Brain Pickings

Our Microbes, Ourselves: How the Trillions of Tiny Organisms Living Inside Us Are Redefining What It Means to Be Human


“You are mostly not you… We are not individuals; we are ecosystems.”

Being alone may be the central anxiety of our time but, as it turns out, you are never really alone — at least in a biological sense: Every single cell of you — that is, every cell made of human DNA — is kept company by ten cells of microbes that call your body home. And because microbes are single-celled organisms that each carry their own DNA, the difference is even starker in genetic terms — you carry approximately twenty thousand human genes and two to twenty million microbial ones, which makes you 99% microbe. What’s more, although you and I are 99.99% identical in our human DNA, we are vastly different in our individual microbiomes — you have only one in ten of my microbes. Even more striking than the sheer number of these silent and invisible cohabitants is their power over what we consider our human experience — they influence everything from our energy level to how we handle illness to our moods to how tasty we are to mosquitoes.

The enormous implications of this micro-scale relationship, implicated in conditions as diverse as obesity, anxiety, arthritis, autism, and depression, are what Rob Knight explores in the deeply fascinating Follow Your Gut: The Enormous Impact of Tiny Microbes (public library) from TED Books, who have previously published journalist Pico Iyer on the art of stillness and mathematician Hannah Fry on the mathematics of love.

Knight, a Professor of Pediatrics and Computer Science & Engineering and Director of the Microbiome Initiative at the University of California, San Diego, writes:

You are made up of about ten trillion human cells — but there are about a hundred trillion microbial cells in and on your body. Which means: you are mostly not you.

But we are not, as we have thought, merely the unlucky hosts to the occasional bad bug that gives us an infection. In fact, we live in balance with a whole community of microbes all the time. Far from being inert passengers, these little organisms play essential roles in the most fundamental processes of our lives, including digestion, immune responses, and even behavior.

Our inner community of microbes is actually more like a collection of different communities. Different sets of species inhabit different parts of the body, where they play specialized roles. The microbes that live in your mouth are distinct from those residing on your skin or in your gut. We are not individuals; we are ecosystems.


We’re discovering that microbes are deeply integrated into almost all aspects of our lives. Indeed, microbes are redefining what it means to be human.

And yet all this incredible complexity was practically unknown to us a mere forty years ago — a sobering testament to how inconstant knowledge is and how illusory our sense of its completeness. (Astrophysicist Marcelo Gleiser captures this beautifully in his manifesto for living with mystery, in which he writes: “We strive toward knowledge, always more knowledge, but must understand that we are, and will remain, surrounded by mystery.”) Knight considers the staggering disconnect between our longtime obliviousness to the single-celled universe and its far-reaching dominion:

Single-celled organisms are more diverse than all of the plants and animals combined. As it turns out, animals, plants, and fungi; every human, jellyfish, and dung beetle; every strand of kelp, patch of moss, and soaring redwood; and every lichen and mushroom — all the life we can see with our eyes — amount to three short twigs at the end of one branch on the tree of life.

So staggering is this diversity that not only are the microbes on your hands 85% different from those on mine — meaning we each have a microbial fingerprint — but the microbes on your left hand are even different from those on your very own right hand.

Inspired by the theory of biogeography developed by the great British biologist and anthropologist Alfred Russel Wallace — Wallace, Darwin’s contemporary and the underdog of the race for evolutionary theory, mapped the relationship between land area and species diversity — Knight collaborated with University of Colorado evolutionary biology and ecology professor Noah Fierer to develop a similar way of mapping computer keyboard area and microbial species diversity. They came up with what they call the “Wallace line” between the letters G and H — the fault line of mingling for the microbial populations of your left and right hand, which each colonize the respective half of the keyboard.

Here is some perspective for our human solipsism, which tends to grasp things not in absolute terms but in terms relative to us: You carry about three pounds of microbes in your body, which renders your microbiome one of your largest organs — around the same weight as your brain. But more than a mere static presence, this hefty microbiome is an active agent in your dynamic state of being. Knight points to one particularly pause-giving point of impact — the growing body of evidence that our microbiome affects our behavior, shaping “who we become and how we feel”:

It turns out that, rather than too few mechanisms, there are almost too many to contemplate.

From their throne in our guts, microbes not only influence how we digest food, absorb drugs, and produce hormones, but they can also interact with our immune systems to affect our brains. Together the various interactions between microbes and the brain are called the microbiome-gut-brain axis, and understanding this axis could have profound implications for our understanding of psychiatric disorders and our nervous system.

