The Zoo In You: You Thought You Were Human. But You're Not.

Oct 1, 2015



There are ten times more bacterial cells in our bodies than human cells.
Put another way, we are 90 percent bacteria.

“I think so,” I venture. I recognize the label. “It’s made right down the street.” “Fantastic!” Betsy exclaims. The office manager for her husband’s medical practice, Betsy Hicks is also author of the book, Picky Eating Solutions: Bringing the Joy of Real Food Back to the Table.

She piles a heap of sauerkraut next to the scrambled eggs on her plate with the enthusiasm of a kid in a candy store.

Why is she so happy? Because, like a growing number of medical practitioners and scientific researchers, Betsy and John Hicks have seen marked improvements in children’s health and behavior when their parents start feeding them a small amount of lacto-fermented foods, like this sauerkraut, at every meal. In fact, the addition of fermented foods and the change to a whole foods diet (“If it came from a plant, eat it; if it was made in a plant, don’t,” as journalist Michael Pollan puts it) can make such a big difference to children with autism spectrum disorders that it is the first thing Dr. Hicks—who has been practicing medicine for forty years and specializing in helping heal children with autism for over a decade—recommends to families.

Fermentation is a huge supporter of immune function. It increases B vitamins, omega-3 fatty acids, digestive enzymes, lactase and lactic acid that fight off harmful bacteria.

As we sit down to eat our breakfast, the Hicks tell me they have even started giving breastfeeding infants daily drops of fermented brine to help colonize their intestines with beneficial bacteria and get them accustomed to the sour taste early.

Why fermented foods? These foods are rich in what scientists are now referring to as “beneficial bacteria”—single-celled microorganisms that play a wide variety of crucial health functions in the human body, from helping us fight off infections of invasive disease-causing bacteria and viruses to breaking down our food into usable nutrients.

There are ten times more bacterial cells in our bodies than human cells. Put another way, we are 90 percent bacteria. We like to think of ourselves as human beings but in the past ten years or so medical science has come to realize that bacteria are an inseparable and crucial part of our bodies, and that we are literally teeming with non-human life.

We are walking microcosms of bacteria, fungi, and even worms.

There’s a veritable zoo in you.

Weird, huh?

“We live in a symbiotic relationship with the bacteria in our body,” explains Paul Thomas, M.D., a pediatrician in private practice in Portland, Oregon, who also encourages his patients to eat as much whole real food as possible. “They live off the food we send down the pipe and we benefit as they help us digest our food, ferment our food, absorb nutrients, and manufacture vitamins. Beneficial bacteria also help our immune systems, reducing the likelihood of pathogenic bacteria taking hold and making us ill.”

Though you’ve probably heard this before, or read about it somewhere, the idea that bacteria have so much benefit that we should be eating the good ones, letting them grow on our skin, and even colonizing ourselves with them in other ways (like fecal microbiota transplants, where you use donor feces to recolonize a sick person’s colon) isn’t an easy concept to accept.

At least not for me.

I grew up in the 1970s at a time when public health officials were pushing the benefits of good hygiene and the harms of “germs.” One of my favorite books was about big, bad bacteria. GERMS MAKE YOU SICK was the message that blared out from every page, illustrated with pen and ink drawings of intimidating bacteria and accompanied by admonishments to always wash your hands.

The messaging that “bacteria is bad” has become so ingrained in the public consciousness that in America today you find antibacterial hand sanitizer at every supermarket entrance, antibacterial soap in every doctor’s office bathroom, and antibiotic cream in every pharmacy.

It is unquestionable that an overgrowth of certain bacteria, fungi, and other organisms (like worms) can make humans very sick, and no one contests the idea that good sanitation has helped stop the spread of many diseases. But there is a growing body of research that suggests that we may be taking our fear of bacteria, and even our practice of good hygiene, too far.

Stopping The Spread Of Diseases

In the mid-19th century, a Hungarian doctor who was working in Vienna, Ignaz Semmelweis, first suggested to doctors that they themselves were spreading childbed fever to birthing moms because they did not wash their hands. Semmelweis had noticed that laboring women under the care of doctors had extremely high mortality rates, triple the rates of women cared for by midwives. He also observed that his colleagues often came to births after dissecting cadavers or visiting sick patients in other wards.

