by the invention of agriculture.

Maybe human genes do change that slowly (although they have changed more since the Paleolithic era than Paleo orthodoxy would suggest). The population of the microbiome, however, changes extremely rapidly -- often, within a single day.

After all, the average lifespan of a microbe is only 20 minutes. That's long enough for your entire microbiome to change its composition.

And when your microbiome changes, its genes change too. You literally could wake up with one set of microbial genes on Monday and a whole other set of microbial genes on Tuesday.

What changes the population of your microbiome? A number of factors, including environment, exercise, sleep, and stress. But the most important factor is diet. How you eat determines which microbes live happily within your gut and which die off and disappear.

So the Paleo people have it exactly backwards. It's not that our genes have programmed us to eat only a certain diet. Rather, our diet "programs" our microbiome -- and its genes.

You Are What Your Bacteria Eat
A breakthrough study from Harvard's Peter J. Turnbaugh and Duke's Lawrence David reveals some of the ways in which our diet shapes our microbiome -- and thereby affects our ability to digest various types of food. In 2011, the researchers fed volunteers two very different diets. One group was given a high-protein diet consisting of bacon and eggs, spareribs, brisket, salami, cheese, and pork rinds. The other was fed a very high-fiber diet of fruits, vegetables, grains, and beans. Bacterial analysis of fecal samples collected before, during, and after the experiment showed that what each group ate had a huge -- and almost immediate -- effect on their gut bacteria.

Lo and behold, each group began to develop the very type of bacteria that would most help them digest the particular types of food they had just eaten. In just 24 hours, meat eaters saw an increase in bacteria that are resistant to bile acids (bile acids are a byproduct of the breakdown of meat). If you're a meat-eater, you need those bacteria -- so the microbiome responded. The vegetarian group had far fewer bile-resistant bacteria, because, given their diet, they didn't need them. The microbiome was responding to them, too. Even the long-term vegetarian who agreed to eat meat for this study saw a rapid microbial shift.

The microbiome's dynamic ability to respond to our diet is why our bodies can adapt to so many different ways of eating -- regardless of how long it might take for our genes themselves to change. Our genes aren't what matter -- our microbiome's genes are the key. We don't have to move at the millennial pace of genetic evolution. We come equipped with a mechanism that is exquisitely responsive to a number of different types of foods, which is why humans all over the world can survive on a remarkably wide range of diets.

We Can Eat Almost Anything -- But Should We?
The Paleo diet varies depending on which expert you listen to, but they all agree on one thing: We humans can't digest grain. They say that our genes just haven't evolved enough to metabolize it properly, and that therefore grain is responsible for all sorts of serious disorders.

Not only is that bad genetics, it's bad nutrition. Numerous studies have shown that whole grains have protective effects against heart disease, obesity, and diabetes. We're beginning to see that at least some of these protective effects come from the way that the fiber in grains nourishes the microbiome.

That's why I tell my patients that they can enjoy quite a bit of flexibility in their diets -- as long as they support their microbiome. You don't want to eat too much meat -- the 55 percent of daily calories that some Paleo experts recommend -- because studies have shown that much meat is detrimental to the microbiome. Nor do you want to consume a typical Western diet -- refined flour, sugar, unhealthy fats, additives, preservatives, and artificial sweeteners -- because those ingredients also feed exactly the wrong kind of bacteria.

On the other hand, lots of fresh, whole fruits and vegetables, legumes, and whole grains are terrific "microbiome food." Asparagus, carrots, garlic, Jerusalem artichokes, jicama, leeks, onions, radishes, and tomatoes are Microbiome Superfoods, with exactly the kind of fiber that feed many beneficial species. Fermented foods -- kimchi, raw sauerkraut, fermented vegetables, and kefir (a type of fermented milk) -- are natural probiotics that replenish your friendly bacteria. Probiotics -- capsules, pills, or powders that contain live bacteria -- can supplement a healthy diet.

There is no "one size fits all" when it comes to the microbiome. You could be a vegetarian who eats all those grains and legumes that the Paleo people demonize -- and be extremely healthy. You could also eat a diet full of whole, fresh foods with moderate amounts of chicken and fish, and small amounts of beef or lamb -- and also be extremely healthy. The key is to keep supporting your little friends inside -- your microbiome.