Dirt Is Good: The Advantage of Germs for Your Child's Developing Immune System

By Jack Gilbert and Rob Knight

From two of the world’s top scientists and one of the world’s top science writers (all parents), Dirt Is Good is a q&a-based guide to everything you need to know about kids & germs.

“Is it OK for my child to eat dirt?”

That’s just one of the many questions authors Jack Gilbert and Rob Knight are bombarded with every week from parents all over the world. They've heard everything from “My two-year-old gets constant ear infections. Should I give her antibiotics? Or probiotics?” to “I heard that my son’s asthma was caused by a lack of microbial exposure. Is this true, and if so what can I do about it now?”

Google these questions, and you’ll be overwhelmed with answers. The internet is rife with speculation and misinformation about the risks and benefits of what most parents think of as simply germs, but which scientists now call the microbiome: the combined activity of all the tiny organisms inside our bodies and the surrounding environment that have an enormous impact on our health and well-being. Who better to turn to for answers than Drs. Gilbert and Knight, two of the top scientists leading the investigation into the microbiome—an investigation that is producing fascinating discoveries and bringing answers to parents who want to do the best for their young children. Dirt Is Good is a comprehensive, authoritative, accessible guide you've been searching for.

• Language: English
• Publisher: Macmillan Publishers
• Release date: Jun 6, 2017
• ISBN: 9781250132628

Jack Gilbert

JACK GILBERT, PhD is a Professor of Surgery at the University of Chicago and Director of the Microbiome Institute. Dirt is Good is his first book.

Book preview

Introduction

Is it okay for my kid to eat dirt?

That’s just one of the many questions we’re bombarded with every day from parents all over the world who are worried about their children’s health and confused about what they’re reading on the Internet.

Why are they asking us?

Because we’re two of the scientists leading the investigation of the human microbiome. That’s often misunderstood as meaning germs, but it’s really the community of friendly microbes that populate the human body, as well as a few that, in the wrong context, aren’t so good. This diverse multitude of tiny, invisible creatures helps us out in all kinds of ways, such as digesting food, making vitamins, protecting us from diseases, sculpting our organs, tuning our immune systems, and even shaping our behavior.

The notion that most bacteria, or germs, are intrinsically bad—and must be killed by any means possible—is widespread. But it’s wrong, dangerously wrong. New methods of studying the microbial world reveal that most of the bacteria we encounter on a daily basis, and those that reside in and on our bodies, are not just friendly but even essential for keeping us alive. We exterminate them at our peril. In our zeal to vanquish all those classical plagues, we have inadvertently unleashed a Pandora’s box of modern plagues—the array of slow-killing, miserable, chronic health problems that have become prevalent across the modern world: obesity, asthma, allergies, diabetes, celiac disease, irritable bowel syndrome, multiple sclerosis, rheumatoid arthritis, and many others.

The science of the microbiome is leading to fascinating discoveries, and in just the last few years it has gone from a wonkish subfield of biomedical research to a topic of intense public interest. You’ll find it lionized in magazine and newspaper articles, TED talks (including ours), documentaries, radio and television talk shows, podcasts. And of course, it seems ubiquitous on the Internet, where it is inducing an enormous amount of hype and misinformation—and adding to the confusion and anxiety of parents who want to do the best for their young children.

Because of our expertise, we find ourselves being asked for our advice from all sorts of people in all sorts of situations.

After hearing a talk on the role of family dogs and a healthy microbiome, an audiovisual technician approaches the lectern. A bit nervously, he says, My son loves our local playground, especially the sandbox and the jungle gym. He wants to go there every day. But the place looks filthy to me. I mean, gum wrappers, dog poop, pigeons everywhere. Should I worry about him catching a disease?

After engaging in a short conversation about work, a balding taxi driver turns his head around and shoots a pained expression. Oh my god, maybe you can help me. My son has diabetes. He’s extremely overweight and he’s only three. My wife and I don’t know what to do.

A janitor at work stops us in the hall with a concerned look. We’re supposed to use antibacterial products on everything we clean, but is that a good idea? I work in two elementary schools and I have a five-year-old at home.

The questions pop up even when we’re not being recognized for our expertise. In the Whole Foods supplements aisle a woman scrutinizing shelves of probiotics turns to ask, of anyone, Do you have a clue as to which of these brands really work? My little girl has diarrhea. She’s not getting better. I’m frantic!

We can relate. In raising our own children, we have dealt with numerous frightening episodes where their health was challenged and we didn’t know what to do, starting with birth itself. Each of our firstborns experienced rather terrifying (or at least we thought so at the time) events in the delivery room.

