Your Body Is A Wonderland (Of Microbes): An Introduction To The Microbiomes Of The Human Body


When we hear the word microbiome, most of us think of gut bacteria, and for good reason. The digestive tract is where the majority of your 38 trillion microbes live and work. It’s also the primary destination for most prebiotic and probiotic products, including Seed’s Daily Synbiotic. But did you know there at least a dozen microbiomes across the human body?

It’s true! Scientists have identified distinct communities of microorganisms in our mouth, eyes, nose, lungs, bladder, urethra, and skin. For men, there’s a microbiome of the penis. For women, there’s a microbiome of the vagina, breasts, and breast milk. And there are likely many more we have yet to uncover. Each is intricately linked to the rest, and each contains species and strains that can be found nowhere else.

To understand the role these ‘micro’ microbiomes play in our health, and it’s vital that we do, we must first change the way we look at our biology. Our exploration of the microbial world inside us, made possible by next generation technologies like metagenomic sequencing, has taught us that we are not singular organisms, but rather superorganisms—50% human and 50% microbe by cell count (1).

That means each of us is a living, breathing ecosystem, not dissimilar to the planet we call home. And that may just be the best way to look at the human microbiome—as a vast, interconnected world filled with unique landscapes, climates, flora, and fauna. Using this visualization, we can begin to see how the various microbiomes of the body (and their peculiar inhabitants) work together for the benefit of the whole—that is, you.

The Gut Microbiome: Rainforest

Though tropical forests only cover 6% of the Earth’s land surface area, they are home to approximately 50% of all terrestrial plant and animal species. They’re incredibly productive, too, absorbing 2.4 billion metric tonnes of carbon dioxide from the atmosphere each year. Rainforests are also major exporters of water vapor, the atmospheric gas that drives the world’s weather and climate cycles. Clouds formed by tropical forests drift across entire continents, sustaining life thousands of miles away.

It’s no wonder the Amazon Basin has been described as the world’s largest pharmacy, the lungs of the planet, and Earth’s sweat glands. The gut microbiome is not so different. The bacterial content of the colon, alone, exceeds every other organ in the human body by at least two orders of magnitude (2). That means the vast majority (>95%) of microbes in your microbiome can be found in your large intestine.

And just like a rainforest, the products and outputs of this community travel far beyond the boundaries of the digestive system. The human body is complex and interconnected, and the gastrointestinal tract sits at the core of it all. It influences everything from immunity and metabolic function to cardiovascular, skin, and urogenital health. It may even impact our mood and behavior, as recent research into the gut-brain axis has suggested (3).

Our gut bacteria—and the metabolites they release into our bodies—drive much of this activity. Some strains help determine what should and shouldn’t pass through the protective barrier lining your intestines. Others serve as microscopic factories for vitamins B and K. Some even produce neurotransmitters that stimulate muscle contractions, leading to easier bowel movements. And the list goes on (4).

Both the rainforest and the gut microbiome owe their productivity to the sheer volume and diversity of species within them. Each one plays a unique role that keeps the whole ecosystem humming. That’s why a biodiverse gut is a critical component for human health (5). And it’s why we must protect the Amazon at all costs.

The Skin Microbiome: Desert

Deserts are, in many ways, the opposite of rainforests. They are desolate and arid, and contain a fraction of the biodiversity found in places like the Amazon. However, they play a surprisingly large role in the stability of all life on Earth. Most desert and dryland regions are covered in biological soil crust, or biocrust, a razor-thin layer of rugged, photosynthetic microorganisms—cyanobacteria, mosses, lichens, and fungi—that thrive in extreme climates.

In recent years, scientists have found that biocrusts are the key to improving water absorption and reducing soil erosion in low-productivity ecosystems (6). They also help add nitrogen and carbon to the soil, allowing plantlife to grow in nutrient-poor conditions (7). Together, these processes keep violent dust storms at bay, and ultimately help prevent desertification—the process by which fertile land becomes desert. A stable biocrust means a stable planet.

The skin microbiome is much the same. We’ve long known that the body’s largest organ serves as a passive physical barrier, protecting us from harmful substances and chemicals that would otherwise leak into the body (8). However, it wasn’t until very recently that we started to identify the unique organisms that call this dry, perilous landscape home, and unravel the role they play in our outermost defense system.

We now know that the skin serves as an active immunological barrier as well (9). That means it hosts a community of hardy microbes that patrol its surface, day and night. Whenever a foreign intruder is detected, they partner with your epithelial and immune cells to address the threat. This is called innate immunity. Over time, another group of cells, led by dendritic and T cells, learn from these confrontations. This is called adaptive immunity.

Just as desert-dwelling microbes help protect our planet from desertification, skin-dwelling microbes help shield our bodies from infection. It’s no wonder scientists refer to biocrust as the ‘living skin of the earth.’ Resilient ecosystems breed resilient organisms, and resilient organisms lay the foundation for more complex life to thrive—including us.

The Oral Microbiome: Coral Reef

Tropical forests may contain a higher volume of species than any other ecosystem, but coral reefs are the most biodiverse when adjusted for size. They cover less than 0.1% of the Earth’s total surface area, but may be home to as many as 9 million different species of plants, animals, and microorganisms (10). As the “rainforests of the sea,” they’re also a primary source of food for 25% of all marine life.

