Going With Our Gut

Michael Pollan has done it again. Ten years ago, with the publication of The Omnivore’s Dilemma, he transformed farm-to-table philosophy into a movement for food system change. Now, in the space of just three years, he’s helped focus the national spotlight on the microbiome, the communities of microorganisms that live within the human body, other animals, soil, crops and the ocean. Since his 2013 article “Some of My Best Friends Are Germs” in the New York Times Magazine, we have seen a surge of interest: new scientific research, books and an exhibit at the American Museum of Natural History in New York. One artist in Montreal has even created a series of psychedelic self-portraits based on the bacteria living in and on his own body.

There’s federal funding, too. In May, the White House launched the National Microbiome Initiative that promises more than $500 million to help scientists better understand the microbiome and the connections between us and our planet.

The intellectual appeal of the microbiome is easy to understand, at least when the ever-eloquent Pollan is doing the explaining. This community of invisible organisms—100 trillion or so on every human body—regulates and, in some cases, controls our health and well-being. According to Pollan, the human microbiome helps to modulate our immune systems, metabolisms, even our stress levels and temperaments. No wonder that some scientists are calling the microbiome the “second genome.”

What we feed this vibrant community of organisms matters. Scientists estimate that our guts are fully colonized by the time we are about three years old. The typical Western diet, low on fiber and heavy on meat and processed foods, limits diversity in the microbiome, as well as its resilience. The same is true for the microbiomes of soils, crops and the ocean. Like us, they are what they eat.

In soil, for example, a variety of bacteria and fungi help to cycle nutrients and water to plants. They work, as Mike Amaranthus and Bruce J. Allyn explain in an article in The Atlantic, as a stomach for plants, digesting materials so that the plant can feed on important nutrients such as nitrogen and phosphorus. The lesson, the authors note, is that “reintroducing the right bacteria and fungi to facilitate the dark fermentation process in depleted and sterile soils is analogous to eating yogurt…to restore the right microbiota deep in your digestive tract.”

A number of writers have explored the parallels between the earth’s and humans’ microbiomes. (Stone Barns Center is currently exploring the theme in its lecture series, The Prescription: How Better Farming Leads to Better Health.) In The Hidden Half of Nature, husband and wife David R. Montgomery and Anne Biklé show readers how they transformed a neglected lawn on the side of their home into a productive vegetable garden by feeding the soil’s microbial community. Later, when Ms. Biklé is diagnosed with cancer, they explore the body’s microbes and their effect on our immune systems, concluding that our gardens and our bodies need healthy, biodiverse communities of microorganisms. In The Dirt Cure, pediatric neurologist Maya Shetreat-Klein takes the argument one step further, arguing that fresh food from vibrant soil is key to a healthy gut and a healthy life. She also suggests that just being outside—on a farm or in a park—can help protect children against allergies and boost immune systems.

It’s an intriguing theory, and one that makes sense particularly to the farmers’ market set. (And even if she’s wrong, it probably can’t hurt to eat more fresh and fermented foods and spend more time outside.) But the scientific understanding of the microbiome is still so new that it’s hard to nail down connections between healthy soil and a healthy gut.

What we do know is that there is much more to learn. And we are on our way. The American Gut Project aims to shed light on the connections between the microbiome and human health. Headquartered at University of California, San Diego, its lab analyzes more than 1,000 samples every week, enabling participants to learn about their own microbes while also contributing to a greater understanding of the human microbiome. New studies also have attempted to define what a healthy microbiome looks like and discovered that our microbiome can control inflammation as well as our circadian rhythms. The work gives a whole new meaning to the idea of listening to your gut. Now is the time to pay close attention.

Originally published on July 7, 2016