Read an Excerpt
Introduction
When I was working on my book about mushrooms, Mycophilia, I asked the mycologist Tom Volk whether bacteria lived inside fungi the way they live in us.
“If you ask me,” he said, “I think there are probably bacteria in everything.” That quote lingered in my mind for years. If bacteria (and, I would later learn, other microscopic organisms) live in everything, did that mean all living things are connected by microbes?
I started looking for the answer in books about microbiology. That’s where I hit my first snag. I had no microbiology background. Actually, I had almost no biology background at all. I was an English major in college not only because I loved to read and write but also because I was convinced I was hopeless at science and math. So the books I read may have contained the answer, but if they did, I couldn’t see it.
That’s why I went back to college, at 55 years old, to study biology. Going back to school turned out to be a kind of unraveling of my ego, where I had to deal with being bad at something all the time. It wasn’t fun, but it turned out to be necessary, because humility is the entry point for understanding nature. One of the many things I learned in college was the deeper you look, the more complex life is.
I also learned that learning is not something you age out of. In fact, it can change everything, no matter how old you are. I went to college to study biology in order to expand my perception of life. And it did, but not in the way I expected. I found out that life itself is a vast conspiracy of microbes.
Microbiology, the study of organisms too small to see with the naked eye, is really difficult to comprehend at 55 or any other age. You can’t use your senses to perceive these tiny life-forms. Unless you have a microscope, you have no primary observation of them, only secondary sensing. You can see the burp of methane bubbles in Los Angeles’s greasy La Brea Tar Pits, but you can’t see the archaea that are producing the gas. It’s challenging to describe microscopic organisms with words for the same reason. Throughout the process of writing this book, I kept losing track of my voice, the truth-speak that comes directly from the writer’s personality. And it occurred to me my problems were founded in the very limited number of adjectives I could use. I mean, the descriptive tools of my trade—sight, sound, smell, and touch—don’t really apply to a bacterium. It seemed like my writerly challenges were synonymous with the challenges I faced in understanding the biology of the microscopic world. My worldview, which includes my way of communicating, is locked into a scale relative to my experience. But the microscopic world
operates on a very different scale.
That’s a problem, because we can understand nature and ourselves in a deeper way through the lens of a microscope. New discoveries about the impacts of bacteria on our lives occur every day, and while the headlines grab some of us, many of these breakthroughs seem beyond the capacity of most people to understand. But microbiology is where it is happening. This is the age of bacteria, said the evolutionary biologist Stephen Jay Gould, “as it was in the beginning, is now, and ever shall be.”
Microbiology is like a foreign country. It is very difficult to get around without a basic vocabulary. That’s what the biology course I took at Columbia University (my alma mater: I graduated from Barnard College during the Reagan administration) gave me. I acquired the tools necessary to read most papers by microbiologists and understand their presentations. I only developed tourist biologese—I couldn’t learn enough in a year to master weedy, acronym-stuffed papers—but it was enough to get around. And by the second semester, something began to change. I started to see that life, every aspect of life, is sustained by microbes.
I experienced revelation after revelation about the impact of microbes on our lives. For example, microbes link the nonliving and living spheres of the planet. They convert chemicals in the atmosphere into food that can travel up the food chain. And they maintain the balance of chemicals on the planet. If lions and elephants went extinct, life would still go on. But as the biologist Tom Curtis wrote in the journal Nature Reviews Microbiology , “If we accidentally poisoned the last two species of ammonia-oxidizing bacteria, that would be another matter.”
I learned that inside our cells reside the remnants of ancient bacteria that convert the oxygen we breathe into energy. They are called mitochondria, and without them, we wouldn’t exist. I realized that on the microscopic level, the whole idea of species just falls apart because the pace of microbial evolution is so fast that by the time a scientist has identified a bacterial species and picked out a name, its progeny may have evolved into something else.
I found out that mats of microbes, not unlike the orange muck of an intertidal zone, are complex communities composed of microscopic friends and enemies, food makers and degraders of the dead. Ancient microbial mats were the protosoil; they made the colonization of terrestrial Earth possible. I learned that soil is living and dying and dead microbes interacting with a matrix of minerals, upgraded with living and dying and dead plants and animals. Without microbes, soil is just dirt.
Another revelation was the notion that feeding and fighting were invented by microbes, and they have been doing those jobs for every organism that came after them on the timeline of life. Microbes deliver nutrients and provide defenses for fungi, plants, and animals. All complex life evolved with microbes that do these jobs. It’s the microbes living on our skin that keep pathogens at bay; it’s the microbes in our guts that break down the plants we eat.
Indeed, my whole understanding of how to take care of my body changed. What we eat feeds the microbes in us. Eat a lot of sugar and you feed microbes that ferment sugar, and their population numbers rise. Sugar fermenters produce molecular by-products like lactic acid, which cause tooth decay. Eat a lot of kale and other species thrive, species that produce other by-products, some of which we depend on to make everything from hormones to neurotransmitters. Our food choices affect the population dynamics of our microbes, which in turn affect us.
