If you’ve participated in foodie dinner table conversation in the past year, you’ve likely heard the term “microbiome” more than once.  Due in part to exceptional expository pieces such as Michael Pollan’s “Some of My Best Friends Are Germs,” the popular lexicon now includes some incredible statistics about the body’s ecosystem of 100 trillion bacteria. For instance: a count of the cells within the human form will yield a tally of nine non-human microbes for every human cell. Moreover, 99% of the total genetic information in our corpus is microbial. We’re taught to think of life as a turf war between “us” humans and “them” germs; yet, it turns out that “us” is mostly “them.”

And many of the bugs inside us – the denizens of our microbiome – are doing us quite a bit of good. In babies, Bifidobacterium Longum helps stave off pernicious bacterial infections, while Lactobacillus Johnsonii aids in the digestion of mother’s milk. In adults, Bacteroides Thetaiotamicron and Escherichia Coli (different from unsavory strains of E. Coli) are critical to digesting plants and extracting vital vitamins from our food. Moreover, our internal bacteria can even determine our susceptibility to arthritis, our predilection for metabolic disorder, whether we are fat or thin, whether we develop the type of arterial plaque that causes heart disease, and even how we think. Whoa.

Knowing this, we have begun to own up to the need for a paradigm shift concerning microorganisms. As one author puts it: “We are moving from a multi-decade focus on killing ALL bacteria via soaps, detergents, antibiotics and hand sanitizer, to a new understanding of the complex bacterial system in our bodies and in the world around us.” Famous fermenter Sandor Katz further elucidates this point in Michael Pollan’s Cooked: “’To declare war on ninety-nine percent of bacteria when less than one percent of them threaten our health makes no sense. Many of the bacteria we’re killing are our protectors.’”

So how do we best cultivate our individual microbiomes to effect benevolent health outcomes? One way to preserve your gut ecology is to avoid the haphazard consumption of antibiotics. Antibiotics are the “nuclear option” in regulating our foreign fauna: they wipe the slate clean, eliminating good bacteria along with bad. Similarly, it’s good to lay off the Purell and antibacterial soaps. But what about promoting the growth of undersized friendly germ colonies, or sowing new communities that aren’t currently present in our bodies?

Is this the domain of food, or medicine? How might we optimally shepherd the hardy, cunning, and inexhaustible soldiers of our internal infantry? If control is the most valuable currency we can amass in our daily grapple with the swirl of feral nature, then this is a major question indeed.

Food

What we eat for our own nourishment also happens to be the fuel for our microbiome. And the bacteria that enter our body along with our food often become a part of the microbiome. Indeed, the evolution of our internal microbe colony has historically depended heavily on the consumption of a variety of “living” foods.

Today, food safety regulations all but ensure that the living elements of our food are annihilated in the course of preparation, packaging and delivery. Much as we use the blunt instrument of antibiotics to destroy bacteria in our bodies, we use heat (Pasteurization) or high-pressure processing (HPP) “kill steps”, engender abundant acidity, thoroughly dehydrate, and seal our food in protective packaging to ensure that microorganisms are obliterated. We codified these safety procedures to ensure that we eliminate a short list of pernicious pathogens (such as e. coli, salmonella, and listeria) that sometimes exist within the large community of microorganisms that are present on raw food.

By requiring that our packaged food be heated, acidified, and desiccated, we are rendering it “dead” in every sense. Valuable enzymes, vitamins, minerals, and antioxidants are forever lost. And so are the myriad harmless and benevolent microorganisms that we have benignly ingested for centuries. Accordingly, processed food fails to stir up microbiome magic.

“Living Food”

Lately, there has been a resurgence of food as medicine for the microbiome. Michael Pollan’s latest book, Cooked, offers a robust look at a productive class of artisan fermenters that create living foods as varied as cheese, yogurt, kimchi, sauerkraut, miso, prosciutto, pickles, etc. (Cooked also delves eloquently into the science of fermentation, a mind-blowing process wherein humans cultivate microorganisms that transform foods for us.) Fermented foods contain beneficial live cultures known as probiotics, while other foods contain prebiotics, the nourishing molecules that sustain probiotic organisms.

(Important side note: many mass-produced “fermented” foods are not actually fermented by living organisms. They use chemical processes to mimic the effect of microbial action. For instance, supermarket pickles are pickled by vinegar, not microbes. These non-living foods are cheaper to make and more uniform in taste. But they lack probiotic function.)