Semmelweis began tracking maternal deaths and showed that simple handwashing in a chlorine solution could stop the spread of childbed fever and drastically reduce maternal mortality. But though he adopted a handwashing policy in his clinic that showed nearly instant good results, his new way of practicing was unwelcome among his colleagues. Some doctors were even offended by the suggestion that they, as gentlemen, would need to wash their hands. Semmelweis was soundly ridiculed by the medical profession, so much so that he had to leave Vienna. Though his ideas gained widespread acceptance just a few years after his death, he died tragically at age 47 two weeks after being committed to a mental institution and being beaten by the guards.

Though Semmelweis identified the mechanism by which childbed fever was spread (dirty hands) and concluded that medical professionals spread “cadaverous particles” on their hands to the birthing ward, he did not ascertain the exact cause of the infection.

It was just a few years later that Louis Pasteur, a French chemist, microbiologist, and inventor, hypothesized that microbes—tiny organisms that had first been seen and identified under the microscope by a Dutch scientist in the 17th century—were the agents that caused disease.

Pasteur argued that people got ill from food because of contamination from live disease-causing microbes. For Semmelweis, the key to safe childbirth was simple hygiene. Pasteur took the importance of hygiene one step further and developed what every American child learns about in high school science classes, a process called pasteurization that kills all the bacteria in a food by heating it to very high temperatures.

Have We Become Too Sterile?

Though Pasteur’s realization that some bacteria can harm us and that we can protect our food supply by destroying these disease agents has long been considered a huge advance, scientists are increasingly coming to realize that we may have taken Pasteur’s lessons too far. (For the philosopher buffs among my readers, does this push-me-pull-you sound familiar? It is an elegant example of the Hegelian dialectic.) The problem is that Pasteur’s process of sterilizating food not only kills harmful bacteria, it also kills beneficial microorganisms, a realization that has led some Oregonians to go back to drinking raw milk.

If you walk into a hospital today, everything is as sterile as possible: counters are scrubbed with chemical disinfectant, bed sheets are bleached, infected human waste is immediately removed and incinerated. Using sterile utensils and meticulous hygiene have drastically stopped the spread of infection, of course, especially when dealing with surgery, wound care, and open body sores.

But there’s a rub that we are just starting to understand. When you use a broad spectrum antibiotic to rid the body of harmful bacteria, you also rid the body of good bacteria, creating an environment that is more hospitable to fungal overgrowth and to vigorous, opportunistic bacteria that are able to take over because there are no longer beneficial bacteria to keep them in check.

If you kill off all the bacteria in the human digestive tract, for example, opportunistic bacteria (often Clostridium difficile) take over, resulting in debilitating, sometimes fatal, diarrhea. That’s where the fecal transplants I mentioned before come in. We now know that we can repopulate a person’s intestines by inoculating them with fecal bacteria, a practice first documented by the Chinese in the 4th century.

Fecal transfers may cure debilitating and sometimes fatal Clostridium difficile infections.

Understanding the need for a balanced biota and the complexity of the human microbiome has profound implications for childbirth as well. Think about it: before his discovery, the midwives Semmelweis observed weren’t disinfecting their hands either. They also weren’t carrying harmful pathogens on their unwashed hands, since they were not performing autopsies or caring for other patients with infectious diseases. These midwives weren’t sterile and did not practice good hygiene but they weren’t introducing pathogenic bacteria that the doctors contacted in other wards and in the morgue and nonetheless they had much better outcomes than the doctors.

Has it been a positive advance for childbirth to create a germ-free environment for the laboring mother and baby so as not to introduce pathogens? Yes and no. We must always be vigilant about spreading infections to vulnerable newborns but we are now seeing that it is actually not in the best interest of human health to sterilize mothers and babies. The mother’s vagina and rectum are teeming with thousands of different kinds of bacteria. These bacteria, passed from the mother to the baby via the birth canal, are now thought to be beneficial, essential even, as are the bacteria that the baby imbibes in the mother’s colostrum and breast milk.

In addition, several studies have suggested that babies should not be washed after birth. Not only does the vernix (a white creamy substance on an infant’s body that develops in the womb) have powerful protective properties, but keeping a baby unwashed promotes bonding between the mother (whose brain responds with euphoria to the scent of her baby) and the baby (who recognizes the smell of his own amniotic fluid). While many midwives have stopped washing newborns, American hospitals continue to wash babies, depriving them of the bacteria-rich substances they are born with and exposing them unnecessarily to antibiotic soap.

