By Tom Parker

Anne Biklé’s journey into the hidden world of microbiomes began in the least likely way possible: house-hunting. Actually, yard-hunting. In Seattle. To hear her tell it, the house was practically secondary, nothing more than a place to decompress while she transformed a boring patch of lawn into a lavish and intricate vegetative community, some edible, some not. The house she and her husband, David Montgomery, finally settled on fit all her basic requirements: four walls, roof, big yard.

It was built in 1918 by, Biklé suspected, Norwegians. “Norwegians did not come from a gardening race,” she said. “Norwegians left us a hodgepodge of a yard. It looked green, but it wasn’t biologically interesting or rich.”

Biklé, a biologist, is all about biology, and an unbroken expanse of sod was a violation of the natural order. With the meticulousness of an architect, she set out to draft a botanical blueprint. She schemed and dreamed, drew diagrams, charted the sun’s trajectory, and improvised dozens of composites of photographs and texts that littered the house. They looked like ransom notes from crazed botanists, Montgomery said.

And then they ripped up the sod. The underlying soil wasn’t dark and friable; it was khaki-colored concrete. Technically, it consisted of bits of Canada scraped off by a mile-high wall of ice, bulldozed down over the Puget lowlands, and compressed into a hardpan nearly impossible to sink a shovel into. There wasn’t a single worm in it.

“This was the beginning of my education as a gardener in what I call the Organic Matter Chronicles,” she said. She bought a wheelbarrow and painted it with flames to make it look speedier. In retrospect, she said, she should have painted it with microorganisms.

Biklé’s chronicle, which eventually expanded into a book, “The Hidden Half of Nature: The Microbial Roots of Life and Health,” was shared in a keynote address at the Kansas Rural Center’s annual Food and Farm Conference, held Nov. 16-17 in Wichita. Other speakers included Montgomery, a geologist, who expanded on the history of soil and its relationship to the demise of ancient civilizations, while Biklé honed in on the soil biome and the human gut biome.

Most of the world’s lifeforms are hidden from view. They burrow beneath the ground in incomprehensible numbers, they swarm beneath our skin in an intricate choreography that can enable, enhance or destroy life. Some are visible to the naked eye; the rest require specialized equipment.

Microbiomes are the one-celled microbial community found in every living entity, Biklé said. They’re native to a particular soil or host organism, whether human, dog, wombat, oak, or dandelion. Yeasts that ferment grapes into wine or milk into yogurt are one-celled organisms, and so, in some senses, are mushrooms. Because their cells are not completely closed off from one another, their cytoplasm flows like a river throughout the entire fungal body, making them a single-celled organism spreading both above- and belowground.

Even the dirt in Biklé’s yard had its own unique microbiome, though to be sure there wasn’t much of it. For her to have a successful garden, she would have to build that microbiome, in essence to create a healthy living soil teeming with microorganisms from a foundation uncannily similar to beach sand. She needed organic matter, and lots of it.

Anything she could get her hands on went into the mixture: wood chips fuzzy with fungi, fresh leaves, grass clippings, coffee grounds, pine needles, zoo doo (animal waste from the zoo), worm compost. That first summer, the soil started changing in color, darkening to a light mocha. Each year after it grew darker still, and more pliable, too. She planted a forest of maple trees, flowers and vegetables radiating outward from a small lawn. An eco-lawn, she called it, harvesting the grass clippings for the nitrogen. Within a geologic fraction of a second — 10 years, in human terms — the soil took on a life of its own. It wasn’t as fertile as Midwestern soil, but it was growing at a pace that far outstripped anything in nature.

“It takes nature about 100 years to build an inch of soil,” she said. “Who’d have thought you could change soil that rapidly? I thought I was doing all the heavy lifting, but what was really doing the work was soil organisms.”

Witnessing it firsthand led her deeper into the world of microbiomes, and she began to glimpse their importance not only for plants and agriculture, but for people and medicine and health. Although humans aren’t rooted in the soil, their bodies have at least one microbial cell for each of their own, and in some cases as many as three. Adding the genes we inherited from our parents, the bacterial members of our microbiome, and all the rest, it’s estimated that our bodies contain between four to six million genes.

“Suddenly, we’re not who we think we are,” she said. “That’s either creepy or it’s kind of cool, or maybe it’s both.”

The field of the human microbiome has exploded over the past 20 years, and new discoveries have led to a revised view of our digestive system that sounds a lot like plant biology. Our bodies are an ecosystem unto themselves, and its heart is the large intestine, or colon. Everything we eat ends up there, which makes the colon a nutrient-rich, all-you-can-eat buffet for microbes. Most members of the body’s biome live in a thick layer of mucus lining the interior of the colon. Most of the body’s immune system cells and tissues, on the other hand, are wrapped around the outside of the colon. A complex system of interaction between the biomes and the immune system either keeps the system in balance or sends it wildly out of control.

“We should be thinking of gardening our gut, because it is an ecosystem after all, and we know the kinds of things the critters inside that system are after,” she said. “And when they do well, we do well. This is our internal landscape.”

Scientists know that what affects our genes and our environment influences our health and well-being. They charted a decrease in infectious and chronic diseases in the postwar years following the introduction of clean water, antibiotics and vaccines, while at the same time noting an increase in other infectious diseases from 1950 until the present time. They theorized that some of our microbes were missing. But why?

The inappropriate use of antibiotics certainly contributed, Biklé said, but something else was responsible, something not so obvious. The culprit, they discovered, was our diet.

Most food contains carbohydrates, composed of fiber, starch and sugar, which the body breaks down into simple sugars, the main source of energy for the body. Modern people consume about the same amount of carbohydrates as their ancestors did in 1910, but back then carbohydrates derived primarily from whole plants or grains. Now they’re “busted up,” Biklé said, processed into various forms of component parts, and our digestive system can’t process them as well. The end result is that few nutrients ever make it down to the microbiome, and the microbiome goes hungry. Many scientists believe that our modern diet of high-carb processed foods is responsible for the explosion of Type 2 diabetes cases.

“We know that it matters what we eat,” she said, “but we don’t know what the role is in the agronomic system that produces those foods.” Biklé and Montgomery are currently researching that topic for another book.

The subject of microbiomes is infinitesimally deep and complex, and it doesn’t help that microorganisms are tiny and small and full of surprises. “Just when you think you have them figured out, some new piece of information comes along and throws your world upside down,” Biklé said. To keep it simple, she suggested, it helps to remember that our bodies are no different than the soil or the plants. Our gut is our root system, and when it’s well, we’re well.

“There are only six words you need to remember,” Biklé said. “Mulch your soil inside and out. That’s what it all comes down to.”

Parker is a freelance writer from Blue Rapids.