The Magnificent Microbiome
“If you don’t like bacteria, you’re on the wrong planet.”
—Stewart Brand, American photographer and writer
Inside your mouth are millions and millions of tiny bugs. Most of them are harmless, many of them are very beneficial, and a few of them cause diseases. Imagine your mouth, teeming with these invisible bugs. If this gives you the willies, you aren’t the only one. We have a long history of hating bacteria and seeing them as the bad guys that cause infections, fever, pain, and suffering. But we have learned in recent decades that many of these bacteria are good for us.
The truth is, we are not just human beings. We are superorganisms. According to “The Oral Microbiome—An Update for Oral Healthcare Professionals,” “for millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a ‘superorganism’…with the microbiome playing a significant role in our physiology and health.” We carry around trillions of microscopic bugs all day, every day, for our whole lives. These microbes help us fight disease, boost our nutrition, protect us from infections, and tune the metabolism.
It turns out that there are about as many bacterial cells in the body as there are human cells, though many scientists believe the number of bacterial cells may be even higher. There are millions of bacteria in every crack and crevice of the body. They inhabit most organs of the body, especially the ones that are open to the outside world, like the gastrointestinal tract, skin, eyes, genitals, and more.
“Microbiome,” “Microbiota,” or “Bugs?”
The bacteria, viruses, fungi, and other microscopic organisms that live inside and on your body make up your microbiota. The DNA codes (or genomes) of those bugs make up your microbiome.1 However, when we are talking about a community of bugs that lives inside the body, we also call it a microbiome. You’ll see this word over and over again, so it’s worth remembering. The human microbiome is a super-hot area of research. It’s like exploring a whole new universe—one that lives within.
I often use the word “microbiome” to talk about the microbes or microscopic organisms that live all over and inside of you. But sometimes I think it’s simpler to just call them “bugs” Don’t let that word—bugs—scare you off. The majority of your microbiome is made up of good bugs. And we aren’t talking about insects.
When we talk about the human microbiome, bacteria are the major players. Bacteria are single-cell organisms that don’t have the same cellular makeup that we do. Bacteria are tiny. If you line up 1,000 bacterial cells, they would fit across a pencil eraser. Under a microscope, a bacterium can look like a ball, a rod, or a spiral. Bacteria are the dominant living creatures on Earth and they can survive in almost any climate, including in the Yellowstone hot springs, under Antarctic ice, or in the human digestive tract. It has been estimated that there are 5 × 1030 (a nonillion) bacteria on Earth, which accounts for much of the Earth’s biomass, more than that of all plants and animals combined.
Sometimes people talk about only bacteria when they talk about the human microbiome, but other life forms are there too, it’s just that they are a little easier to overlook. Fungi and viruses don’t make up as big a piece of the pie and they aren’t as widely studied as bacteria. So are other, even smaller, bugs that we are learning more about all the time.2 Viruses are ultra-small infectious agents that replicate inside of other cells. You know about cold viruses, and there are others that live in the mouth, such as the herpes virus. Beyond human viruses, there are viruses that attack bacteria. Wherever bacteria are, so go bacteriophages; these bacteria-infecting viruses outnumber bacteria, humans, whales, trees, and everything else put together.3
Figure 1.1: Bacterial composition in different microbiomes of the human body.
Fungi, such as mushrooms and yeast, have a different cellular makeup than animals or plants. Certain fungi thrive in the human body, contributing to the microbiome. You have probably heard of fungal infections causing vaginal yeast infections, jock itch, or athlete’s foot. Still, bacteria make up the large majority of the microbiome.
There are at least 100 trillion bacteria living in the human intestinal tract, and taken together they have at least 100 times as many genes as our own genome.4
There are big microbiomes and then there are small microbiomes. When we talk about the human microbiome, we are talking about the compilation of all of the bugs that live throughout the whole body. Each particular place in the body may have its own specific microbiome. There is the oral microbiome, the gut microbiome, the vaginal microbiome, the skin microbiome, the urinary tract microbiome, and the list goes on and on. It’s a universe that we are only beginning to explore. Each of these unique areas of the body has a distinctive community of bacteria, fungi, viruses, and more. In ecology, we call it a “niche.” A niche is an environment with a certain set of conditions that favors a certain kind of life. In turn, the lifeforms can affect the environment. We will talk more about ecological niches when we tour the mouth in Chapter 3.
