Exploring the Microbiomes of Your Body

When you hear the word microbiome, what comes to mind? You probably think of the gut microbiome, and for good reason. Of the 38 trillion bacteria living on and in you, the vast majority of them reside in your digestive tract.¹ But did you know there are at least a dozen microbiomes across the human body?

That’s right. Scientists have identified distinct communities of microorganisms in the mouth, eyes, nose, lungs, bladder, urethra, skin, and more. The penis, testes, vagina, breasts, and even breast milk all harbor their own unique microbiome. And there are likely many more that have yet to be uncovered. Each is intricately linked to the rest, and contains species and strains that can be found nowhere else. Collectively, this community of microbiomes are involved in most, if not all, aspects of your health and well-being. 

To understand the role each plays in your health, you must first shift the way you look at your biology. The exploration of the microbial world inside you, made possible by next generation technologies like metagenomic sequencing, has revealed that humans are not singular organisms, but rather superorganisms (a group of organisms functioning as a whole). In fact, you are 50% human and 50% bacteria by cell count, and that’s not even including the viruses, fungi, and archaea that contribute to your microbiome.¹

That means you are 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, you 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.

Here, we’ll explore some of the most impactful microbiomes of your body and uncover seven research-informed ways you can support your microbial half.

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The Gut Microbiome: Rainforest

Though tropical forests only cover 6% of the Earth’s land surface area, they are home to approximately 80% of all terrestrial plant and animal species.² They’re incredibly productive, too, removing approximately 29% of annual CO2 emissions—or 15.6 gigatons of CO2—each year.³ 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—it’s a hub of biodiversity that supports the health of the whole planet (in this case, you!). 

The vast majority (read: 95%) of microbes in your microbiome can be found in your large intestine (a.k.a. the colon).⁴ And the bacterial content of the colon alone exceeds every other organ in the human body by at least two orders of magnitude.¹

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 to heart health, skin health, metabolism, and sleep. It can even impact your mood, appetite, cognition, memory, and behavior, as research into the gut-brain axis has revealed.⁵ 

Your gut microbes—and the metabolites (compounds) they produce in your body—drive much of this activity. For instance, some microbes produce short-chain fatty acids that help maintain the integrity of your gut barrier, fuel the cells of the colon, manage the production of certain immune cells, and maintain blood sugar levels.⁶ Some act as microscopic factories for vitamins B and K. While others defend against pathogens (harmful microbes), reduce oxidative stress (an imbalance between damaging free radicals and detoxifying antioxidants), balance pH, and support the production of neurotransmitters that stimulate muscle contractions, leading to easy bowel movements. And the list goes on.^6,7 

Both the rainforest and the gut microbiome owe their productivity to the sheer volume and diversity of species within them. In a healthy state, 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.⁸

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. 

Biocrusts are key to life in the desert, improving water absorption and reducing soil erosion in low-productivity ecosystems.⁹  They also help add nitrogen and carbon to the soil, allowing plant life to grow in nutrient-poor conditions.¹⁰ 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. 

It’s a dry, perilous landscape with a community of microbes that help maintain homeostasis and contribute to your outermost defense system: your skin. As the body’s largest organ, the skin serves as a passive physical barrier to the outside world, protecting you from harmful substances and chemicals that would otherwise penetrate  into the body.¹¹ However, it wasn’t until very recently that we started to identify the unique organisms that call your skin home and unravel their specific functions. One of the most important roles of your skin microbes is to inhibit the growth of pathogens and eliminate any that take root. They do this in a variety of ways: They can produce enzymes and their own antibiotics, secrete antimicrobials, modify the local environment of the skin, and compete for space and nutrients.¹² 

In addition to these protective roles, skin microbes can also enhance the skin’s barrier function and stimulate the immune system. This is important because the skin not only serves as a physiological barrier, but an active immunological barrier as well.¹³ It hosts a community of hardy microbes that patrol its surface, day and night. Whenever a foreign intruder is detected, these microbes partner with your epithelial and immune cells to address the threat. 

Just as desert-dwelling microbes help protect the planet from desertification, skin-dwelling microbes help shield your body from infection. Scientists actually refer to biocrust as the “living skin of the earth.” But in the same way shifting climates disrupt a stable biocrust, environmental and lifestyle factors can disrupt a stable skin microbiome, so it’s important to make decisions each day that will nurture—rather than harm—these communities.

The Oral Microbiome: Coral Reef

Tropical forests may contain a higher volume of species than any other ecosystem, but coral reefs contain the most biodiversity 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.¹⁴ As the “rainforests of the sea,” they’re also a primary source of food for 25% of all marine life.¹⁵

Coral reefs are one of the planet’s oldest ecosystems as well.¹⁶ 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. 

Although 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, influencing everything from bad breath to tooth decay and cavities.¹⁷ They can even impact systemic health. For instance, research has connected the oral microbiome to diabetes, inflammatory bowel disease, heart disease, and more.^18,19 But optimal conditions don’t always mean stable conditions.

