New Shit

Bacteriotherapy and the universe in your gut

by Doreen St. Félix

Illustration by Layla Ehsan

published February 28, 2014

I’ve come into the habit of considering myself a human being. Dr. Charles Raison seems to disagree with me.

     Biologically, my human body evidences itself. I am land-borne, bipedal, masterful at the art of deceit. I feel embarrassment. Part of our human species classification is that we belong to the class Mammalia—breasts, backbones, odd number of toes on each foot, possessive of culture, naturally covered with a thin coat of hair. Humans are mammals, I thought. The National Institute of Health-funded Human Microbiota Project (HMP) is generating data that could prove that we are actually bacteria.

     Dr. Raison, associate professor in the Department of Psychiatry at the University of Arizona’s Medical School, doesn’t mean this genetically, of course. He’s talking about sheer body composition. My mother, who is in her early sixties and otherwise deceptively vital, has colitis, inflammation of the colon caused by Clostridium difficile, an unremitting, spore-forming bacteria cluster known to bloom in the gut. I subscribe to a number of colitis-related newsletters for her. I got an email from this past September, titled “In a Very Real Way, We Are What We Poop.” In the article, Dr. Raison sent grainy pictures of a new galaxy, at once primordial and from the future: “Only one in every ten cells in your body is mammalian. By cell count each of us is about 90 percent bacterial.” Over 100 trillion bacteria, using our body space commensally, symbiotically—and in the only relationship dangerous to overall health, pathogenically—form an ecological community: a microbiome.


This universe weighs less than five pounds. Bacteria populate the entire body; currently, the NIH and dozens of privately-funded research enterprises in the US and abroad are pouring millions into exploring, sequencing, and characterizing individual microbiomes. Microflora teem in the mouth, the vagina, the skin, but the largest reservoir of bacteria resides in the gut, and the easiest way to study it is to extract samples from excrement.

     Over one hundred million neurons in the ENS (enteric nervous system) communicate with microflora to execute the complex daily industry of digestion. The ENS, your second brain, consists of the esophagus, stomach, small intestine, and colon. Diverse bacterial species populate the bowels, and “good” bacteria balance the bad ones also living in the gut. That gut flora are marvelously industrious laborers—churning, liquidating, extracting, and eliminating our recurring waste on the clock—has been well established.

     But microbiologists have known about this shit for a while. Intrepid scientists like Dr. David Relman at Stanford aren’t poring over excreta just to uncover further machinations of the digestive system. That’s old school.

     “Humans are like coral, an assemblage of life-forms living together,” he told the New York Times. My mother’s gastroenterologist, who prefers to remain anonymous, is more explicit. “The bacteria are the ones in charge,” she told me over the phone. “If we have a better understanding of what they do and don’t do, who knows, we can more effectively treat a lot of ‘incurable’ intestinal diseases.”

     Intestinal flora have also been linked to disorders like autism, asthma, depression, anxiety, obesity, and hypertension. Recent neurological studies on mice tease citizen-scientists with enticing prospects. In one study, replacing the pathogenic microbiota with healthy species alleviated core behavioral aspects of the autism spectrum. In another, obese mice injected with bacteria from thin humans dropped in BMI; in another, mice known to exhibit anxiety-prone behaviors “became much more adventurous explorers” when they received infusions from their bolder rodent cohorts.

     Microflora influence homeostasis so essentially, says Christine Gorman, health editor at The Scientific American, that “there is simply no way that the gut environment does not also contribute to psychological states.”

     Influence, originally an astrological term. A process of streaming ethereal power from the stars to act upon the character or destiny of men; a body infusion. External factors influence your behavior, but some mystical autonomy should persist. That internal microorganisms could control my mood utterly leaves me intrigued and deeply, deeply disturbed.

     Evidence is mounting against me, but I think I’m still human, that my mother is.

     Her gastroenterologist tells me to look up something called an FMT, a fecal microbiota transplant. She says that my mother isn’t interested in the procedure, for “aesthetic issues.” Some doctors are willing to perform transplants and the whole thing is over with quickly. If not, and many will refuse because of new restrictions imposed on the procedure by the FDA, FMTs can be done at home. It requires few tools: a blender, a sieve, saline, an enema tubing, healthy human excrement from a donor, and lots and lots of newspaper. A commenter on an experimental therapies blog performs routine fecal transplants on herself,  “when [she’s] feeling low or down about something.” She believes her young son’s stool is healthier than hers, that it takes her out of small depressions. She’s gotten so good at it she can do it in the tub.


Our storytellers knew gut might influence mood. Ivan Ilyich could not think well, and the problem flourished from his blind gut. A deep intestinal gurgle traps Ignatius J. Relly in his seat in the faculty men’s room. Beloved’s stomach violence grows bigger and bigger. Soon she eats the whole house, and Denver is disgusted.

     Repulsion is loaded. What disgusts you? As an evolutionary mechanism, repulsion safeguards your body from foreign agents. Socially, it pads your prejudices. You’re disgusted by that moldy sandwich (throw it out) and you’re disgusted by the homeless man on the corner (refuse him his dollar). The person repulsed by her own diarrhea recoils her shoulders in a manner similar to the person repulsed by young black men.

