Essays An ode to germs, guts and gardens When calamity strikes, a gardener finds her way back to the basics.

The location is beautiful and the soil sucks. I live below the first buckle of foothills of Colorado’s Rocky Mountains, waves of mountains to the west and grasslands in all other directions. The only problem? The dirt is as bad as the view is good. Instead of the deep brown rich soil that other locations on the planet naturally enjoy, this stuff is composed of sand and clay. But even worse, underneath the thin top layer of soil that supports all the glorious grama and bluestem and sage is, well, rock. Rock and more rock.

It’s good that the view is so inspirational, because it’s given me patience during the 10 years I’ve spent trying to foster soil that was gardenable. Like many people, I’ve been busy and harried, but I also had a vague but purposeful plan: Building soil that would foster vegetables, vegetables that would foster good health.

More or less, this all worked in a haphazard way. Despite the weeds, the drip-irrigation system that got pulled all over the place by the dog, and the persistent plentiful deer, there was, in fact, a nice crop of veggies.

But then catastrophe struck. It struck in the way that catastrophe often does: in a series of unrelated chaotic events. My particular calamities involved a septic tank, a bulldozer, an infected tooth and antibiotics. From the chaos of all that, I learned to sing songs of praise to microorganisms, both in my garden and my gut.

Brooke Warren

It started with an ice storm, which froze the ground, which caused the septic tank to burble out foul-smelling contents in the middle of winter. The appropriate people were called; a new septic tank, they told me, would cost nearly $10,000, and, more painfully, would need to be moved because of new regulations. The only place to put it, they added, was where the garden bed now sat.

After years of amending the soil, I found that news disturbing, but then, voilà! I had the excellent idea to ask the gentlemen to save this stuff; they could scrape and bulldoze it to the side or something, right?

But no. Alas.

The crew came while I was gone on a short errand, and before I returned, my hard-earned soil was buried in a huge pit many feet below the surface of the ground. I stood on top of the rocky “parent material,” as it is called, and stared down at it, as if my vision might penetrate and bring up the dark good soil below. The stuff below me had no organic material, no nothing. The chickens, who had followed me out there, looked up at me. Then they looked down at the crappy soil, looked up at me again. Not even they liked this soil. No bugs in it — nothing really to do except take a dirt bath.

People who live in such areas will understand my sorrow. All those pickup loads of manure, compost, even gently relocating worms from the street in the hope they would loosen the compacted soil (and because I felt sorry for them). All that again?

But I didn’t have time to grieve, because I also had an aching face. Soon after, and yes, nearly $10,000 later, the correct two teeth had been identified, root-canaled, infected, my gums cut and stitched, infection again, a perforated sinus cavity, gums cut and stitched again, and then finally pulled. Which required round after round of antibiotics. Which caused my stomach to hurt, because my good microorganisms had been killed, too.

My guts were as barren as the dirt outside.

Francesca Yorke/Getty

When things look bad, I figure, a person can check out, or she can stand defiantly and shake her fist at the skies. I opted for the second. Fixing these two problems — the barren garden dirt, the barren guts — became related, not only in the sequence of time, but in the very core of the way they functioned. Indeed, soil fertility and human health are directly related; the word “human,” after all, is related to “humus,” meaning “earth or soil.”

Humans are just beginning to understand exactly what that means — both the human gut and the layer of dirt are somewhat unexplored territory. There are 100 trillion bacterial cells in a human body, 10 times the number of human cells — on a DNA level, at least, we are more microbial than human. There are 100 million to 1 billion bacterial cells in one teaspoon of healthy soil, which makes me think Leonardo da Vinci had it about right: “We know more about the movement of celestial bodies than about the soil underfoot.”

There’s been a paradigm shift of late, wherein the terms “microbiology” and “neuroscience,” formerly two disciplines that rarely came into contact, are almost colliding headlong in the same sentences. Recent science suggests that several health problems may be related to a disruption in this relationship between bodies and the microbial symbionts with whom we coevolved. Like garden dirt, our guts need microorganisms — but due to our farming and eating and kitchen practices, we aren’t getting that good broad spectrum of bacteria anymore. And that, ultimately, is related to dirt.

So I turned my attention to the soil. As someone who is always a little too busy, and a little haphazard, I have never quite known what exactly I am supposed to be doing to my garden dirt. But I do have the vague sense that garden dirt is supposed to be dark and full of organic matter, and I also believe that perfectionism is dangerous, and that it’s best to stick to the general idea, which is this: Stewarding good soil is one of those good things to do; fostering humus is fostering humanity. The more humus, the more fertile the soil is. Indeed, humus is the most critical aspect of soil composition, and humus is not what I had.

“We might say that the earth has the spirit of growth; that its flesh is the soil.”

— Leonardo da Vinci

So I started over again: Food scraps out to the compost bin, manure brought in, the chickens let loose to scratch and scat. Slowly, over the course of winter, and into spring, things started to decay. By spring, that parent material looked at least semi-gardenable.

Meanwhile, I was trying to help amend the microorganisms in my guts, too. They do more than digest food; the little creatures in our digestive tract help our immune system and might even be responsible for our mood, stress and temperament. As acclaimed science writer Michael Pollan points out, when gut microbes from easygoing, adventurous mice were transplanted into the guts of anxious and timid mice, those mice became more adventurous. And it’s the gut microbes in locusts that cause locusts to swarm — the microbes release chemical signals that cause locusts to physically change in shape and develop a radical new behavior. The expression “thinking with your gut” is truer than we thought.

I moved from Clindamycin to Z-Pak to others, but my teeth did not heal, and the seriousness of my predicament started to grow. My stomach really hurt as the microbes died. The scariest part was this: One course of antibiotics may bring shifts in the population of bacteria, but usually, the guts can recover. Several rounds of antibiotics, though, can change your gut forever.

So out went the sugar and processed foods, and in came foods with prebiotics and probiotics. I ate yogurt, garlic, lemon, beets, sauerkraut. And I went back out to the garden — I’ve always been an advocate of relaxing the sanitary regime in homes, washing veggies less and spending more time in dirt and with animals, thereby deliberately increasing exposure to what Pollan calls the “great patina of life.”

In the end, the “great patina” solved both problems. And pretty quickly, too. Within a few months, the garden soil was better. Turns out, it’s not so hard to parent the parent material, after all. My health improved, too. For a mere $20,000, I sometimes joke, I’ve had a crash course in the deep appreciation of the power of microbes to do their dance of health. I now feel it in my bones: We are from the soil and we’ll go back to the soil. While here, we can work to steward both body and earth.

Lately, I’ve been standing in my garden and watching the sun set over the blue waves of foothills. The garden offered up plenty. The deer sometimes walk by, a bear leaves evidence of its wanderings, the golden retriever pounces at the occasional falling yellow cottonwood leaf, the chickens wander. All of it mixed together — the view, the garden, the body, the life — is a territory no longer hostile. A home.

Laura Pritchett’s most recent novel, Red Lightning, was just released. This essay is from an anthology entitled Dirt: A Love Story (University of New England Press), which was released this fall. See www.laurapritchett.com and ­­www.dirtalovestory.com