Like a shallow water reef, the oral cavity is very exposed. Conditions change with every breath you take and every word you speak. Thankfully, your 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.^19,20

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, your mouth can easily fall into dysbiosis (an imbalance in the composition), too. It may only take one swig of antibacterial mouthwash to throw the whole ecosystem temporarily out of balance.²¹ 

The Vaginal Microbiome: Fresh Water

Though water covers more than 70% of Earth’s surface, only a small fraction of it (2.5-3%) is fresh. Of that 2.5%, an even smaller fraction (about 1%) is accessible and can be used.²² The rest is largely untapped, 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.²³

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 78% of our renewable power.²⁴ As a result, our reliance on it has grown dramatically.

The vaginal microbiome is just as vital. 

Like fresh water, the microbes residing in the vagina represent a small but incredibly important fraction of all the microbes living in and on the human body. This complex, dynamic, and protective ecosystem is primarily dominated by Lactobacillus species. These Lactobacillus microbes reside on the vaginal walls and metabolize sugars to produce lactic acid, resulting in a low, acidic pH that naturally inhibits the growth of harmful bacteria, yeast, and viruses. Beyond this protective barrier, they also secrete bacteriocins—natural antibiotic-like substances—that safeguard against pathogenic invaders.²⁵ In this way, you can think of the vaginal microbiome as a “vaginal immune system”.

These defenses are crucial for maintaining vaginal health, and in their optimal state, protect against a myriad of reproductive and urogenital issues, and support positive health effects. Yet, in the same way pollution, runoff from agricultural and urban areas, climate change, and drought can jeopardize the quality and availability of freshwater, the vaginal ecosystem is vulnerable to many threats of its own. Its balance is easily tipped by everyday events like hormone fluctuations, menstruation, douching, stress, the use of antibiotics, and even activities as routine as having sex.^26,27,28 These disruptions can cause temporary deviations from an optimal Lactobacillus-dominated state, and research is revealing that this dysbiosis is the underlying cause of many vaginal symptoms, infections, and conditions that affect millions of women worldwide.^29,30,31

Fortunately, in the same way fresh water opened the door for countless human innovations across our history, growing knowledge of the vaginal microbiome is paving the way for a new chapter of innovation not just in medical science, but the future of women’s health.

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.³² Oceanographers like to put it this way—we know more about the surface of the moon than we do about the ocean floor.³³ 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.

The same is true for the human body. In addition to the four microbiomes we explored here, there are several other microbiomes of the body that have been characterized. Here’s a quick look:

• The areolar and breast milk microbiome: Maternal milk and areolar skin each have their own distinct bacterial communities that contribute to the developing infant microbiome and immune system (in a process known as seeding). In fact, a 2017 study revealed that breastfed infants received 27.7% of their gut bacteria from breast milk and 10.4% from areolar skin during the first month of life.³⁴ It has also been proposed that the breast microbiome contributes to the maintenance of healthy breast tissue by stimulating resident immune cells.³⁵
• The nasal microbiome: This diverse community of microbes is thought to influence respiratory health, immune responses, allergies, and susceptibility to infections. Dysbiosis of the nasal microbiome has been associated with several diseases, including chronic rhinosinusitis (CRS), asthma, bronchiolitis, the flu, and ear infections.³⁶
• The ocular microbiome: This ecosystem is characterized by low diversity, possibly because the enzymes in tears have antimicrobial properties.³⁷ The ocular microbiome is believed to maintain balance in the eye and regulate immune function. Imbalances in this community could increase the risk of various eye diseases, such as keratitis (inflammation of the cornea), dry eyes, and blepharitis (inflammation of the eyelid).^38,39,40
• The penile/urogenital microbiome: The microbiome of the male genital tract is gaining scientific interest because of its connections to male reproductive health, fertility, and sexual behavior. This microbiome consists of a diverse array of microbes from nearby areas such as the perineum, skin, gut, and even urine.⁴¹ Recent work highlights its potential role as a risk factor for STI occurrence, and some evidence indicates the microbiome of semen (seminal microbiome), specifically, has important implications for the health of men, their partners, and even offspring.^42,43
• The pulmonary microbiome: The microbiome of the lungs is transient and mobile, meaning the microbes are not permanently established and can be easily cleared by mechanisms like coughing, the movement of respiratory cilia (tiny hair-like structures in the airways), and alveolar surfactant (a substance that lines the air sacs and prevents growth of certain bacteria). When the lung microbiome is in balance, it helps maintain a clean and safe environment by participating in the immune response and preventing excessive inflammation.⁴⁴ Dysbiosis of this microbiome, however, can impact diseases like chronic obstructive pulmonary disease (COPD), pneumonia, and bronchial diseases.^45,46,47
• The belly button microbiome: In 2011, the Belly Button Biodiversity Project investigated the microbes living in people’s belly buttons. Researchers discovered 2,368 different species of bacteria, more than half of which could be “new” to science. Eight of these species were common in most, while the remaining were extremely rare.⁴⁸ One belly button, for instance, housed two bacteria typically found in extreme locations: ice caps near the poles and thermal vents deep in the ocean. While these insights revealed fascinating information about the composition of the belly button microbiome, its function remains largely unexplored.