Among the potential applications of this understanding is the promise of alleviating the physiological and psychoemotional burdens of obesity:

Sometimes our genes determine which bacteria live inside us, and then those bacteria turn right around and influence how we behave. This is very well demonstrated in mice lacking a gene called Tlr5, which makes them overeat and subsequently become obese. Mice missing Tlr5 have microbes that make them hungrier; they overeat and become fat. We can prove it’s the microbes doing this in two separate experiments. In one, we transfer the Tlr5-less mice’s microbes into other genetically normal mice, which then overeat and become fat. In the other study, we use antibiotics to wipe out the microbes in the Tlr5-less mice and watch as their appetites return to normal. It’s amazing to think a genetic tweak can create gut microbes that affect behavior and that this behavior can be transferred into another stomach and alter the behavior of its formerly normal host.

Knight points to similar studies being done on inhibiting anxiety by introducing microbes from anxiety-free mice to anxious mice, and considers the imminent development of vaccines against stress, PTSD, and depression. He points to one particularly promising area of study:

According to the World Health Organization, depression is now the leading cause of disability in the United States and is rapidly becoming more common in the developing world. This increase in depression rates matches the rise of other diseases frequently considered to be Western, such as inflammatory bowel disease, multiple sclerosis, and diabetes, all of which, we now know, have both immune and microbial components. Could our estranged soil bacteria, which modulate the immune system, be playing a role? In experiments in mice, Mycobacterium vaccae, a soil bacterium, has reduced anxiety. Intriguingly, in a social stress situation (essentially, smaller mice are put in a cage with a much larger, dominant mouse, which beats them up), M. vaccae treatment makes the mice much more resilient against the effects of stress, possibly providing a model for treating stress disorders in humans.

But far beyond the realm of lab mice, we’re conducting everyday experiments on our human microbiome all the time, usually without realizing it — Knight points out that everything from our diet (for instance, the balance of grains and proteins we eat and our your alcohol intake) to the antimicrobial hand-soap we buy to our use of antibiotics alters our microbiome.

Indeed, one of the most important aspects of Knight’s book, far beyond its scientific fascination, is its role as a vital public service announcement against the misuse and overuse of antibiotics — an outcry against the monoculture of mainstream medicine and a call for reclaiming our agency in the handling of our own bodies.

Pointing out that vaccines have “saved more lives throughout the world than any innovation except clean water” and are thus “humanity’s greatest triumph in public health,” he turns a critical eye toward the ludicrous anti-vaccination movement, lamenting “how much people worry about vaccines and how little they worry about antibiotics.”

A quick primer here: Antibiotics work by killing harmful bacteria in our bodies with poison that is more toxic to them than it is to us. But because bacteria breed rapidly, they also adapt to evolutionary pressures fast. Antibiotics exert one such pressure, which means bacteria swiftly sidestep the poison’s effect by developing resistance to it. Like the spammers who are constantly outsmarting and bypassing our anti-spam systems, we end up bombarded with unwanted, harmful material despite our ephemeral defenses.

But apart from being largely ineffective in the long run, antibiotics have a darker and far more significant downside — they tamper with our microbiome, sometimes modifying it to a dangerous degree. They are especially perilous for newborns and young children — Knight notes that antibiotics in the first six months are associated with weight gain (which is hardly surprising, given we use antibiotics to fatten up livestock) and may put the child at greater risk for obesity in adulthood:

Antibiotics can have a profound effect on a child’s microbial development, which may account for their apparent influence on later obesity.


Antibiotic treatment of newborns, even briefly, causes significant alterations to the composition of their gut bacteria. Perhaps more worrisome, antibiotics disturb the normal patterns of colonization of Bifidobacterium, one of the beneficial microbes. Colonization by Bifidobacterium plays a critical role in the development of a child’s immune system. Antibiotic use early in life may thus elevate the risks of allergies and allergic asthma by reducing the beneficial effects of microbial exposure.

But we are creatures of instant gratification, which is probably why we are so much more accepting of antibiotics, even if they are far more dangerous, than we are of vaccines — we take antibiotics when we are ill and they make us feel better almost immediately, almost miraculously; we are given vaccines when we are healthy, in the hope that they prevent some far-off future illness which, if they perform their respective medical miracle and work, we actually never get to experience. It’s easy to choose something that works easily and quickly, however perilous the side effects, to something that works invisibly and with greatly delayed gratification, even if it’s the safest life-saver.

In the remainder of the altogether illuminating Follow Your Gut, Knight goes on to explore how we get our microbiome and what we can do to optimize it for better physical and psychological health, both as individuals and as a culture. Complement it with Knight’s TED talk, which planted the seed for the book:

Illustrations by Olivia de Salve Villedieu

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E.B. White on Idea-Incubation and the Two Faces of Discipline


How to ride the “wave of emotion” in creative work on a raft of conscientious revision.