Jack’s son, Dylan, was born in his own meconium, the dark greenish excrement produced by newborns. Because he had pooped in the birth canal, he was immediately given antibiotics and was kept in the hospital overnight for observation. This was done as a precaution against the possibility he had inhaled some of it, which in his new lungs could have caused a nasty infection. Dylan had multiple bouts of diarrhea by the time he was six months old and later suffered several flares of a yeast infection, or thrush, all over his body. This rash has raised white patches on a scarlet background. He had ear infections and developed a cry that always sounded like a bark or a cough. At age six, he was diagnosed with high-functioning autism, now increasingly linked to the microbiome.

When Rob’s unborn daughter went into distress after a prolonged labor, the anxious parents reluctantly consented to a cesarean section. But they were not about to give up entirely on a vaginal delivery, which Rob’s research strongly suggests confers benefits on newborns. An hour later, after the hospital staff had left them in their room alone, Rob pulled out some cotton swabs. Using these, he collected vaginal fluids from his partner Amanda and transferred them to his daughter’s mouth, nose, ears, face, skin, and perineum. He inoculated her with her microbial birthright, which had been denied by the C-section. He did this because he had knowledge of the best available scientific evidence about what would be good for his newborn; he had even participated in that discovery.

Our goal in this book is to present you, too, with the best scientific advice available about the microbiome and your children’s health and development. What procedures, drugs, foods, environmental exposures, and everyday practices can help or harm your children early in life? What can you do to protect their health and development? What works and what doesn’t? How will you know if your child is heading in the right or wrong direction? What is being hyped and whom can you trust?

Not being medical doctors, we can’t give medical advice. But as scientists who together have been involved in generating a substantial amount of the data that underlie the research that is now relied upon by physicians and other medical clinicians throughout the world, we can offer evidence-based answers to your questions and reliable ways to think about microbes and health. We answer these questions, where possible, with information about clinical trials performed in humans. However, often it’s not possible or ethical to do the definitive experiment in humans, and in those cases we rely on a combination of observational studies (looking at differences between groups of people) and experiments in animals or in test-tube settings. Often, an observation in people (for example, that lean and obese people have different microbes) leads to detailed experiments (say, that mice given a particular microbe isolated from lean people will slim down itself). In general, this translation from bench to bedside allows us to know a lot more in terms of biological mechanisms than would be possible if we looked only at human studies. However, it’s important to remember that the translation isn’t always perfect, and the further you move away from a human study the less likely the results are to apply.

After a brief explanation of microbes and the human microbiome, we’ve organized this book to follow your child from pregnancy through birth and infancy, and then the toddler and preschool years. We pay special attention to medical conditions, assessments, and interventions that cut across those ages. Within each section, we answer the questions we are most commonly asked. You’ll find that answers often lead right into the very next question you were about to ask, as well as its answer. We’ve tried our best to turn this book into a conversation, as if we were in the room with you.

Like it or not, the microbiome has permanently joined the long list of parental worries.

1

The Microbiome

Earth formed about 4.5 billion years ago when a disc-shaped cloud of dust and gas collapsed into a primordial sphere. It was lifeless and molten and reeked of lethal gases. When it finally cooled, a newly solid crust allowed liquid water (via special delivery from comets) to collect on the surface.

A billion years later, this hellish planet had been transformed. It was now slathered with free-living, single-cell organisms called prokaryotes and archaea. They amassed themselves into shallow microbial mats at the bottom of the ocean and on the sides of towering volcanoes. In fact, these original inhabitants survive to this day in the coldest and hottest regions of land and sea. And they can feed on just about anything, including ammonia, hydrogen, sulfur, and iron.

One of the great mysteries of biology is, how did all this life arise? How did nonliving chemicals manage to invent cell membranes and self-replication, to feed and repair themselves? Scientists used to think that a primordial soup was struck by lighting and suddenly organic life sparked into being—a la Frankenstein.

Current theories are only a little more prosaic. More recent evidence, based on a genetic analysis of known microbes, traces life’s origins to deep-sea hydrothermal vents that spew out boiling gases.¹ In other words, the first cell we can know about by analyzing modern genes fed on hydrogen gas in a hot, pitch-dark, iron-rich, sulfurous environment. It had figured out how to obtain energy to live.

For millions of years, microbial mats pretty much ran things. Gradually, through countless real-life experiments driven by evolutionary forces, some of the microbes developed the ability to use the energy in sunlight to turn carbon dioxide and water into food. This process, known as photosynthesis, released massive amounts of oxygen. The air you breathe was made by those microbes. It still is.

We mention this background to help you get your head around a fact that is difficult to grasp: we humans live on a planet that is run by and for invisible microbes. For 3 billion years, they were its sole owners. They created our biosphere, maintaining global cycles involving carbon, nitrogen, sulfur, phosphorus, and other nutrients. They made all the soil. Last but not least, they set the conditions for the evolution of multicellular life, meaning plants and animals, including us.