One reason I call it the “magnificent” microbiome is because it does so many good things for us. Let’s start with the bacteria in the gut, which we know so much about. Bacteria in your gut make vitamins that you need for blood clotting and metabolism, vitamin K and biotin.5 They “talk” to your immune system to tell it how to respond—they can tell it to calm down or ramp up an attack. They can soothe and calm down angry, inflamed tissue. Bacteria help to keep a strong barrier between your gut and bloodstream, which protects you from disease. Your microbiota help you get nutrients and calories from your food, and they fine-tune your metabolism. But perhaps the most important role of your good bacteria is that they protect you from infection. They serve as a biological defense against bad bugs that might want to invade and cause disease.
On the flip side, when your gut bacteria are out of balance, it can cause obesity, nutritional deficiencies, inflammatory bowel disease, autoimmune disease, nervous system disease, asthma, eczema, or cancer. We absolutely, 100 percent, need our good bacteria for optimum health. We would be very sick and weak without these microbes living inside and on us.6, 7, 8, 9
Bacteria were on Earth at least 3 billion years before humans.
Another reason our microbiome is so magnificent is because it is unimaginably complex. Let’s use a rainforest ecosystem as an example of how microbial ecology in the body works. In a rainforest, all of the components work together to build a healthy forest ecology that nurtures and sustains life. There are tall trees that need access to the sun. There are shrubs under those trees, which grow much better in shade. There are spots where the bright sun beams down all day, and certain plants grow well there. There is dark, rich soil. There are bacteria and fungi that help chew up old, dead trees and plants and turn them to dirt again. The more plants, trees, animals, and insects that live in this environment, the more diverse it is, and the healthier it is. Biological diversity, or a broad spectrum of different organisms, is often considered to be a sign of a healthy ecosystem.
Each of these special environments with particular characteristics (sun, shade, etc.) is considered an ecological niche, because it hosts a certain type of plant and that plant in turn affects its environment. Ecological niches are central to the field of ecology, and we will talk about them more as we take a tour of the mouth in Chapter 3.
Let’s continue this comparison of a rainforest ecological system with the gut microbiome. The gut microbiome is also a specific environment housing a sophisticated community of lifeforms. The gut provides an environment that bugs love: It is rich in nutrition and mucus. The gut thrives with lots of different kinds of bacteria, indicating biological diversity. Some bacteria are in high amounts, some are in low amounts. Some survive better if they live close together with their neighbors. Bacteria produce chemicals that are beneficial to the gut and to the immune system. They make chemicals that other bacteria eat or that repel certain bacteria. To keep the gut microbiome healthy, then, you have to think about it more as an ecological system with communities of bacteria and an environment it depends on. It’s wild and wondrous.
The microorganisms living in the human oral cavity make up the oral microbiome. It also covers microbes in adjacent areas such as the nose, pharynx, and the upper portions of the esophagus and lungs. The oral microbiome has one of the most diverse bacterial populations in the body, second only to the gut microbiome.10 You will notice that we often talk about the oral microbiome in the context of the gut microbiome (see page 49). Much of what we know about the microbes that live inside our bodies comes from the research on the gastrointestinal tract microbiota. It’s a good jumping-off point, and most of it applies to the oral cavity, as well. It’s been a major subject of research and everyone, including me, has been interested and excited about the gut microbiome in recent years.
You are swallowing at least 140 billion bacteria each day, seeding your gastrointestinal tract with the microbes from your mouth.
But, what lies at the beginning of the gut? The mouth and nose. This means that the oral microbiome and the gut microbiome are inextricably linked. What happens in the mouth also happens in the gut. With its critical position at the front entrance to the gastrointestinal tract, your mouth supplies millions of bacteria to your gut every time you swallow!
The gut has gotten the lion’s share of the headlines. But the oral microbiome is equally impressive. Amazingly, the oral microbiome influences health or disease in many other systems of the body, not just the gut. The well-documented link between the oral microbiome and heart disease, diabetes, joint disease, and gut health proves that the oral microbiome is ready to take its rightful place on center stage.
Until now, the oral microbiome has been largely forgotten. My goal is to dust off the research on the oral microbiome, bring it to light, and make it easier to understand. That will be the topic of Chapter 5.