“One must continually watch what one is doing, without being carried away by it … [but] another kind of discipline is needed for using the mind with support from the imagination,” Simone Weil wrote in contemplating the key to discipline in 1933. Indeed, fruitful creative work — especially writing — is predicated on this porous relationship between structure and spontaneity, discipline and imaginative freedom. That’s what E.B. White addresses in his contribution to the fantastic volume The Paris Review Interviews, vol. IV (public library) — a compendium of wonderfully wide-ranging conversations with literary legends like Maya Angelou, Haruki Murakami, Ezra Pound, Marilynne Robinson, and William Styron.

In the same superb 1969 conversation that gave us White’s wisdom on how to write for children and the writer’s responsibility to society, he considers the question of discipline in writing:

There are two faces to discipline. If a man (who writes) feels like going to a zoo, he should by all means go to a zoo. He might even be lucky, as I once was when I paid a call at the Bronx Zoo and found myself attending the birth of twin fawns. It was a fine sight, and I lost no time writing a piece about it. The other face of discipline is that, zoo or no zoo, diversion or no diversion, in the end a man must sit down and get the words on paper, and against great odds. This takes stamina and resolution. Having got them on paper, he must still have the discipline to discard them if they fail to measure up; he must view them with a jaundiced eye and do the whole thing over as many times as is necessary to achieve excellence, or as close to excellence as he can get. This varies from one time to maybe twenty.

But this discipline of discarding mediocrity in the editing process must be preceded by the appropriate gestational period for ideas, or what T.S. Eliot called “a long incubation.” White reflects on his own experience of “sneezing” Charlotte’s Web:

When I finished Charlotte’s Web, I put it away, feeling that something was wrong. The story had taken me two years to write, working on and off, but I was in no particular hurry. I took another year to rewrite it, and it was a year well spent. If I write something and feel doubtful about it, I soak it away. The passage of time can be a help in evaluating it. But in general, I tend to rush into print, riding a wave of emotion.

And yet even this “wave of emotion” — which the perhaps more coolly rational Virginia Woolf famously called “a wave in the mind” — must be ridden on the raft of revision:

I revise a great deal. I know when something is right because bells begin ringing and lights flash. I’m not at all sure what the “necessary equipment” is for a writer [but] I do think the ability to evaluate one’s own stuff with reasonable accuracy is a helpful piece of equipment.

Complement with the cognitive science of the perfect writing routine and Anna Deavere Smith on what discipline means for an artist, then revisit this evolving library of advice on writing from some of humanity’s greatest writers and White’s warm letter of assurance to a man who had lost faith in humanity.

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The Miraculous in the Mundane: Annie Dillard on Reclaiming Our Capacity for Joy and Wonder


“The world is fairly studded and strewn with pennies cast broadside from a generous hand.”

Annie Dillard (b. April 30, 1945) has a way of coaxing the miraculous out of the mundane with such commanding gentleness that ordinary life has no choice but to unmask its extraordinary dimensions. She does this over and over in her 1974 masterwork Pilgrim at Tinker Creek (public library) — one of the most beautiful books to bless a lifetime with, which also gave us her magnificent meditation on the art of seeing and the two ways of looking.

I find myself returning to one particular passage that strikes with the grandeur Dillard is able to extract from the humblest of acts and the most middling of moments. She writes:

When I was six or seven years old, growing up in Pittsburgh, I used to take a precious penny of my own and hide it for someone else to find. It was a curious compulsion; sadly, I’ve never been seized by it since. For some reason I always “hid” the penny along the same stretch of sidewalk up the street. I would cradle it at the roots of a sycamore, say, or in a hole left by a chipped-off piece of sidewalk. Then I would take a piece of chalk, and, starting at either end of the block, draw huge arrows leading up to the penny from both directions. After I learned to write I labeled the arrows: SURPRISE AHEAD or MONEY THIS WAY. I was greatly excited, during all this arrow-drawing, at the thought of the first lucky passer-by who would receive in this way, regardless of merit, a free gift from the universe. But I never lurked about. I would go straight home and not give the matter another thought, until, some months later, I would be gripped again by the impulse to hide another penny.

Illustration by Sydney Smith from 'Sidewalk Flowers' by JonArno Lawson, a wordless ode to living with presence. Click image for more.

The joy of this, of course, comes not from reveling in the self-appointed godliness of orchestrating a mundane micro-miracle — it comes, rather, from the unexpected grace of allowing such an unremarkable event to fill the soul with such remarkable delight. But the very act of allowing is something we unlearn as we go through life and forget what it means to be truly awake. To relearn it, Dillard suggests, is to reclaim our capacity for joy and wonder:

The world is fairly studded and strewn with pennies cast broadside from a generous hand. But — and this is the point — who gets excited by a mere penny?