It’s wild to think that this is still just a snapshot of the microbiomes of your body— just like the ocean, there is even more that has yet to be mapped. 

Also 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.⁴⁹ 

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 several years.⁵⁰

In fact, we’re well on our way already.⁵¹

7 Ways to Support a Thriving Ecosystem 

The more we learn about the various microbiomes of the human body, the better we can nurture them. While certain body sites have “best practices” that are most applicable to that particular microbial community—for example, flossing and brushing regularly will have the biggest impact on the oral microbiome—there are some general, research-informed guidelines to support your microbial ecosystem as a whole. These include:

• Prioritize a diverse, balanced diet rich in plant-derived compounds like fiber and polyphenols.^52,53 Diet is one of the most impactful ways to support your microbes. In the mouth and the gut, fiber intake has been shown to increase bacterial diversity and decrease “bad” bacteria.^52,54 A plant rich diet has also been associated with healthier skin due to its ability to enrich the gut microbiome, and polyphenols have been shown to have anti-inflammatory effects on the skin.⁵⁵ There’s also some evidence that a low-fat diet and increased intake of folate, vitamin A, and calcium may protect the balance of the vaginal microbiome and reduce the risk of bacterial vaginosis.⁵⁶ 
• Manage stress. When you’re stressed, your microbes feel it too. Sustained physical and/or emotional stress sets off a chain of reactions in your body—think: the release of certain hormones, blood flow redistribution, increased inflammation, altered immune system function, and shifts in vagus nerve signaling—all of which can negatively impact your microbes. For instance, catecholamines (hormones made by your adrenal glands, which are secreted into your blood when you’re stressed) can enter the bloodstream directly modify microbial growth.⁵⁷ Changes in the activity of immune cells residing along the GI tract can alter the composition and function of gut microbes.⁵⁸ Furthermore, heightened inflammation during stress may trigger blooms of pathogenic bacteria that contribute to dysbiosis.⁵⁹ 
• Take a high-quality probiotic. While they’re most often thought of in the context of gut health, probiotics can deliver an array of benefits across the body, depending on the specific strain and its actions within the body. For instance, some strains support an optimal gut environment by reinforcing the gut wall and/or supporting the production of short-chain fatty acids.⁶⁰ Others support “cross-talk” between the gut and skin.⁶¹ Vaginal probiotics can repopulate and maintain an optimal vaginal community. Research even suggests that there are probiotic strains that may affect the population of your oral microbiome and reduce the number of pathogenic bacteria.⁶² Keep in mind, not all probiotic products are created equal. It’s important to look for one(s) with scientifically and clinically validated strains to support the particular benefits you’re looking for.
• Get outside. Nature exposure introduces diverse microbes to your ecosystem, which may positively influence your microbial composition. This is especially important for children—one study involving 54 children showed that after 10 weeks engaged in nature activities, kids showed fewer signs of stress and a more diverse microbiome.⁶³ But this recommendation applies to adults too: A small 2020 study showed that when participants interacted with urban green spaces by digging in the dirt, brushing up against the plants, etc., the diversity of their skin and nose microbiomes increased.⁶⁴ Another 2022 study found that consistent contact with gardening soil resulted in the transfer of soil-derived bacteria to humans, which was associated with a more diverse gut microbial structure.⁶⁵ 
• Move. Studies indicate at least 150 minutes of moderate exercise a week can enhance the number of beneficial microbial species and improve diversity in the gut.^66,67 But what exercise is best? The answer is any that you can keep up consistently, whether that’s yoga, cycling, or walks. Research suggests that when it comes to your microbes, consistency matters more than intensity and even duration.⁶⁸ 
• Limit known microbiome disruptors like alcohol, smoking, excess sugar, and anti-inflammatory drugs (NSAIDs). Various aspects of modern living are known to perturb your microbes. Certain inputs like alcohol, for instance, affect the composition of microbes in your mouth and your gut, which can lead to dysbiosis.^69,70 Smoking has also been shown to alter microbial ecology of the mouth, increasing the acidity of saliva, depleting oxygen, and imparting host immunity.^71,72,73 Excess sugar can affect the balance of bacteria in the gut, promoting inflammation.⁷⁴ NSAIDs, too, can promote overgrowth of certain bacteria that may weaken the gut’s defenses and make it easier for gut damage to occur.⁷⁵ 
• Use antibiotics only when necessary By nature, antibiotics wipe out bacteria. And they do so indiscriminately, meaning they get rid of the “bad” AND the “good”. Many studies have shown that antibiotics can affect the number and diversity of gut and oral microbes, and the functions of these microbiomes may be drastically changed as a result of antibiotic treatment.^76,77 The microbiome can “grow back” after antibiotics—often in a matter of days or weeks—but it won’t always return to the same state as it was before. Of course, there are times when antibiotic use is necessary, as in the case of life-threatening infections, but far too often they’re prescribed for conditions or diseases that would resolve on their own given time—and even sometimes when it’s unclear whether an illness is bacterial or viral in origin. Fortunately, these practices are changing, as more healthcare providers come to recognize the importance of the delicate balance within.