In 1890, Willoughby Miller wrote the first book implicating oral bacteria as a cause of tooth decay. Called Micro-Organisms of the Human Mouth, it sparked a worldwide movement of toothbrushing and flossing.11
The gut microbiome has been wildly popular in the last ten years, and you have probably heard it mentioned in the news, in books, on the internet, or even when talking with friends. There are books about the gut microbiome and even cookbooks that tell you how to “feed” your magnificent microbiome. Or maybe you have just heard people talking about the drawbacks of antibiotics, which can damage the gut microbiome.
The gut microbiome refers to the microbes living in the gastrointestinal tract. While the gastrointestinal tract officially includes the mouth, pharynx, esophagus, stomach, small intestines, large intestines, and rectum, usually people are talking about microbes living in the small and large intestines when they mention the “gut microbiome.”
“To Boldly Go Where No Man Has Gone Before”
What started all of this? I would venture to say it was the Human Microbiome Project, initiated by the National Institutes of Health in 2008. They started what seemed like an impossible feat: to characterize the entire human microbiome. Perhaps after sequencing the entire human genome (or the human DNA code), it seemed like a natural next step to figure out what the DNA of our microbiome looked like. I’m sure the scientific community took a collective gasp of anticipation at the thought of exploring and identifying all the microbes that colonize the human body! It was no small undertaking.
The gut microbiome and oral microbiome have so many similarities that I refer to them as “kissing cousins,” and you will see my reasoning in Chapter 7. Much of what you learn about the oral microbiome in this book can be applied to the gut microbiome, as well.
An Unlikely Pregnancy Test
Gracie visited her dental hygienist, Margaret, for her regular cleaning. Margaret had taken care of Gracie’s teeth many times over the years. She noticed that Gracie’s gums looked different this time. They were rolled, swollen, and puffy. Margaret asked Gracie if she was on her period, as hormonal shifts could sometimes cause these changes. Gracie said no. Margaret asked if she was about to start her period. Again, Gracie said that it wasn’t the case. Margaret said, “Well, from the standpoint of your gums, it looks like you could be pregnant.” They carried on through the dental cleaning without another mention of it. One week later, Margaret got a call from Gracie. She told her, “You were right! I am pregnant!” Margaret had predicted Gracie’s pregnancy even before the typical pregnancy tests. And Gracie’s story of finding out she was pregnant at the dentist’s office made it into her newborn’s baby book, too.
The Human Microbiome Project studied the microbes in 300 healthy people to figure out what bugs were there, what they were doing, and how they differed from one person to another. After figuring out what a “healthy microbiome” looked like, they could move on to study how the microbiome changes with certain diseases, such as inflammatory bowel disease or diabetes.
One thing that was so special about this project is it used the most cutting-edge technology available, a method called quantitative polymerase chain reaction (qPCR) that identifies microbes based on their DNA code. Just like sequencing the human genome launched us into a whole new realm of exploration and scientific understanding, so did characterizing the DNA of the microbes that live on and in us. With this technique, the number of bacteria that we could identify skyrocketed.
Historically, we have identified bacteria based on if and how they grow in a petri dish. These bacteria are usually taken from a blood, stool, or urine culture. It worked for many, many years, and clinical laboratories still diagnose infections based on this technique. But it has flaws. The biggest flaw is that it misses bacteria that don’t like to grow in artificial conditions. DNA methods like those used in the Human Microbiome Project made it possible to see 50 percent more microbes than had ever been seen before.12,13,14, This was a tremendous success and fundamentally changed our understanding of the human microbiome forever!
In this book, we will explore the magnificent oral microbiome and how keeping it in balance can promote health from head to toe. We will tour the oral cavity, get familiar with the immune system that defends the mouth, and review the most common oral diseases that crop up when the oral microbiome is out of balance. We will review the evidence about oral health and natural, safe things you can do to optimize your oral microbiome. The oral microbiome is the next big thing since the gut microbiome, and you’ll find out why keeping your oral microbiome healthy can lower your risk of heart disease, stomach ulcers, rheumatoid arthritis, diabetes, and even lower your blood pressure.
Takeaways
• You are made up of at least as many microbial cells as human cells, and probably more.
• Your “good bugs” promote health and ward off disease.
• The bacteria, viruses, fungi, and other microscopic organisms that live inside and on your body make up your microbiome.
• The gut microbiome is diverse and complex, like a tropical rainforest.
• The Human Microbiome Project led the way in microbiome research.
• The oral microbiome and gut microbiome are inextricably linked.