It is dire poverty indeed when a man is so malnourished and fatigued that he won’t stoop to pick up a penny. But if you cultivate a healthy poverty and simplicity, so that finding a penny will literally make your day, then, since the world is in fact planted in pennies, you have with your poverty bought a lifetime of days. It is that simple.

After all, as Dillard herself has written elsewhere, “how we spend our days is, of course, how we spend our lives.”

Complement Pilgrim at Tinker Creek, which is as much a life-changing read as it is a life-changing reread every time, with Dillard on writing.

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An Adventure in Paris with Pussy and Lovey: Alice B. Toklas and Gertrude Stein Become Babysitters


A positively pleasing illustrated take on a true story.

The fateful first meeting of Gertrude Stein and Alice B. Toklas sparked a lifelong romance that lasted not merely until Stein’s death but, as Toklas’s moving memoir suggests, until her own death twenty years later. During their reign as the quintessential Americans in Paris, they became an epicenter of creative culture, around which such rising stars as Picasso, Matisse, Hemingway, and Fitzgerald orbited. In 1954, Toklas captured their extraordinary partnership in The Alice B. Toklas Cookbook — a delicious memoir in disguise, written in a style similar to Stein’s autobiography and peppered with warm recollections of the couple’s life and love.

Although their story is yet to join the finest picture-book biographies of great artists, writers, and scientists, a most delightful fragment of it comes to life in Gertrude and Alice and Fritz and Tom: An Artful Adventure with Gertrude Stein and Alice B. Toklas (public library) by longtime Stein and Toklas collector Hans Gallas. Illustrated by comic artist and New Yorker cartoonist Tom Hachtman, creator of the comic strip Gertrude’s Follies, this marvelous picture book for all ages is loosely based on a chapter from the memoir of Fritz Peters, who went to a boarding school near Paris in the 1920s with his younger brother Tom and did indeed visit with Stein and Toklas one holiday.

The story begins with an affectionate primer on Stein and Toklas and their home in Paris amid “masterful modern paintings that covered the walls, floor to ceiling,” including a “positively pleasing portrait of Gertrude” by the couple’s dear friend Picasso.

Gertrude was a really remarkable writer and sometimes Alice called her “Lovey.”

Alice was a constantly creative cook and sometimes Gertrude called her “Pussy.”

One day, they receive a letter from an American friend asking them to babysit her “beautifully behaved boys, Fritz and Tom,” over Thanksgiving.

“There, there,” said Gertrude, “What to do? What to do? What to do?”

“Lovey,” said Alice, “I’ve heard Fritz and Tom can be a horrible handful. They play pesky pranks at school and are not fond of challenging chores.”

“Horrible handful? Pussy, you mean beastly brats who play pesky pranks and are not fond of challenging chores?

How beastly can the brats be? We have two dogs, Basket and Pépé.

Rose is a rose is a rose is a rose.”

After some deliberation over Tibetan tea and Alice’s “truly tasty teacakes,” the couple decides to let the boys visit. From the moment they arrive and begin pressing their noses against Stein’s prized art, festive chaos ensues.

After their Thanksgiving feast, appropriately reflective of Toklas’s culinary creativity, the foursome take to the streets of Paris for sightseeing and adventures in Stein’s famous car, Lady Godiva.

Eventually, the boys depart and the couple resumes life as usual.

Then, one morning, Alice discovers a sweet thank-you note from Fritz and Tom tucked behind her favorite teapot and runs to show it to Gertrude, who is enjoying one of her beloved bubble baths.

“Pussy, don’t drop it in the tub,” said Gertrude. “This is one of the nicest notes we have ever received.”

“Lovey, it is positively pleasing, and I think we would make two amusing American aunts,” said Alice B. Toklas.

“Now finish your belated bubble bath, you have some really remarkable writing to do!”

“And you have some constantly creative cooking to do!” said Gertrude Stein.

Complement the altogether positively pleasing Gertrude and Alice and Fritz and Tom with Stein’s loving “word portrait” of Toklas and Toklas’s recollection of the magical moment they first met, then revisit Lisa Congdon’s wonderful illustrated inventory of Stein’s favorite objects.

Donating = Loving

Bringing you (ad-free) Brain Pickings takes hundreds of hours each month. If you find any joy and stimulation here, please consider becoming a Supporting Member with a recurring monthly donation of your choosing, between a cup of tea and a good dinner.

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Brain Pickings has a free weekly newsletter. It comes out on Sundays and offers the week’s best articles. Here’s what to expect. Like? Sign up.