     The curative potential of shit troubles repulsion, and it should. Not only does the site of rejection come from you; it restores you. In the wake of commercialized medicine, the possibility of a doctor tailoring treatment to her patient’s ecological makeup sounds radical, futuristic. Enough to surmount the recoiling instinct.

     Little critical theory exists because scatalogical waste does not hold any intrinsic value. Joshua Reno, an anthropologist and biosemiotician at SUNY Binghamton, challenges the prevailing non-account of human waste in western cultural discourse. Last month, he published “Toward a New Theory of Waste: From ‘Matter Out of Place’ to Signs of Life.” I suspect that he’s conferencing with the microbiologists.

     Reno situates the problem of theorizing waste in our fondness for opposites. Symbolically, “excreta has no opposite,” he explains. Unlike garbage, we reject it because we must; unlike dirt, it pollutes because a body has already extracted nearly all its value. Cross-culturally, excrement is offensive, animal, and disease-baring. Less dead than it is useless, shit is matter with no right to functional space. Our self-blinding, of course, disguises pure performance; shit is certainly “caught up in the same systems of valuation and distinction as are other rejectamenta.” You peer into the toilet to evaluate. If you’ve been eating many fruits and vegetables, you’re proud of your newfound regularity.

     Repulsion unlearns itself when there is health to gain. Tracy Mac, Zen practitioner and editor of, teaches her e-patients this. “In 2011, a series of fecal microbiota transplants at FMT pioneer professor Thomas Borody’s Centre for Digestive Diseases in Sydney…gave me the physical and mental strength to keep on fighting,” she writes. Her hair is shiny and thick in the picture, her skin glowy and sun-kissed. She provides information to people suffering from intestinal distress, so that they can perform safe DIY FMTs.

     My mother wonders what antidote will give her back her intimacy and still make her feel like a person. The anti-inflammatories cause her stomach to bloat. Nervousness sometimes stops her when she goes to bed with my father. Philip Roth found it wrenching to write of his father sweating against the bathroom tiles in that basic state, the whole room doused in his uncontrolled shit. Shit was the word he used. She has never asked me for help when she gets sick. She’s not compelled to show her shit. She can clean it all up herself.


When Darwin concluded that the indomitable human species evolved from apes, John Hooker seethed, “it was like confessing a murder.” What would Hooker say about this bitter satire, that human shit might be reintroduced to balance the body’s mental and physical states? What are we saying to that?

     Evidently, the scientists and the doctors and the gut-conscious are saying “yes.” To an interviewer’s inquiry about bacterial attack, Julie Segre of the National Human Genome Research Institute requests, “I would like to lose the language of warfare. It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.”  Certain bacteria, probiotics and other species, that can do things for you and that kind is not only good, it’s essential. The probiotic food and supplement industry is chic and lucrative—the global market will top $30 billion in the next fiscal year.

     Microorganisms, though, are fickle; the benevolent microflora you inherit from pushing against your mother’s vaginal wall at birth may ominously switch course. Influenced by environmental factors and foreign agents, the microbiome may turn, bringing about irritable bowel diseases similar to the condition my mother lives with, contributing to obesity, perhaps even triggering anxiety and depression.

     That unpredictability worries Dr. Andi L. Shane, a contributor for The Atlantic. He treats infectious diseases, specializing in the gut.  Antiobitic resistance is a growing problem and Shane concedes that FMTs serve as an attractive alternative. He’s still worried about people “practicing unscrupulous and unsterile procedures.” This is his greatest concern: “that I will be unable to offer them the best care and they will seek treatment from the black market, where their risk for complication is unknown.”

     A healthy stool donor and an enema may treat diseases that kill tens of thousands every year, especially young children in slum areas across the global South plagued with life-threatening diarrhea, E. Coli, and other parasitic infections. So far, FMTs performed in the United States boast an unheard of 90% cure rate: “there is no drug or anything with a rate that high,” according to a 2011 article on fecal transplants in Wired. The sample size remains small; the vast diversity of gut flora has yet to be fully catalogued.

     In 2012, the Human Microbiota Project released an ambitious five-year report detailing how changes or full transplantations of the microbiome might be associated with disease. Scientists at nearly 100 institutions across the US studied and sequenced the microbiomes of 245 individuals.  According to Dr. Relman, the study “barely scratches the surface [of microbiota diversity] but is the first step in trying to improve health by deliberately altering the microbiome.” Packed with extensive investigation of the human microbiome, a particular innovation struck me quite dumb. I had understood bacteriotherapy as offering a progressive individual-centered approach to treatment, but—

     By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter). (Nature, 2011)

     Like the common bloodtypes, an enterotype would group individuals based on common bacterial diversity, linking potential donors with stool transplant candidates. The shit would get very formal, very corporate, very fast.