Surgical birth is another microbe-depleting practice. When babies are born via Cesarean section, they do not get inoculated with the mother’s beneficial vaginal bacteria but instead colonized by other bacteria found on the mother’s skin and even in the hospital itself. To combat this problem, an increasing number of forward-thinking evidence-based obstetricians, often at the urging of midwives, have started inoculating babies born via C-section with their mother’s vaginal secretions. 

A few months after having breakfast with the Hicks, I visit John Kloetzel, a cell biologist who earned his Ph.D. from Johns Hopkins, taught at the University of Maryland for 37 years, and moved to Southern Oregon in 2007.

John Kloetzel, Ph.D.
Credit Kloetzel Family

  Kloetzel ushers me into his brightly lit and tidy home on the north side of Ashland and his wife brings me a glass of iced tea. Sitting in a rocking chair, he sports a white beard, a white Polo shirt, and blue shorts as he recounts that these days he teaches classes on the human microbiome at the Oregon Lifelong Learning Institute. He explains that the ability to do DNA sequencing is what has proved to scientists that there is a rich diversity of “bugs in our guts” and that the field of microbiome research has really taken off recently because of scientists’ keen interest in the implications this knowledge might have to human health.

Like a good scientist, Kloetzel does not have definitive answers. Instead he has a lot of questions:

Is the explosion in autoimmune diseases, obesity, and autism, which has paralleled a decline in infectious disease, somehow linked to the microbes in our bodies?

Do we need infectious diseases to attack so that our immune systems—always on the alert—will not attack ourselves?

“We’re in the early stages of understanding what’s in us and on us,” Kloetzel explains. “We’re like the first explorers in the Amazon paddling in dug-out canoes … It’s a field that’s just getting rolling.”

Though he is keenly enthusiastic about the human microbiome, Kloetzel is skeptical when I tell him about some of the benefits that Dr. Hicks is seeing among the children in his practice. He wonders if the healthy bacteria in fermented foods can really survive the harsh environment of the stomach, withstand the acid, and colonize our guts. He points out that more than 90 percent of the microbes in our guts cannot be grown in a petri dish in standard lab conditions. Many of them are “obligate anaerobes” (they cannot survive in the presence of oxygen). He wonders out loud if taking probiotics and eating fermented foods truly have a health benefit or if they are just another diet craze.

“I can’t say it’s bad for you,” Kloetzel laughs. “I took some probiotics myself when I had a condition for which I had to take antibiotics. But a lot of research is still needed before we really understand if taking this or that probiotic is really going to help you, because we don’t really know what the optimal biome should be.”

One of Kloetzel’s colleagues, Andy Kumitz, M.D., a family practice doctor with 36 years of experience in private practice in Southern Oregon, tells me a few weeks later that while he agrees there is still a tremendous amount to learn about which bacteria are beneficial to humans, he thinks probiotic treatments will be the future of modern medicine.

“We just catalogued the normal bacteria in the last year and a half,” Kumitz explains when I reach him by phone. “We’ve identified bacteria that helps us lose weight and ones that make us gain weight using germ-free mice … without changing their diet … It’s the bacteria that really drive our metabolism.”

So one day I’ll be able to swallow a pill full of microscopic bugs that will help me get thin?

I like the sound of this.

So does Dr. Kumitz.

“The future holds probiotics as a way to cure specific diseases,” he insists. “Yes, there’s still a lot to be worked out. It’s all extremely exciting and promising.”

The Overuse Of Antibiotics

What neither Kumitz or Kloetzel is happy about, however, is the fact that doctors are continuing to overprescribe antibiotics and parents continue to give them to their children much too often, a practice that destroys the beneficial bacteria in a child’s body and disrupts the immune system, setting the stage for more virulent and antibiotic-resistant infections.

Kloetzel tells me people do not realize that they are often ingesting antibiotics on a daily basis, every time they eat meat and other animal products. Ranchers give antibiotics to their cattle and other livestock not just to treat infections but also because antibiotics have been shown to help animals put on more weight. When you are paid by the pound, it’s a “no brainer” to do anything you can to make your livestock weigh more, Kloetzel points out.

So now antibiotics are in our food supply, in our drinking water, in over-the-counter medications like first aid cream, in hand sanitizers, hand soaps, dishwashing soaps, and prescription medications.

“We’re way overusing them.” Kloetzel shakes his head. “It’s bad for our microbes.”

