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Your Microbes, Yourself

In his new book, Rodney Dietert argues that it’s time to re-configure our relationship with germs: Instead of fearing them, we should cooperate with them — and accept that our bodies are incomplete without a colorful palette of microbial species.

By Louise Fabiani


Microbes. (Serendigity/Flickr)

If, after squeezing on and off a crowded bus on a hot summer day, your impulse is to make a beeline to the nearest shower, hoping to scrub every last stinking bacterium from your hair and skin, don’t. Even if it were possible to do so, you really wouldn’t want to, for the simple fact that there would be far less of “you” as a result.

According to Rodney Dietert in his new book, The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life, all animals not only contain microbes (we all know about what goes on in the gut), they are also significantly composed of bacteria and other microbiota. In human beings, these “foreign” (non-mammalian) cells, which include around 10,000 different species, constitute the human microbiome. In other words, we are less a single, autonomous animal than a conglomeration of organisms — something like a coral reef. Dietert, a professor of immunotoxicology at Cornell University, argues that the sooner medical professionals adopt this shift in perspective, the better they can treat individuals and communities beset by non-communicable diseases (NCDs), such as obesity and Type 1 diabetes, as well as many cancers. It’s a captivating idea, but, like all potential panaceas, it is also a dangerous one.

In human beings, these “foreign” (non-mammalian) cells, which include around 10,000 different species, constitute the human microbiome. In other words, we are less a single, autonomous animal than a conglomeration of organisms — something like a coral reef.

Among the most absorbing parts of the book are when Dietert stands back a moment and asks “What is human?” in the context of his thesis. The ecosystem model of human health (of anything, to tell the truth) is hardly orthodoxy. Clearly, all of us have to relinquish more than a few cherished assumptions about ourselves, as individuals and as a species, if what Dietert calls “the new biology” is ever going to come to pass.

In Dietert’s account, humanity is overly hung-up on competition as a concept, which we apply pretty much across the board. In the health-care realm, this “us versus them” mentality regards “purging the microbes and creating a biologically pure human as the ideal outcome.” A more holistic view would use cooperation instead: we scratch their backs, they scratch ours. While the microbes on and in us can certainly live up to their bad reputations as pathogens from time to time, their influence is predominantly neutral or benign. Those benefits are often more than nice perks too; they can be vital to well-being. In developed nations, NCDs are the top causes of death (and of lengthy disability leading up to it). NCDs like asthma and food allergies cost billions in health care and lost workdays, not to mention untold misery for patients and their families. There are more than enough reasons to keep our microscopic buddies as happy as possible. The first step is learning how to adjust our thinking.

If our microbiome is incomplete or otherwise unhealthy, there are any number of ways it got like that. Dietert says that we aim for unnatural purity “in our modernized world of antibiotic-administered, formula-fed, cesarean-delivered babies growing up in urban environments, surrounded by hand sanitizers and antibacterial soaps.” This quest for purity can leave us bereft of the life-enhancing (sometimes life-saving) “ecosystem services” granted, almost free of charge, by our little roommates. All they ever ask in return are food and lodging.

The hazards of microbiophobia, as it were, continue throughout a child’s life. Inappropriate, excessive, or haphazard use of antibiotics can wipe out good bacteria as well as pathogens, allowing other bad guys enough room to maneuver. Diets low in fiber and other such microbe-pleasing foods will also throw things out of whack, though less dramatically than the careless use of antibiotics. Life in urban wastelands, far away from natural areas where the body can encounter a wide assortment of microbes that live on wild plants and animals, impoverishes us on many levels. A key element of ecosystem health is biological diversity. Contact with many other sources of microbial life cannot help but boost our personal species roster — for better or for worse.

Most absences or imbalances, however, can be remedied. One of the medical trends already in the works is something called personalized, or precision, medicine. Dietert outlines the new biology approach to treating patients with NCDs, which tends to start with re-seeding, or “rebiosis,” of the patient’s system: replacing any beneficial microbes that have gone missing, from either a dose of antibiotics, a steady diet of processed food, or exposure to environmental toxins.