As my knowledge of microbiology deepened, I became more adept at teasing out the commercial hype and fearmongering in the news. Flesh-eating bacteria, for example, are rare; they’re not the microbes to worry about even though an infection by them is truly horrific. The ones to worry about are antibiotic-resistant microbes, which experts estimate will kill 10 million people every year by 2050 unless we find some new medicines. Probiotics, live bacteria and fungi that increase the population of particular species in your gut, work if you suffer from certain kinds of diarrhea, but beyond that, meh. And prebiotics are just bacteria (and fungi) food, mainly fiber that feeds those microbes that produce healthful benefits. An apple is a prebiotic.
I came to understand that everything that lives has a microbiome, multiple microbiomes, in fact. There are microbiomes all over plants, microbiomes of the seed and the fruit and the leaves, and microbiomes all over us, in our noses and our ears (one fellow, after dealing with a persistent bacterial infection in one ear, finally had the bright idea to transfer some wax from his healthy ear to his infected ear, and within days his infection disappeared), in our belly buttons, on our hands, in our mouths, between our toes, under our arms, in our genitals—everywhere.
Microbes even define family. Each of us travels through life in a unique cloud of microscopic debris that we shed from our skin and hair and breath and clothes and farts, an aura composed of a million microscopic particles. Depending on how much time and what degree of contact a person has, two or more people’s airborne microbial clouds may homogenize. Couples share
more microbes than roommates, and families with young children share the most of all.
As I was nearing the end of this book, I met an artist named Andrew Cziraki, who explores social issues using science to construct art forms. I’d heard about a piece he was working on called The Holy Water Project. Part of the project included collecting samples of water from holy water fonts, the basins of blessed water often placed inside the entrance of Catholic churches, into which parishioners dunk their fingers before making the sign of the cross. He conducted DNA analyses of each sample in order to determine what organisms were present. He was on the lookout for something that would illuminate the relationship between the community and the church through an analysis of the water. He found bacteria and yeast, and human DNA, but also DNA that correlated with the locations of the New York City churches: carp DNA in the Chinatown church, parasites like roundworms and tapeworms in the church near Pennsylvania Station, “which kind of made sense because there are a lot of homeless people sleeping there,” he said.
Andrew is interested in this because holy water is where people drop off and pick up microbes. The metaphor of the church, that religion binds the community, is literal here. “The community shares itself in this font of microbes,” he said. The font is a symbol of sacrament, of purification, “and yet,” said Andrew, “what it really does is transmit. I learned it doesn’t matter who or what
you are. We are all connected.”
All along I’d been sensing it: microbes are bridge organisms that connect the living and nonliving, the soil and plants, the plants and people, and people with each other. But now, I understand. We are all connected to everything by microbial life. We hardly perceive the connections, but we are living them, every day.
Microbia tracks my year studying biology—what I learned and what it was like learning it. College life today differs from when I was young. A lot has changed. The science is new, the technology is new, and the pressures and stresses are on a level I don’t recall. But much is the same. Students still get morally outraged, they still protest, they still have wickedly funny senses of humor. And everyone is still looking for love, or at least that age-old exchange of microbes we call sex.
When I first registered for classes, I was frustrated to discover I couldn’t take courses in microbiology without studying biology and chemistry first. I didn’t want to wait a few years before I could dig into what most interested me, so I augmented my biology classes with a pretty vigorous schedule of off-campus reading, interviews, seminars, and lectures. The science I report on comes from all those sources.
But as the mycologist Nicholas Money wrote in his book The Amoeba in the Room, “The more we probe, the more we see.” I am quite sure that by the time you read this book, there will be many new microbiological discoveries, probably very significant ones. The flood of data is accelerating, and I could have continued to write indefinitely. So obviously, I had to make compromises. For starters, I didn’t write about ocean microbiology; nor did I explore the microbiology of different soils, or get into comparative microbiomes between different kinds of animals and plants, or look in depth into the effects of climate change on microbial life, which is significant. For example, researchers have found that the warming climate leads to loss of microbiome diversity in common lizards, which can undermine the lizard’s ability to survive environmental conditions such as, well, a warming climate. All these are fascinating and important subjects, and lots of great science is being done. But I chose to focus on the immediate and familiar: farmland, corn, us.
I had a great deal of assistance on this book, from my professors at Columbia and from many microbiologists in the field who kindly clarified—and then clarified again—what was for me very challenging material. At one point over lunch at a hummus restaurant in New York City, Nicholas Money pointed out that maybe it was something of an advantage to come at microbiology as a naif. I don’t know if that is true, though I hope so. Because if I’ve achieved what I set out to do, which was to share the euphoria (and the humiliations) of my learning curve and dejargonize the basic current thinking about microbes, then maybe the breakthroughs in microbiology that you read about in the papers will be a bit more accessible and make a bit more sense. We are just starting to understand microbial life. The term microbiome wasn’t even coined until 2001, by the molecular biologist Joshua Lederberg. There are a lot of discoveries on
the horizon, and it’s going to help to have a little microbial literacy under our belts. “The planet is half-owned by microbes,” sighed the microbiologist Moselio Schaechter, in his rich Italian accent. “Which means, if we don’t know something about microbes, we don’t know half of ourselves.”
He’s right. For all our technology, we still don’t know the half of it. For me, studying invisible life expanded my perspective of the world, and it broadened my definition of life to include organisms that were beyond my ken. But once I understood that these creatures invented living and, as a result, are implicated in every aspect of every life, it raised my own soggy consciousness. I glimpsed another world and found out I share it with everything else on Earth. By looking into the unseen, my sight cleared.
