Trust Thy Gut: Healing in the Age of the Microbiome

I was diagnosed with ulcerative colitis in May, 2002. On the day of my diagnosis, I refused my doctor’s prognosis, as well as the drugs, and commenced a journey to heal—a twelve-month experiment, absent any conventional medical guidance whatsoever, that ended midway through my honeymoon, when my new wife admitted me to the ER.

For twelve months, I devoted my life to an obsessive and fastidious investigation. Hunched over my desk, I spent day after day Googling. For a phrase like “ulcerative colitis natural cure,” I’d click twenty pages deep, reading every word on every site—every blog, every forum. Certain opportune comments led to new searches in new windows, fresh rounds of clicking.

When I risked leaving the house, I’d visit the book store, where I’d scan the indexes of books, seeking the slightest reference to “colitis,” or “autoimmune.” Inevitably, though, turning from my screen, or trudging from the store briefly lifted by some tidbit, I’d come to think of the only definitive cure: death.

I do not believe my obsessive investigation, nor my despair, were unique. In my experience, most people who experience illness–from colds to colitis–engage in some form of this fanaticism. And many, discovering confusing or contradictory advice, have yielded to despair. My search led to life.

I’ve learned to heal my symptoms–without drugs.

And yet, each year for many years, around March or April, just as the weather warms, I would suffer a relapse, or “flair.” The severity of these flairs varied–yet I knew how to recover.

In May 2013, however, I suffered a particularly bad flair. My go-to remedies–a horridly wine-free lifestyle, VSL#3, and Metagenics–seemed to fail. Worse, the severity of the symptoms transported me back in time, to 2002, when I felt my despair most acutely.

My wife, who witnessed my behavior over the years, acclimated herself to my eccentricities. But even she was startled, that year, when I walked into our infant daughter’s nursery, and pointed to the dirty diaper laying on the changing table.

“Save that,” I said.

“What?” she asked.

“Save that,” I said, and to state the case plainly, I added, with conviction, “I’m doing a fecal transplant enema.”

Nearly all DNA in our bodies belongs to microorganisms: they outnumber our cells nine to one.
– Burkhard Bilger, writing in The New Yorker 

Fecal Transplant Enemas: A Brief History

Although the provenance seems to be disputed–by this guy, for example–the fecal transplant enema is generally accepted (by the folks at Wikipedia, and elsewhere, at least) to have been first described in 1958, when the Chief of Surgery at Denver Hospital, Dr. Ben Eisman, reported in the Journal of Clinical Gastroenterology, on four patients who had been cured of pseudomembranous colitis (commonly known as C. difficile colitis or C. diff).

Eisman described a novel treatment: Enemas containing feces from healthy colons had been transplanted into the patient’s colons, and had successfully replenished the patient’s bacterial ecosystems, effectively curing the patients.

The next documented success occurred in the mid-1980s, when an Australian gastroenterologist, Dr. Thomas Borody, was faced with a particularly challenging case. A traveler, recently home from Fiji, had contracted an especially pernicious form of colitis. Searching the medical literature for a potential cure, Borody discovered Eisman’s article, and decided to give it a try.

Writing in The Scientist, Cristina Luiggi explained Eisman’s procedure quite candidly in her article “Same Poop, Different Gut“:

“He collected stool from the woman’s brother, and after screening it for known pathogens, he stuck it in a blender, added some brine, and filtered it to get rid of any undigested material. The stool, now turned into slush, was administered to the patient—who had her gastrointestinal tract previously flushed—via two enemas over the course of two days. The results were nothing short of surprising, Borody said. Within days her colitis was gone, never to return.”

This is the method I’d considered in the spring of 2013. Obviously, like any reasonable human, I would’ve preferred to administer this treatment with a doctor.

Unfortunately, despite the mounting evidence of the treatment’s success–including the first randomized control study–the FDA had made the procedure essentially untenable for any liability-minded doctor. Even though some doctors believed the regulations had become too strict., it was nearly impossible to find a reliable source of treatment.

(Happily, updated guidelines recommend the treatment for C. diff.)

Faced with this climate in 2013, but suffering acutely, I found myself standing in my daughter’s room pointing at her diaper, envisioning my own guerrilla campaign.

All I’d need, I told my wife, was a “dedicated” blender and a little poop.

Michael Pollan’s 2013 lead article for The New York Times Magazine, introduced the microbiome to many readers:  “To the extent that we are bearers of genetic information, ” Pollan wrote, “more than 99 percent of it is microbial. And it appears increasingly likely that this ‘second genome’…exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents.”


Sterility, Cleanliness, & Purity

I believe the FDA’s regulations mirror a cultural obsession with sterility–and as Kathleen Barnes, a Johns Hopkins Medical School researcher, said in a Science Talk podcast on the “hygiene hypotheses,” this obsession may be harming our health:

“The hypothesis is that as we make the shift from dirt to sterile that you are changing the direction of your immune response. And so in the context of asthma, and frankly in other autoimmune diseases and diseases of inflammation, it’s this imbalance from that side of our immune response that we believe evolved to protect us against things like bacteria and viruses and malarial parasites to the other side of our immune system that, frankly, when it’s revved up causes diseases like allergies and some of these other diseases of inflammation.”