The number of bacteria on Earth is estimated to be a nonillion: 10³⁰ (10 to the 30th power, i.e., 10 followed by 30 zeros). That’s more than the number of stars in our galaxy. The number of viruses is at least two orders of magnitude greater. According to a new estimate, there are about 1 trillion species of microbes on Earth and 99.999 percent of them have yet to be discovered.² If we lined them all up end to end, the bug chain would stretch to the Sun and back 200 trillion times.

That means all of microbiology is built on less than 1 percent of microbial life. We have only sequenced fifty thousand of their genomes for our databases. The rest are mysterious. We can’t grow them in our labs. They have no names. Their functions are not known. We are surrounded by microbial dark matter.

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Organisms that we call microbes are grouped into three domains: Bacteria, Archaea, and Eukaryota. These domains are radically different from one another—far more different genetically than humans are from a squid or even a pine tree.

Microbes in the first domain, Bacteria, are what most of us think of when we talk about bugs or germs. They are single-cell organisms lacking a nucleus. But they are not primitive. They can move, eat, eliminate waste, defend against enemies, and reproduce with remarkable efficiency.

Microbes in the second domain, Archaea, are single-cell organisms that look very much like bacteria under a microscope but have unique ways of making a living. They stem from a different branch on the tree of life, with different genes and biochemistry. Many of them are extremophiles that thrive in environments like boiling hot springs and salty lakes. But others live in milder climates, in the oceans and even in the human gut and skin.

The third domain is the Eukaryota, in which we find the microbes of the Fungi and Protista kingdoms. These Fungi are not toadstools in a forest but a single-celled version of this kind of life. You are undoubtedly familiar with yeasts, valuable for making bread, beer, and wine. But some, such as Candida, can also cause unpleasant infections. The Protista are single-celled relatives of plants, animals, and fungi. They are the latest incarnation of our microbial ancestors.

Finally, and somewhat contentiously, we have the viruses. While it’s debatable whether they’re alive, there’s no doubt that they are incredibly efficient at replicating themselves by harvesting the cellular machinery of cells around them.

Collectively, these microbiota—the bacteria, archaea, fungi, protists, and viruses—constitute the microbiome of a particular plant, animal, or ecosystem.

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Nevertheless, we have some pretty good ideas for how life operates and how simple rules give rise to complexity. All of biology is based on principles of evolution, competition, and cooperation. And microbes are masters at cooperation. The waste product of one microbe helps feed its neighbor. They care where they are and who is with them. And they share genetic information, passing it not only to their progeny but to their neighbors as well—even across species.

As for competition, the microbial world is a stage for endless war. Bugs that eat the same foods struggle to find ways to outwit their neighbors. As sworn enemies, bacteria and viruses have been duking it out for billions of years and, in so doing, have invented just about every chemical reaction, every defensive and offensive strategy imaginable, every survival trick in the book of life.

Another mind-boggling fact is that all these invisible microbes outweigh all visible life by a factor of 100 million. Collectively they are heavier than all the plants and animals—all the whales, elephants, and rain forests—that you can see around you.

Visible life is overwhelmingly composed of eukaryotes—single cells that contain a nucleus and that evolved over the last 600 million years into everything big. You are a eukaryote because the cells that make up your body are eukaryotic. Yet unlike microbial eukaryotes, which only have a single cell, your body is made up of tens of trillions of cells that have differentiated into all the different body parts—each of which still has your genetic code locked in its nucleus. As we’ll see in Chapter 2, collectively, your eukaryotic cells have developed many special relationships with microbes.

But before we get to the human microbiome, let us entertain you with some of the more hostile habitats that microbes call home.

Bacteria and archaea have been discovered living in Martian-like conditions on volcanoes in South America, with no water, extreme temperatures, and intense levels of ultraviolet light. They extract energy and carbon from wisps of gases flowing from Earth’s interior.

The oceans contain at least 20 million kinds of marine microbes that make up 50 to 90 percent of the ocean’s biomass. There is a mat of bacteria on the seafloor off the west coast of South America that covers an area roughly the size of Greece. Mud pulled from more than five thousand feet below the seafloor off Newfoundland was found to be teeming with microbes.

Bacteria at hydrothermal vents inhabit everything—rocks, the seafloor, and the insides of mussels and tube worms. They thrive in highly acidic, alkaline, or salty boiling water under high pressure and heat. Some heat-loving thermophiles grow at 235 degrees Fahrenheit. They lend the deep blue, green, and orange colors to Yellowstone’s boiling ponds.

Microbes dwell in the rocks found in the world’s deepest gold mines. In fact, they can eat gold, sequestering it like Lilliputian miners.

Recently, a new genus of bacteria, Candidatus frackibacter, has been found living inside hydraulic fracturing wells in Appalachian Basin shale beds. Similarly, acid-loving microbes make their home in mine drainage sites.