Coral reefs are one of the planet’s oldest ecosystems as well (11). Their success is a function of the cooperation of their inhabitants. Corals provide shelter for countless organisms, from microscopic algae to giant sea turtles. Many of these creatures, in turn, provide nutrients and protection for polyps—the architects of reefs. These reciprocal relationships are as complex as they are delicate, and scientists are only just beginning to understand them.

The oral microbiome shares many of these same traits. Though minor in size compared to the skin and gut microbiomes, its dark, damp, nutrient-rich environment provides optimal conditions for microscopic life. Indeed, nearly 700 different species can be found here, performing roles such as nutrient absorption, food digestion, and energy generation (12). But optimal conditions don’t always mean stable conditions.

The oral cavity, like a shallow water reef, is also very exposed. Atmospheric conditions change with every breath we take, and every word we speak. Thankfully, our microbes have evolved to thrive in spite of the chaos. Like the polyps in a reef, the key is communal housing. To guard against the elements and stop ‘bad’ bacteria from gaining a foothold, mouth-dwelling microbes construct multilayered colonies, bound together by a slimy matrix called biofilm (13).

The bacterial colonies of the oral microbiome may be resilient, but they’re not indestructible. Just as a coral reef is highly susceptible to ‘bleaching’ from temperature changes and pollutants, our mouths can easily fall into dysbiosis, too. It may only take one swig of antibacterial mouthwash to throw the whole ecosystem out of balance (14).

The Maternal Microbiome: Fresh Water

Though water covers more than 70% of Earth’s surface, only a small fraction of it (2.5%) is fresh. Of that 2.5%, an even smaller fraction (0.3%) can be found in accessible lakes and rivers. The rest is frozen, or trapped underground. That’s pretty incredible, considering that every land-based plant and animal species depends on it for survival. Humans are especially reliant—we can go a few months without food, but only a few days without a drink.

Fresh water isn’t just a critical resource for our bodies either. Over the course of history, humans have found innovative ways to use it to expand our territory, and our population. Water irrigates countless acres of crops, nourishes vast quantities of livestock, and supports high-yielding fisheries. It generates 16% of the world’s total power, and up to 70% of our renewable power (15). As a result, our reliance on it has grown dramatically.

The maternal microbiome, which includes the vaginal, breast, and breast milk microbiomes, is just as vital. To understand why, you must first understand where your microbiome came from. The answer, in short, is your mother (16). Her microbes are the first ones you were exposed to when you were born—through the birth canal, skin-to-skin contact, and breastfeeding. You get microbes from the environment, too, but your mother’s strains are better adapted for survival inside you (17).

This process of receiving foundational microbes is called seeding, and it is a critical part of early biological development. Our first microbes impact metabolism, immune system function, and brain development (18). Without them, your body wouldn’t know how to distinguish between benign substances, like food, and enemy invaders, like pathogens. You also wouldn’t be able to digest certain carbohydrates (i.e. fiber) that are critical for your health (19).

Like fresh water, our reliance on the maternal microbiome has grown stronger over time through coevolution. This has made us vulnerable. The introduction of just a single strain of ‘bad’ bacteria to either ecosystem can lead to severe health problems for all who are exposed (20, 21). That’s why it’s so important to treat both with the respect and care they deserve.

The Remaining Microbiomes: Open Ocean

According to the National Oceanic and Atmospheric Administration (NOAA), up to 80% of the world’s oceans remain unmapped, unobserved, and unexplored. Oceanographers like to put it this way—we know more about the surface of the moon than we do about the ocean floor. Thanks to new tools and technologies that make it easier to explore hard-to-reach places like the Mariana trench, that’s finally beginning to change.

Over the last few decades, we’ve learned that our oceans play a much bigger, more complex role in the health of our planet than previously thought (22). For example, we now know that up to 50% of the world’s oxygen is produced by microscopic algae called phytoplankton, which drift through the open ocean in incalculable numbers. We also know these phytoplankton form the foundation of the whole oceanic food web. That means every marine creature on earth depends on them in some way, from the tiniest zooplankton to the biggest blue whales (23).

These kinds of connections are invaluable for us to understand if we are to have any hope of bringing the global ecosystem back into balance. The same may very well be true of the microbiomes of the body that we have yet to explore in depth. While we may not find a microbe as universally important as phytoplankton in our ear microbiome, or our lung microbiome, we’ll more than likely find that these distinct ecosystems play a vital role in our health.

And just like the ocean, we now have the technology to explore and characterize all of the microbiomes of the body with unprecedented accuracy and detail. That means we can go beyond simply identifying the unique microbes that call these places home, and begin to unravel the mechanisms that they use to interact with our human halves. After all, it is the functions that microbes perform in the body that matter most, not their classification or taxonomy (24).

Like our inquiry into the underexplored ecosystems of our planet, our research into the lesser understood microbiomes of the human body may very well lead to new insights and interventions that improve (or even save) the lives of millions of people. This is exactly the kind of research that scientists plan to conduct over the next ten years.

In fact, we’re well on our way already (25).