What is a Microbiome?

Before we can understand probiotics, it’s essential to understand the answer to this question: what is a microbiome? The word describes a microscopic ecosystem—a community of microorganisms in a particular habit. When it comes to our bodies, we actually have several microbiomes: the communities of microbes on our skin, in our mouths, our airways, and our GI tracts are all different, as well as unique from person to person. But these are commonly and collectively known as the human microbiome, consisting of trillions of different microbes, from thousands of species. Their numbers are so immense in size and so key to our bodies’ healthy functions that they have even been labeled a supporting organ system.

The most famous microbes are the ones with the potential to harm us: pathogens that possess the ability to cause disease. But most of our microbes are symbiotic: our bodies provide them with a place to live and nutrients to survive on, and in turn, they perform essential functions and produce substances that help our bodies and our health.


How Do Microbes Support Our Bodies?

Recent advancements in technology have given scientists the ability to examine microbes’ contributions and influence on our health like never before. As our depth of understanding about these microscopic communities grows, it’s becoming more and more apparent that there’s almost nothing our bodies do that isn’t connected to microbes.

In our gut microbiome—the largest and most famous of our microbiomes—microbes maintain our immune system’s balance, break down complex food compounds, extract nutrients, and synthesize vitamins. They also produce vital substances that include short-chain fatty acids (SCFA). SCFAs are not only used by the body as nutrients, but they also help reduce inflammation in the gut and body and support our metabolism.

Data continues to emerge connecting our gut microbes’ influence not just to our immune and gastric systems, but to our function and behavior as well. Research has shown stress to alter our gut’s microbial makeup to the point where gut barrier function is decreased, and fewer short-chain fatty acids are produced—amplifying bodily inflammation. Another study found that introducing short-chain fatty acids to the guts of mice significantly reduced stress and anxiety-based behaviors.

It’s All About the Microbial Balance

Through continued research like the Human Microbiome Project, we understand that each person’s microbiome makeup is unique, like a fingerprint, making a “healthy” microbiome hard to define. But we do know this: microbiomes are systems, and in a healthy one, the beneficial populations control the growth of the harmful, or pathogenic populations, keeping the balance in check.

In our guts, where more than 70% of our immune system resides, beneficial microbes not only fight to outcompete pathogens for space and nutrients, they also form a single-cell lining in our intestines, providing a barrier that prevents potentially hazardous bacteria from entering our blood stream and traveling to other organs. Their metabolites—bioactive substances produced as a result of their metabolisms—help maintain an acidic environment that makes it difficult for pathogens to survive.

It’s when this balance is disturbed that something called dysbiosis emerges, increasing our bodies’ susceptibility to disease.


What Factors Impact our Microbiomes?

Our microbiomes are as unique to each of us as our fingerprints, but they all begin at birth. Through the birth canal and breastfeeding, our mothers inoculate our microbiomes, and from this foundation, we continue to build the core of our microbial populations until semi-stabilizing around age 3.

And there may not be a singular definition of a healthy microbiome, there are several factors that continue to influence the balance of our various microbiomes throughout our lives. These factors are important levers within our control to help support and optimize our microbiomes, so that they in turn support and optimize our health.


In our guts, one of our beneficial microbes’ primary roles is to break down and ferment foods and absorb and process nutrients for us, turning them into energy. Many of the beneficial microbes that are efficient at this process can be fed by complex carbohydrates—including whole grains, vegetables, leafy greens, and fruits—that contain what is known as prebiotic fiber. And it’s when fermenting fiber in your gut that microbes produce those all-important short-chain fatty acids.

Eating fermented foods—like yogurts, sauerkraut, kimchi, and kombucha—can also introduce and add beneficial populations to your gut microbiome.

This makes diet one of the most important levers for influencing your gut’s microbial population, and therefore, your digestive and immune health. If you nourish yourself with foods that feed your beneficial microbes—and subsequently, your body—those populations can flourish. If your diet is heavy in added sugars and simple carbohydrates, the more harmful microbes can flourish instead.


Need another reason to get more exercise? Previous associations have been made with exercise and microbial differences in the guts of athletes versus sedentary people. But new research is emerging with evidence that exercise itself may affect and change the makeup of gut microbiomes. What’s more, the researchers also found changes in many of the microbes’ gene expressions.

Each volunteer participant—a non-exerciser at the start—was asked to follow a six-week supervised exercise routine, followed by a six-week return to non-exercise. Each participant had a unique gut that also responded uniquely to the exercise. But the similarities the researchers found included increases throughout the group in certain microbes that help produce short-chain fatty acids, which are believed to help reduce inflammation throughout our bodies, fight insulin resistance, and help our metabolisms function.

When the participants stopped exercising, though, nearly all these changes to their microbiomes stopped, and reverted to their state at the beginning of the study.

Medications and Products

Intuitively and culturally, we may tend to believe that wiping out every possible microbial threat will make us safer. There’s no question that antibiotics have been lifesaving since their invention, but we also know now that they’ve been contributing to the rapid evolution of antibiotic-resistant pathogens; their use can cause targeted bacteria to change and create new defenses that are even more threatening.

While antibiotics may still be the best route for treating infections, a single course of them can wipe out your internal microbiome. Made to kill off bacteria, they act broadly, killing all bacteria—including your beneficial populations. If you do need to take a course of antibiotics, pairing that with probiotics, along with pre- and probiotic-rich food as you’re able to consume them, can help.


We are surrounded by microorganisms—they’re literally everywhere, from the ground we walk on to the surfaces we touch. And as it turns out, our interactions with these microorganisms—again, mostly neutral and beneficial—help train our immune systems so that they can appropriately assess threats and react accordingly.

Pets, especially dogs, can help introduce a diverse group of beneficial microorganisms; studies have found that children who have even just one dog have a nearly 13 percent reduction in their chance of developing asthma. And soil, which is full of beneficial microorganisms that help plants thrive, is beneficial as well. Children who grow up on farms, for example, have a nearly 50 percent reduction in the chance they’ll develop asthma, allergies, or other immune diseases.

Interacting with plants inside and outside the home can help increase beneficial microbial exposure, and rather than using antibacterial soaps and cleaners to kill all microorganisms, probiotic-powered cleaners can be used to reduce the populations of harmful microbes and encourage the growth of friendly ones. All of which may help boost your microbiome’s health and diversity.

What About Probiotics?

Probiotics are technically defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit to the host.” As supplements, they represent a rapidly growing group of diverse products that contain live, beneficial microorganisms meant to be consumed as a way of inoculating our bodies with helpful microbes.

We’ve been studying and crafting our proprietary community of beneficial microbes for 20+ years. Learn more about what the science says about probiotics.