The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life. (Photo: Penguin Random House)

Some social-psychological changes along these lines may already be underway, gradually eroding beliefs written in stone since the mid-1800s, when Louis Pasteur and Robert Koch first brought us germ theory. Increasingly aware of the dire consequences, physicians are now less apt to yield to parental demands for antibiotics when children present certain common symptoms, many which are probably viral in origin anyway. More recently, sales of probiotic foods, such as live-culture yogurts, have been on the rise (as are opportunities for fraudulent claims about the healthiness of these foods). Fecal transplantation gains followers all the time, prompted by rampant hospital-acquired antibiotic-resistant infections, like C. difficile, which kill tens of thousands of vulnerable patients every year. Concepts such as the Hygiene Hypothesis (a strange omission in Dietert’s book-length argument) have also entered the realm of public discourse. Still, most of us cling to the belief that cleanliness is next to godliness, and invest in enough shower gel and antibacterial soap to transform us into earthbound angels. The irony, of course, is that in doing so, we impoverish — and imperil — our very tenure here.

An immunotoxicologist by profession, Dietert speaks about these cutting-edge scientific matters with the zeal of the convert. Indeed, near the end of the book, we learn that he had something of a life-changing experience a few years ago. While visiting Germany for less than a week and eating whatever conference catering provided, Dietert discovered that he was losing weight and enjoying noticeable relief from two chronic conditions: gastric reflux and sinusitis. (The weight loss was all the more unusual because he was sitting in conferences for almost the entire trip.) Upon return home to the United States, he started experimenting, adding this or that component of his travel diet, until he stumbled upon a winning combination. It all but eliminated the inflammation he had suffered for decades.

Inflammation is a key function of the immune system, of course, where it helps fight infection and heal injuries. But it can end up attacking the very organism it was meant to protect. Dietert describes a Who’s Who of 21st-century afflictions, which he proposes can be alleviated, or even wiped out, if we repair or restore the microbiome. He believes that when our non-mammalian side goes awry, its first line of attack is to cause undesired inflammation in the rest of us, which in turn leads to NCDs like rheumatoid arthritis, obesity, irritable bowel syndrome, depression, allergies, arteriosclerosis, and many, many others. Taken together, they have become the plagues of industrial societies (and, increasingly, of developing nations that adopt our processed foods and other modern conveniences), the price we pay for more than 80 years of undeniable success in protecting ourselves and our domesticated animals from pathogens.

Most of us cling to the belief that cleanliness is next to godliness, and invest in enough shower gel and antibacterial soap to transform us into earthbound angels.

Dietert argues a strong case for a more holistic approach to medicine, and, hence, an expanded idea of what “human” means. He draws upon a solid body of evidence — the notes section is a fat one — making it relatively easy to ignore the volume’s flaws, which include Dietert’s tendency to repeat himself and a sometimes annoying degree of conviction in his own narrative.

What is less forgivable is Dietert’s sleight of hand regarding the amount of microbial biomass relative to the mammalian. His whole thesis rests on the mind-blowing disproportion of “them” to “us,” so the reader cannot simply ignore confusing or misleading data. In the introduction, Dietert states that “recent estimates [of relative numbers] of just bacterial cells range from a low of 57 percent to a high of about 90 percent of total human cells.” Yet, for the rest of the book, he does not mention cells at all, only the relative amount of our microbial partners’ genomic information, which, he insists, stands at 99 percent of our total genetic payload. The remaining 1 percent is all us. Those 10 million microbial genes contribute everything from digestive services to serotonin production in the gut (more than the brain does!), and cannot help but appear to dwarf our 22,000-gene human contribution. This may explain why Dietert chooses to support his case by counting genes, not cells. The wow factor is just that much stronger.

How much of you really is a bunch of bacteria, viruses, and so on, instead of mammal? At the beginning of 2016, Cold Spring Harbor Laboratory released a paper that corrected previous, frequently quoted claims that we are 90 percent not-us, by cell count. The real proportions could be closer to 50–50. The paper itself enjoyed its 15 minutes of fame (in science, debunking anything tends to be good copy), then faded from sight. What does Dietert have to say? Well, the strange thing is that not once in the entire text does he refer to the paper, even to disagree with it — but he cites it in the notes. Did he bury it back there because a bolder reference, in the text, would distract his readers and threaten to dilute his argument, namely, that we ought to re-visualize ourselves as superorganisms?

Perhaps that ratio, like age, like so much we obsess over, is just a number. Far more important is Dietert’s challenge to dominant paradigms. He wants to rid the scientific community of the idea that the natural world consists of nothing but essentially homogeneous individuals, all too often at odds with each other — and the virtues of this perspective are as important to medicine as they are to ecology.

Far more worthwhile pondering is what it means to be human. “No man is an island,” wrote poet John Donne, speaking of the social contract. His formulation can serve as a prescription for our increasingly fragmented world, but also for how we can think of our body and its relationship with the microbodies it encounters. It is engaging to imagine each of those countless islands out there as a vibrant, teeming, coral reef, with the potential to connect with all the others.