For me, this obsession with sterility–and by way of sterility, cleanliness and purity–touches the most intimate part of my life: my relationship with food.

For my entire adult life, I’ve been a staunch “health-food” enthusiast. At the age of twenty-one, while traveling in Italy, I became a vegetarian. But even before my trip to Italy, I’d experienced a lifetime of brown rice and Moosewood Cookbook recipes, organic broccoli and honey-sweetened treats. My mother raised me with a special attention to my diet; she also sent me to a school–the Waldorf school–that favored whole food cooking.

I lost touch with this impulse throughout my teenage years. Then, when I was twenty, in college, in the midst a dismal semester eating in the student cafeteria, I came across a surprising image in the cafeteria kitchen: a box of hamburger patties stamped Grade F, But Edible.

Within a week, I was a vegetarian.

For me, vegetarianism, and later veganism, morphed in my twenties into obsession with purity. When I experienced my first symptoms of autoimmune illness, my obsession evolved into what I now view as an eating disorder.

My early symptoms were vague: moving pain, crushing fatigue, listlessness, depression. Blaming certain foods, I refined my diet. For months, I refused to touch anything but organic greens, sprouted grains, wild salmon, brown rice, and tempeh. I drank green drinks. I refused wine. I did not eat one ounce of cheese or bread. I avoided all night-shade vegetables. I never, ever combined proteins and carbohydrates at the same meal.

By the time I received my ulcerative colitis diagnosis my diet was already remarkably limited. The new diagnosis, however, thrust me into a new realm.

At the time, my relationship with food, ritualistic and minutely precise, alienated me from others. When eating lunch, specifically, I simply could not bear company. I dined under strict conditions: on the zero or five, at say, 12:00, 12:05 12:10, and so on, exactly four hours after my last bite of food—a bite I might’ve detained in my mouth, for minutes, if the time did not match my zero/five requirement. For fifteen months, from my ulcerative colitis diagnosis to my wedding day, I never once finished eating on the one, two, three, or four.

For reasons I have yet to entirely fathom, this rigor did not survive dusk. Dinner absolved me—and Karen, from her patient allegiance to my eccentricities. We’d invite others to share the weirdness—to share our chilled Chianti and buttery Castelvetrano olives, our pan-roasted wild salmon and spice-grilled mini sweet potatoes. Easing into these dinners, I eased back to myself—my pre-illness self: the gallant host, the ecstatic narrator.

Today I live for dinner’s absolution, but I am still haunted by my daytime exactitude. My timing is more fluid, but I can only bear company to a point—as long as I’m free to sit in complete silence, and slurp my 1¼ cup seasonal soup, and dip each of my twelve tempeh squares into a tiny ramekin of portioned extra virgin olive oil, and eat my seasonal salad without once glancing to my left or right, but down, to the latest New Yorker.

My Lunch: Every Single Day

My obsession with purity nearly killed me. Refining my diet to an impossible degree, I distorted my relationship with my body and food and those around me. Worse, I’d tricked myself into believing that this diet was the only diet for my symptoms.

Even then, I felt shameful of my illness; shameful of the person I’d become, this ill person with this horridly embarrassing disease. Yet I felt powerless to change. I could hardly utter the word, “colitis,” in private, let alone write about it on a public forum.

In a sense, I was guilty of “kitsch,” as Milan Kundera defines it:

“The absolute denial of shit, in both the literal and figurative senses of the word; kitsch excludes everything from its purview which is essentially unacceptable in human existence.”

My recovery was occasioned by the opposite: an embrace of the chaotic and messy in my life and writing, the literal ingestion of dirt, and an entirely new diet typified by my first bite of meat after eight years of vegetarianism: a juicy, blood red hunk of lamb, cooked rare.

I’d ordered the lamb, spontaneously, with the sort of nervous enthusiasm a person might reserve for a wedding proposal. It was this enthusiasm, this new sense of goofy caprice, that also typified the attitude that inspired me to walk into my infant daughter’s room seeking poop.

Not to say that I hadn’t researched the topic with my typical compulsive energy. I had.

By “goofy caprice,” I simply mean to say that in learning to recover from illness, I’ve opened myself to change, and that in doing so, I’ve also learned to see humor in my vehemence.

For me, humor provides confidence even in the darkest hours. This is something I try to express in my writing. I often write about illness, about how I feel as if I’ve been slapped by life. In part, I want to express an honesty about my feelings of woundedness. However, I don’t want this sense to drive my writing into dour seriousness, but rather give me range to be, at times, slightly goofy, as all celebration is.

In the end, after a series of tedious conversations with my wife, I did not administer a fecal transplant enema. I’ll spare you the details. Instead, as a compromise, I tried the probiotic enema suggested on the website Listen to Your Gut.

