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. In other words, the first cell we can know about by analyzing modern genes fed on hydrogen gas in a hot, pitchdark, 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: 10 (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. 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.
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.CHAPTER 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. 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 health.
Thus the first three years of life are profoundly important. Interventions in the very young can have the largest and most lasting effects on health and disease. Although some things that happen in the first three years are beyond your (or anyone's) control, the people your child interacts with, the foods they eat, the places they go, and the medications they take can have lifelong effects. What they encounter in those early years serves as a critical inoculation for their well-being.
This is why dirt is so good. It exposes your child to a huge array of harmless germs that, while they may not colonize us, have complex traits to train up your baby's immune system. Many people think that an activated immune system, with lots of inflammation, is good, but in fact the reverse is true. A well-trained immune system damps down inflammation when it's not needed, just as a highly trained athlete's heart races during exercise but has a low pulse the rest of the time.
Microbes can come from the strangest places. Rob recalls a friend who said, "The weirdest part of being a mom is saying sentences I never thought I could imagine, like 'Never put your finger in that part of the kitty.'" Think for a moment about our evolutionary history. We evolved as hunter-gatherers and early agriculturalists. Our world was filled with dirt, animals, and wild foods we had to hunt or collect. We've only cleaned things up in the last couple of hundred years.
Your baby comes into the world with a biological program expecting to see conditions similar to that past. You can help by providing missing pieces in a commonsense manner. And that is what the rest of this book is all about.CHAPTER 3
Can my microbiome affect my ability to conceive? Are bacteria related to infertility? We often get asked these questions. Trying to conceive can be difficult.
Everyone wants to know why things are not just happening as they should. Unfortunately, right now there is very little data that could support a solid answer. As we often say, this is a topic of active research.
Examples of this active research include testing to find out whether bacterial vaginosis (BV) — growth of less common kinds of bacteria in the vagina — is related to infertility — and whether it interferes with conception and early pregnancy after in vitro fertilization.
BV is extremely common. Symptoms include a white or gray vaginal discharge with a fishy smell. It usually does not itch or burn. The risk of contracting a sexually transmitted disease such as HIV doubles when you have an active BV infection (although the picture is less clear if you simply have an unusual vaginal microbiome). BV has also been associated with premature birth, a topic being researched in Jack's lab, but no causal link has yet been identified.
BV is caused by an imbalance in vaginal microbes, particularly a reduction in lactobacilli. Women who douche frequently are especially prone to it. So trying to keep the vagina "too clean" in the short run can lead to problems in the long run. The consensus medical advice is that the drawbacks of douching greatly outweigh the benefits. And these drawbacks range from problems conceiving to cervical cancer.