After the Deepwater Horizon oil spill in the Gulf of Mexico in 2010, microbes gorged themselves on oil and natural gas. They chewed through a toxic stew of hydrocarbons.

Microbes eat plastic. As much as 8 million metric tons of the stuff are dumped into our oceans every year. Trouble is, each piece of plastic takes at least 450 years to decompose. The Great Pacific Garbage Patch, a floating vortex of plastic waste far out to sea, is home to about a thousand different kinds of microbes living on the debris. Landfills contain mountains of polyethylene terephthalate, a plastic used to make water bottles, salad spinners, and peanut butter jars. While it’s the most recycled plastic in the United States, two-thirds of it escape our household bins. Researchers recently screened 250 samples of sediment, soil, wastewater, and sludge to see if any microbe might like to eat the plastics. One volunteered: Ideonella sakaiensis.

They even munch uranium. Fungi have been deployed to absorb radiation from tainted water at the Fukushima nuclear reactor in Japan.

Some bugs make their living forty miles high up in the sky. In the upper atmosphere, they help form clouds, snow, and rain. When raindrops land on the leaves of trees and shrubs, the bacteria within them can cause water to freeze, creating ice crystals even when they wouldn’t form otherwise. These crystals damage plant tissues, allowing the microbes to get inside. Once there the microbes can exploit the resources of the plant (of course the plant thinks of this as an infection!).

Bacteria can survive in space. They rode in all the space shuttles and are ensconced in the International Space Station. The Russians exposed microbes to space for a year, outside of the Mir space station, and some survived. NASA scientists suspect that water channels emerge sporadically on Mars and would like Curiosity, the robotic rover that is tooling around, exploring the terrain on Mars, to take a look. But since the rover may carry Earth’s microbes, which would thrive rapidly in the water, they can’t take the chance of getting too close for fear of contaminating this off-world water source.

They also live closer to home. Extremophiles have been found in dishwashers, hot-water heaters, washing machine bleach dispensers, and hot tubs. They are on every household surface and even in your tap water. We harness them to make food, drugs, alcohol, perfumes, and fuel. Nearly every antibiotic is derived from microbes.

And if all this isn’t enough, they eat you when you die.

2

The Human Microbiome

As you saw in Chapter 1, Earth has its own microbiome. It’s everywhere—in soil, air, water, forests, mountains, fracking fluids, gold mines, and hot-water heaters.

But animals have their own microbiome, and like you and your child, they acquire it at birth from their mothers, other animals, and the environment. Baby Komodo dragons share their skin and mouth microbes with their surroundings. Octopus eggs are colonized by friendly bacteria within hours of being fertilized. Vampire bats and koala babies acquire microbes from their mothers that allow them to digest their highly specialized diets.

Every creature has coevolved with its own collection of bugs. Termites can digest wood only because of the bacteria in their guts, which break down the otherwise indigestible cellulose. Cows absorb nutrients from grass thanks to the microbes living in their four stomachs. Aphids depend so heavily on their gut microbes that they have delegated the ability to produce essential nutrients like amino acids to their bacteria. Aphids no longer have the genes to carry out these functions. Their microbes do.

Humans have a microbiome too. Perhaps you’ve read that there are ten times as many microbes in your body as there are human cells. Unfortunately, that ratio came from a back of the envelope estimate made in 1972, and because it was such a compelling image, it stuck. A more recent analysis puts the ratio at 1.3 microbes per human cell.¹ Thus an average guy will have about 40 trillion bacterial cells and 30 trillion human cells. Individual differences in body size and gender skew the ratio, but you get the idea: we are a superorganism. You harbor about ten thousand microbial species that altogether weigh about three pounds—the same as your brain.

Recall the definition of a microbiome. It is all the microbes and all the genes acting in concert.

Here, microbes have the upper hand. There are at least one hundred microbial genes for every human gene, and they are responsible for many of the biochemical activities associated with your body, ranging from digesting carbohydrates in your food to making some of your vitamins.

Importantly, the microbiome is the genome that you can and do change every day. Although our human genome is fixed our whole lives, the genes in our microbiomes change in response to our food, our environment, drugs we take, and even our health. And at no time is this truer than in early childhood.

Our goal in doing research is to learn how to tweak the microbiome to enhance human health. And this raises a critical issue. From birth to age three, your child’s microbiome, especially in the gut, is extremely dynamic. It changes day to day, week to week, following a general pattern that acquires microbes, catch as catch can.

By age three, your toddler’s microbiome will have assumed an adult-like pattern. It is mostly stable and tends to bounce back after challenges. All the key microbial players are there, having taken up residence in all the moist and dry niches of your child’s body. There they stay, fending off pathogens, breaking down fibers, tuning the immune system, and even influencing mental

Reviews for Dirt Is Good

[2wondery_1 · Rating: 4 out of 5 stars]

Moderately interesting, though I've read in more depth elsewhere. A good place to start the subject.