This video, specifically, convinced me as well as the raw testimony of the video’s star, Crohns Boy:

“So to tell you the truth it sucked being sick for the last 2 weeks especially while I was in Hawaii. When I look back at it now I am almost grateful for being sick as it has taught me a lot in the process. I have learned that when I feel awesome and other people are doing shitty I really have to remember how I felt when I was in their shoes-feeling depressed, hopeless, insecure etc and I have to be able to communicate effectively that they will overcome this and that stuff will be lost in the process. I also realized life has a great way of humbling you from time to time even if it came in the form of a flare lol I realize you really have to soak up the GOOD TIMES and enjoy them!! Sunshine is always awesome and appreciated the day after the storm…..simply said.”

Gut bacteria may be the key to preventing or treating some diseases,” says The Harvard Medical School, which recommends fermented foods or probiotics as a healthy option for “good bacteria.” [Photo Source]
Fermented Foods and Probiotics

I am a passionate proselytizer of bugs–specifically the beneficial bacteria found in fermented foods. In my former position at Whole Foods Market, I spoke to hundreds of people over ten years who offered testimony after testimony to the effectiveness of probiotics. And finally, it seems, the idea of “beneficial” bacteria has entered the cultural conversation under the meme of “the microbiome.”

Although the microbiome is meant to describe our entire bodies’ bacterial ecosystem, much of the current talk focuses on the gut, and the profound influence the gut has on our health. Many scientists studying the microbiome are hesitant to make recommendations. In his groundbreaking article, however, Michael Pollan teased enough information out of his sources to discover “the outlines of a new diet.”

Near the end of the article, Pollan writes, “one of the keys to good health may turn out to involve managing our internal fermentation.”

How is this done? If you’re interested in trying a probiotic, I suggest inner-ēco™ Coconut Kefir–a food-based probiotic that follows Pollan’s advice of tending to “internal fermentation.” Another option is eating small amounts of fermented foods, like pickled vegetables.

Recently, I have also tried a relatively new product, Ion Biome. I cannot recommend this product enough. The effects have astonished me. My digestion has improved appreciably, and I am sleeping better. This is a simple addition to any diet.

Nine Years Symptom Free

“I have learned that when I feel awesome and other people are doing shitty I really have to remember how I felt when I was in their shoes-feeling depressed, hopeless, insecure etc and I have to be able to communicate effectively that they will overcome this and that stuff will be lost in the process.” – Crohns Boy.

By the time I’d read this quote from “Crohns Boy,” in mid-April, 2013, I’d already suffered two months of symptoms. I’d been to my doctor three times, and had, for the first time in my life, considered taking the potent anti-inflammatory drugs. I’d lost ten pounds, and had acquired the paperwork to take a LOA from work. Inspired by Crohn’s Boy, I tried the probiotic enema on a memorable date, April 15, 2013: the day of the Boston Marathon Bombings.

That was Monday. By Wednesday, I was completely symptom-free.

I’ve remained symptom-free since then. (Update: As of  April, 2022, nine years later, I am still symptom-free).

I understand that the very nature of my illness might ensure a relapse–perhaps maybe even next spring. With each flare, and each recovery, however, I do believe I’ve learned to become a bit more human.

For me this means, specifically, an acceptance of that which I cannot control.

Each year, I learn to cede a bit more control to life as it is: radically imprecise, often downright messy. Bacteria, and by extension, probiotics and poop, have become metaphors for my growth.

That I can now talk about this so openly seems to prove the point–for me at least.

4 thoughts on “Trust Thy Gut: Healing in the Age of the Microbiome”

  1. Excellent post, Seth. Compelling, revealing, informative, and articulate. Your ventures into alternative remedies remind me of a Radiolab podcast about this dude who goes traipsing barefoot through the African countryside in order to contract a hookworm he believes will mute his severe allergies.( ) What really struck me, however, was not so much the assiduity with which you pursued a cure, but your apparent fearlessness in sharing so many intimate, potentially embarrassing details about your eating habits, past and present.The more deeply you reveal your struggles and neuroses, the more deeply I can understand my own. I thank you kindly, good and noble sir.

  2. Didn't Winston Churchill say something like "when you're going through shit, keep paddling"? As always, your writing tells of courage born of desperation and an endearing pathos, as you grit your teeth, gird your quoit and move on to your next dietary challenge. Informed and highly readable, I always enjoy your posts Seth and look forward to reading the whole story one day soon.

  3. Thanks, Jeremy, as always, for your readership. I'd heard about that podcast from someone at Whole Foods, but I haven't checked it out. Thanks for reminding me–and thanks for the link. I'll check it out.

    When I began work on my memoir, I'd worried that in confronting a range of potentially embarrassing details I'd feel compelled to somehow take advantage of, or worse accentuate, my eccentricities. I'm not really sure if I've done that. In any case, your comment about understanding your own struggles and neuroses by reading about mine humbles me incredibly. This is what I hope to do with the memoir–with all my writing. So thank you, good and noble sir. It's nice to read that sort of feedback. It'll help me sit down tomorrow. 🙂

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