Photo (CC BY 2.0) by Caroline Davis

The Hidden Half of Nature: The Microbial Roots of Life and Health

Note to reader: When we set out to write The Hidden Half of Nature we weren’t sure what to make of our protagonists. Microbes, after all, are invisible. And when most of us think of microbes it’s mostly in terms of their notorious negative side. But once we dug into the new and burgeoning field of microbiomes and looked back in history, we found our story.

It’s taken several hundred years for the true nature of the mercurial microbial world to come into focus. Our own health and that of the soil in which our food grows is as much about the presence of microbial allies as the absence of pathogens. In other words, a focus solely on the adverse aspects of the tiniest creatures on Earth means we’ve been functioning with half a strategy in realms we rely on for our well-being. Across the board, a key tenet in the new view of the tiny multitudes that benefit our lives is to safeguard and cultivate them, even as we combat their pathogenic brethren. Embracing the duality of the microbial world, both philosophically and with new practices, holds much promise for unleashing untapped potential to transform agriculture into a sustainable enterprise and give us new tools to thwart the modern epidemic of chronic diseases. —D.R.M. and A.B.


We can’t help but see the world differently after unearthing the parallels in the essential roles that microbes play in both soil health and human health. While we still can’t see the half of nature hidden beneath our feet, we know it is the root of the life and beauty we see in our garden every day. And we look at ourselves differently too knowing that we are each a tribe of trillions.

Awed by the realization that the animals, plants, and landscapes we see around us are merely the visible tip of nature’s iceberg, we now appreciate how the mysterious world of microbes helps make soil fertile and food nutritious. We had thought most microbes were harmful, foes for our immune system and antibiotics to vanquish. Yet microbial communities are integral to key aspects of our own metabolism. Learning that we reap the harvest of what we feed our soil—inner and outer, for better and worse— widened our view, bringing into focus the extraordinary agricultural and medical value of cultivating beneficial microbes in the soil and in ourselves.

For well over a century humanity has viewed our invisible neighbors as threats. We saw soil life primarily as agricultural pests, and through the lens of germ theory we typecast microbes as agents of death and disease. The solutions that grew from these views—agrochemicals to eradicate pests and antibiotics to kill pathogens—became embedded in our practices. Intent upon killing bad microbes, we haven’t cared much about the collateral damage to innocent microbial bystanders, although we are beginning to glimpse the effects upon ourselves.

While spraying broad-spectrum biocides on fields may take care of agricultural pests over the short run, the pests return with a vengeance in the long run. And there is a direct parallel to aggressive use of antibiotics over recent decades, which have spawned new strains of antibiotic-resistant bacteria, an increasing number of which we now have no defense against. Instead of solving problems, we’ve become addicted to solutions with limited staying power. Dowsing gardens, farms, and people with broad-spectrum biocides should no longer be the de facto solution for gardeners, farmers, and doctors.

What does this all mean? Soil fertility and our immune system—two things critically important to us all—don’t work like we thought they did. Plants with depauperate communities of beneficial microbes around their roots dial back producing the phytochemicals that defend them and nourish us. Of particular relevance for our own health is that it turns out we need most of the microbes we’ve been trying so hard to kill. And scrambling our own microbiome, especially early in life, is increasingly implicated as a factor underlying modern maladies. It’s not that we shouldn’t fight pests and pathogens, but that the approaches we have come to rely upon come with hidden costs.


Subscribe to the Slow Money Minute, a monthly roundup of news and updates.


Looking back on our experience, we believe the difference between a garden and a weed-covered lot can show the way forward. Nature abhors bare ground, and she’ll fill it in her own way. But you can shape a place if you work with her. We intentionally cultivated the soil beneath our tiny patch of Earth to reap flashes of color from flowers, trees to inspire us, and vegetables to eat. The discovery that the real source of the beauty, comfort, and sustenance in our garden lay beneath our feet surprised us, and so did something else about our garden. It has about the same surface area as our digestive tract. Imagine gardening your gut, tending to the life you want and need in the body’s innermost sanctum.

Just as compost, wood chips, and mulch nourish soil life, the same is true of the foods that nourish the symbiotic inhabitants of our gut. While a living soil will ripple above ground to support the health and resilience of a garden or farm, your inner soil supports another kind of garden—your body. If we cultivate the microbes that benefit us, they’ll help fend off their pathogenic cousins and keep our immune system working for us, rather than turning against us.

Tending the garden of our microbiome doesn’t mean forgoing modern medicine. Realistically though, it’s going to take some time to align medical practices and therapies so that they work with our microbiome. In the meantime, we need to ensure we start out with a healthy microbiome and then maintain it with a diet rich in prebiotics. And if our microbiota take a hit, whether after antibiotics, illness, or maybe even a colonoscopy, we might consider doing what a gardener does and replant what we’ve lost and help them get established.

In the end, it boils down to some simple advice. Starve your enemies and feed your friends. And don’t kill off your allies that help keep the enemies in check.


David R. Montgomery and Anne Biklé are married. David is Dean’s professor of geomorphology at the University of Washington and a MacArthur Fellow. Anne is a biologist, gardener, and writer. You can follow them on Twitter @dig2grow. Their website is www.dig2grow.com.

0 replies

Leave a Reply

Want to join the discussion?
Feel free to contribute!

Leave a Reply

Your email address will not be published. Required fields are marked *