Contemporary artisan fermenters have benefited from a revolution in financing and distribution options. For instance: after reading Cooked, I wanted to eat more “living” food, so I ordered some delicious Real Family Foods sauerkraut through Good Eggs, a grocery delivery service that brings a diverse array of goods to my doorstep. A few weeks later, I received an email from peer-to-peer lending platform Kiva Zip with a request to help finance a loan to Real Family Foods. I contributed $25, and within a few days the $2,500 loan was fully funded by 41 of Real Family Foods’ customers. The loan is being used to obtain USDA Organic certification. This case study highlights how easily the modern consumer can vote with their dollars for shifts in the food landscape – without ever leaving home. I supported one of our oldest food production techniques by using some of our newest technology, all in the interest of making my buggy friends happy.

Yet, the exact relationship between which foods we eat and how those foods impact our microbiome is still somewhat murky. We know that fresh organic produce (some exemplars are onions, garlic, and leeks; and, broadly, vegetable fiber is excellent) and fermented foods work wonders. Highly processed foods are bad, as is sugar (for instance, you don’t have to refrigerate honey because bacteria cannot live in a pure sugar solution), and antibiotic-laden meats will shock your gut ecology. Beyond that, it’s hard to say. And there is real risk in consuming raw foods that may be tainted by deadly pathogens. (Note: one of the many remarkable aspects of fermentation is that the fermenting microbes create an acidic environment that is inhospitable to pathogens. Only the good guys can survive.)

Medicine

The traditional role of Western medicine is to react to developed or emerging sickness. The medical establishment has been slow to develop preventative measures or guide patients on how to maintain health, particularly when it comes to food. Layer on to this that our understanding of the microbiome is rudimentary at best, and you can see why most physicians probably don’t have polished advice for their patients when asked: “So, how do I jump-start my internal ecosystem?”

Precision Therapeutics

However, many are looking to the biotech community to develop targeted therapeutics that will help the microbiome flourish. Second Genome is the early leader in this category, and has taken some $19 million in venture financing. But the leaders of Second Genome know that creating therapies for any single person will be difficult given the unique nature of each microbiome. Second Genome CEO Peter DiLaura acknowledges the need for precise therapies: “’We are really focused on the interaction between the microbiome and the host…when we think about therapeutics, it’s about impacting the interaction that is beneficial for disease.’” The company is using DNA sequencing technology to customize solutions, but the cost of doing so is onerous. Peer company Vendata Biosciences is pursuing similar solutions.

At this point, not only are such interventions too costly for mass adoption, but they generate the same slew of privacy concerns that other DNA sequencing technologies have raised. (NPR has an entertaining and illuminative story on this topic, and the accompanying cartoon video on the microbiome is definitely worth a watch.) Nonetheless, endeavors such as the American Gut Project and uBiome are nobly pressing forward to map our collective microbiome, much as the precedent Human Genome Project did in spite of concerns voiced by its detractors.

Right now, the best microbiome solution offered by medicine is inelegant, highly effective, and not for the squeamish. Fecal microbiota transplants (or fecal bacteriotherapy) are exactly what they sound like: taking stool from a person with desirable microbiomic traits and – ahem – sharing it with a person with health issues. The results of the procedure have been inarguably positive, and accordingly the FDA has green-lighted the therapy.

Food or medicine?

The “answer” lies somewhere betwixt the two domains: both food and medicine play a role. With food, cultivation of your microbiome is just the latest in an endless list of reasons to eat more fresh produce and trustworthy raw food. And integrating fermented products into your diet makes good sense: humans have been eating ferments for as long as we’ve been around. Our co-evolution with fermenting microorganisms is a clear synergistic success story.

As far as medicine goes, truly targeted microbiome treatments are not cost-competitive enough to supplant the crude fecal transplants being used today. But those transplants are saving lives in acute disease states. Their applications should be increasingly tested in preventative care.

There are also over-the-counter supplements on the market that purport to service your microbiome. Walk through your local store and you can find a multitude of probiotic pills or “probiotic-enhanced” foods. But any consumer should be seriously skeptical of supplements, and I suggest opting for real probiotic foods instead. Probiotic supplements might be appropriate after a course of antibiotics to catalyze a rebuild of your microbiome, but I suggest doing research on products before buying them.

In the meantime, stay tuned to scientific advances addressing the microbiome, and pay attention to credible literature on what probiotic and prebiotic foods are best suited to positive health outcomes. The next chapter in our long history with our tiny friends is sure to be an interesting one.