     We’re still human, mammalian. Medically, it’s less that we would be better understood as giant, lumbering bacteria on legs, but more that we are bacterial, in essence. We’re human, still, but I’m disturbed by the notion that I have an essence. This feels calculated, non-intimate. The citizen-science community triumphs bacteria as revolution, when really, these therapies may be monetizing shit on the same utilitarian terms on which it was formerly rejected.

     For our feces and the cures mysteriously packed in, there’s now a hallowed but conventional place. This is Bacteriotherapy.


Marie Myung-Ok Lee is known amongst her friends for eating her fruits and vegetables. “It was kind of inevitable, then,” she writes in a New York Times op-ed published last June, that her good friend called Gene would ask her for help. For more than a year, Gene “could do nothing but writhe in bed in pain.” Open sores on his large intestine bloomed, subjecting him to uncontrollable bouts of internal bleeding and diarrhea. He could not eat or drink without extreme pain and discomfort. He lost weight, became anemic. Around half of patients with ulcerative colitis, a form of irritable bowel disease marked by ulcers on the intestinal walls, suffer mild to moderate symptoms, like my mother. Gene’s case was debilitating.

     Gene chose a treatment not suggested to him by his gastroenterologist or technically allowable under the tightened FDA restrictions. His doctor offered him two terrible choices: powerful immunosuppressant drugs or a total colectomy. Gene chose FMT. This is where Lee comes in. She ate a lot of fruits and vegetables. Would she be willing to give him her healthy stool so that he could perform an FMT on himself? She delivered her first donation in a Tupperware container.

     Thought to flourish due to antibiotics disrupting the balance between “bad” and “good” species, dangerous strains colonized Gene’s GI tract to near devastation. The first FMT left Gene feeling better immediately. After more home transplants and a comprehensive colonoscopic FMT from Dr. Shepherd down in Florida, Gene entered a state more mysterious to physicians than pathology: Gene was cured.

     My mother, a cardiac nurse, was not surprised, but she also wasn’t swayed. I suggested to her that she look into it, that maybe it would give her relief. “I’m not just bacteria,” she said. She has her supporters. Worried physicians and scientists agree: recolonizing pathogenic bacteria with screened healthy bacteria positively suppresses symptoms. Yet, “the excitement has led to premature interest among the general public suffering from ailments for which [FMTs] have been unproven,” cautions a recent article in the Boston Globe. Microbial trailblazers like Mark Smith, a graduate student in microbiology at MIT and cofounder of the Boston nonprofit stool bank Open Biome, recognizes the uncertainty. He co-wrote a paper published in Nature last week, along with other researchers from MIT and Brown’s Alpert Medical School. “I have pretty serious concerns,” he told the Globe. “It’s an exciting area of research, but it’s not ready for patients to get their hands on.”


Dormant knowledge of the curative power of fecal bacteria lurks through the ages. Millenia ago, Chinese healers whipped up yellow soup—a watery mix of fecal matter and water for people with diarrhea. An eccentric 20th century Swedish doctor reached brief fame for popularizing the “fermentation diet” of the ’40s. He was rumored to have grazed on his morning stools. In the ’50s, spiffy American veterinarians injected ailing racehorses with healthy animal stool, immediately sending them back on the track to win for their bettors.

     This is Bacteriotherapy, a conglomerate of biology and ecology, of DIY homeopathy and metallic innovation. In a decade, fecal matter will be grown in labs, and Dr. Raison says my psychiatrist will ring me up scripts for anti-depression fecal pills. It feels like a frontier. And it is. Bacteriotherapy may be doomed perpetually de rigeur. Exactly the fact that makes microbiome transplantation possible—that bacteria are always changing, either because of environmental changes, intra-bacterial interactions, or something not yet explained—renders it amorphous. Barbara Methé, a microbiologist at the J. Craig Venter Institute, knows this: “We are stepping back and saying, ‘We don’t really have a population study. What does a normal microbiome look like?’” she told the New York Times. How do we measure homeostasis, calculate the aberrant? Is there such a thing as a stable bacterial state? Researchers cannot definitively say that microflora stabilize over time. The science is not there yet.

     And yet, bacteriotherapy resembles towards the ‘same old shit.’ On the one hand, microbiology spots the underlying imbalance and mines the body’s self-healing capacities. On the other, it medicalizes and reduces a capacity that was always there.

     Applied microbiology starts to smell like recycled Pasteurian essentialism. New Germ Theory shifts the emphasis from bacteria as pathogen to bacteria as remedy. Against a historical bent towards misguided medical conservatism, bacteriotherapy fits in quite nicely. The symbiotic relationship between doctors and Big Pharma requires that people be simple, map-able things. Medical funneling massively complicated human bodies into “environments.” This is political—biological illness should not be considered immutable fact.

     Treat the root, but what of the tree already sprouted? Current institutional financing for microflora research will figure as pennies in comparison to the billion dollar profits pharmaceutical companies will turn on gel caps that cure depression and love handles. Valueless, un-patentable, and regenerating—human shit is the capitalist dream.

     My thinking hadn’t yet turned critical when I first encountered FMTs and these bacterial therapy discoveries. Maybe the little universe inside darkened its influence.

DOREEN ST. FÉLIX B’14 shits gold and her mama does too.