But there’s something Kloetzel argues is worse: spraying glyphosate on food crops. Glyphosate, a broad-spectrum herbicide and the main ingredient in Roundup, targets an important enzymatic pathway found in plant cells. Agricultural and medical scientists have long assumed that it is safe for humans because human cells, like all animal cells, lack that enzymatic pathway. So molecular biologists working in biotechnology have managed to genetically engineer strains of soy and corn to be glyphosate resistant. This allows farmers to spray their fields with glyphosate, which kills the weeds but not the genetically modified crops.

It’s not the genetic engineering that is a problem, Kloetzel argues, it’s the negative effects of the glyphosate on the non-human cells in our bodies.

“It’s a good idea in theory but the problem is that bacteria do have the pathway that is interfered with by the glyphosate,” Kloetzel explains. “If you ingest it, it’s not going to affect your own cells, but it will affect the bacteria in your gut. Our microbes are sensitive to glyphosate.”

It’s pouring rain a few days later when I sit down with Courtlandt Jennings, the founder of Pickled Planet, the artisanal Ashland-based company that made the sauerkraut that made Betsy Hicks so happy. He and his partner Jennifer McCoy, a clinical herbalist, meet me at Sammich, a Chicago-style deli in Ashland, Oregon. We decide to brave the rain and sit outside. And we all choose the same drink—what else?—locally produced fermented sodas. Wylie’s turmeric ale is so bioactive that our sodas fizz and bubble when we pry the caps off.

I share Kloetzel’s skepticism about the claim that eating fermented foods promotes healthy bacteria with Jennings and McCoy.

“There are certain bacteria that don’t but lactobacillus bacteria are able to withstand the harsh environment of the stomach,” Jennings insists.

“I can give you at least a hundred research studies looking at the benefits of gut flora,” adds McCoy.

Watching his mom make sour dough bread first got Jennings interested in fermentation. “You could take this dead flour and make it living,” he says. “It seemed really cool.” So Jennings started experimenting with fermentation—brewing beer and making wine—while he was still in high school. “I was interested that I could make things bubble.”

Jennings says that when he started making big batches of sauerkraut in 2003 there was nothing else like it on the market. It was rough going at first, since Americans did not know about the importance of fermented foods, though now the industry has started to take off.

“We’ve been growing 50 percent each year for the past two years,” he says. “Part of the project is to educate people that you are already covered head to toe with bacteria so you might as well make friends with them.”

The Zoo In You – OMSI's traveling exhibit - is visiting Scienceworks in Ashland, Oct – Dec 2015.
Credit OMSI

  That is what Kloetzel is hoping as well. Before I leave his house, he hands me a flyer. Scienceworks is bringing a 2,000 square foot exhibit from the Oregon Museum of Science and Industry in Portland called “The Zoo in You,” which seeks to educate children and adults about the human microbiome.

“It’s a bit of a hard sell,” Kloetzel, who serves on the Science Advisory Board of Scienceworks (as does Andy Kumitz), confesses. “It’s not dinosaurs.” 

But Steve Jessup, an environmental biologist who has taught university biology and environment science for 18 years (and also happens to be my neighbor), thinks it’s a fascinating subject. “There are more microbes in our bodies than cells related to our own genetics,” he enthuses when I interview him by phone. “We are a highly complex system of bacteria, protozoans, tardigrades, and invertebrates like flatworms and roundworms.”

Tardigrades, I interrupt him, what in the heck are those?

Jessup tells me they are the world’s smallest animals, better known as “water bears,” and they have been touted for their purported ability to survive in outer space. He also says these 8-legged invertebrates live in human tear ducts.

Another scientist at Duke University’s medical school, William Parker, Ph.D., who has published over 100 peer-reviewed scientific papers, tells me that he his research reveals positive effects on the immune systems of both rats and humans when worms, a once integral part of the human biome, are purposefully introduced.

Tardigrades, flatworms, bacteria, oh my.

I’m not sure I’m ready to embrace all the non-human life living in and on my body, but I am looking forward to taking my kids to the exhibit at Scienceworks.

Jennifer Margulis, Ph.D., is an award-winning sauerkraut-eating science journalist and author of Your Baby, Your Way: Taking Charge of Your Pregnancy, Childbirth, and Parenting Decisions for a Happier, Healthier Family (Scribner 2015). Her mother, Lynn Margulis, Ph.D., was a prominent microbiologist who discovered the importance of symbiosis in cell evolution and is responsible for the endosymbiotic hypothesis. Read more about Jennifer and sign up for updates at: