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Understanding the Human Microbiome

What is a microbiome


The existence of good microbes is not news. You’ve probably heard that there are beneficial bacteria in your gut that help digestion. While that is certainly true, it is only the tip of the iceberg. Many of our bodily functions, sleep cycle, mood, and well-being depend on microbes that reside in multiple parts of the body, forming the human microbiome and even outnumbering our very own human cells.

The human microbiome is a hot topic with still a lot to discover, so it is challenging to find accurate information on what exactly the human microbiome does and why it is so important to our health. That’s why we’re tackling the topic of the microbiome in a two-part blog piece. This is part one.

This first part will provide a solid base about the significance of your microbiome, and part 2 will build on it with tips for achieving and maintaining a healthy microbiome.

What Is The Microbiome Anyway?

Before diving in, here is a simple definition to get us started:

Microbiome Definition:

Microbiome: The whole collection of microbes, including all of their functions, interactions, and metabolites, occupying a defined habitat. It is essentially the whole microbial ecosystem in a given location or niche (citation).

When we say “your microbiome,” we mean the microbial ecosystem of your whole body. We can be more specific by identifying the microbiome in a particular part of your body, such as your “skin microbiome” – the microbial ecosystem on the surface of your skin. When just referring to the microbial cells themselves within the ecosystem of a microbiome, we might call them the 'microbiota' or the 'microbial flora’.

microbiome definition split between microbiota and environment

To illustrate how microbes interact with the human body, we’ll use an analogy. Picture a flea market with vendors and visitors. In this analogy, your human cells are the vendors and the microbes are the visitors.

flea market

The relationship between microbes and human cells is bidirectional, meaning they influence each other. Your human cells and your behavior influence what microbes take up residence, AND also (somewhat incredibly) the microbes that take up residence can affect your human cells and change your behavior (yes, you read that right… the microbes in your body can influence the decisions that you make)!

The collection of microbes that make up your microbiome depend on your unique body and your lifestyle (e.g. things like your diet, exercise, stress levels, and sleep), similar to each flea market drawing different visitors depending on which vendors are present, the type of stuff being sold, location, price range, and opening hours.

But those effects go both ways, so your microbiome influences your body, behavior, and even your decisions, too. Just like a flea market adapting to customer behavior and demand (e.g. by altering what it sells, what types of vendors are present, or extending its opening hours), your body is heavily influenced by your microbiome’s activity. This brings on changes in your immune system, skin, brain, mood, appetite, and so much more.

Where Is The Human Microbiome Found?

Considering the microbiome has a wide spectrum of effects on you, it’s not surprising that it is found in many parts of your body. Here, we discuss five of the most important locations: skin, mouth, lungs, vagina, and - the one you’re most likely to be familiar with - gut.

important human microbiomes mouth lungs gut vagina skin

Skin: Being in constant contact with the outside world, the skin is undoubtedly one of the most microbiome-rich parts of the body, with greater numbers and a greater variety of bacteria than anywhere else besides the gut (citation). The skin microbiome not only regulates skin conditions like pH and moisture but also protects the skin against pathogens by producing bactericidal compounds, improving the skin’s immune response, and out-competing pathogens for nutrients. (citation).

Mouth: Protected by saliva, various microbes like bacteria and fungi adhere to the tissue in your mouth and flourish. In healthy individuals, they aid in the first steps of digestion, the protection of the mucosal barrier (i.e. the barrier between the inside of your body and the outside world), the detoxification of chemicals, and the fight against disease-promoting and bad-breath-causing microorganisms (citation).

Vagina: The vaginal microbiota is largely made up of bacteria, and especially Lactobacillus, which protect the vagina against pathogens by producing lactic acid and hydrogen peroxide (citation).

Lungs: The lung microbiome plays a critical role in maintaining lung health, both preventing inflammation and protecting the respiratory tract against pathogens by producing antibacterial substances and out-competing them for nutrients (citation).

Gut: Our familiarity with the gut microbiome is not coincidental, because the gut is, quite frankly, the trendiest spot of the flea market, with hundreds of species of bacteria and other microorganisms. In particular, the colon (part of the gut) has the highest microbial density of any habitat in the body, with 1012 cells per one gram of intestinal content (citation).

The gut microbiome serves several tasks, the most salient one being the fermentation of non-digestible dietary fibers. The resulting short-chain fatty acids have significant effects on our health, such as cardiometabolic regulation, lipid and vitamin (mainly B and K) production, and even liver signaling of gluconeogenesis and hunger/satiation (citation).

But the gut microbiome does much more than digestion. Just one mind-blowing example is its effects on your behavior and mood. This is demonstrated in several animal studies, which have found that mice with no microbiome (called “germ-free mice”) are less social (citation), have poorer memory (citation), and respond more poorly to stress (citation) than mice with microbiomes that were otherwise genetically identical.

Not surprisingly, your appetite can be affected by the gut microbiome. If you experience out-of-the-blue food cravings, you might blame it on different microbes in your gut requiring different food sources for growth, such as Provatella needing carbohydrates and Bacteriodetes needing fats (citation).

These bacteria and others can signal your body when a particular nutrient source is absent. They do so by producing peptide molecules that mimic your appetite-regulating hormones (citation), triggering cravings.

By that logic, constant cravings for sugar might be the result of an overgrowth of specific bacteria that need sugar for energy – an overgrowth that was first caused by an overconsumption of sugar. If you give in to the craving, it feeds and allows further out-growth of these sugar-craving bacteria, which in turn give you more cravings for sugar. This can create a positive feedback loop that is very hard to break!

What Is A Healthy Microbiome?

You probably have come across articles recommending a balanced diet for a healthy microbiome, but that message will make much more sense if you know what a healthy microbiome looks like.

A healthy microbiome is not necessarily about certain “silver bullet” beneficial bacteria; it rather refers to a vast diversity of microbes that carry out myriad functions in a balanced and meaningful way. You might think that human cells are enough to perform these functions, but they only express ~30,000 genes, as opposed to the millions of genes expressed by the human microbiome (citation). If you think about each gene encoding a different function, you can imagine the staggering capacity of functions a microbiome has.

One indicator of a healthy microbiome is its diversity, which has two aspects: richness and evenness. Richness refers to how many different types of microbes you have, while evenness concerns the balance between the numbers of each type.

Two people both with 100 different types of microbes have the same richness. However, if one of those two people has 95% of their microbiome made up of just one of those types and the other 99 types making up the other 5%, that is a very uneven microbiome. Studies confirm that both richness and evenness are equally important for a healthy microbiome and, consequently, a disease-free state (citation).


2 microbiome communities showcasing equal richness and unequal evenness
As an example, Community A and Community B have the same richness, but Community B is much more even, and thus more healthy, from the standpoint of a microbiome.


To get a better picture, let’s go back to the flea market. If your flea market has different vendors offering many different types of merchandise (e.g. furniture, tools, jewelry, clothes, plants, home goods, toys, etc.), but most of your customers only come shopping for furniture, your market would struggle. Not only will you fall short of providing furniture for everyone, since only a fraction of your vendors offer furniture, but also your other vendors won’t generate any revenue. On the other hand, a market with sufficient numbers of visitors in every section will be much better at sustaining itself.

The same is true in your microbiome. You have many functions that need doing, and if you have too much of one type of microbe, then your microbiome will be unbalanced and less functional, which can impact your health.

Unhealthy Microbiome and Disease

Diseases are often associated with certain microbes (e.g. E. coli causes food poisoning, S. aureus causes skin infections, etc.), but interestingly, many of these microbes reside in all of us at all times, interacting with our cells and other bacteria in an equilibrium. Therefore, a more accurate approach is to relate diseases to disturbances in microbiome diversity and balance (i.e. richness and evenness).

Imagine one of the visitors to our flea market has a tendency to litter. They walk around the market buying things, but they drop their trash everywhere. Luckily, some other visitors don’t like seeing trash, so they end up picking up the trash. However, if the littering visitor were to visit a different market that has no cleaning visitors, the litter will accumulate and badly affect the reputation and appeal of the market.

Similarly, we all have microbes that “litter” all the time. However, they actually perform very important functions and are part of a healthy microbiome. Yet, we depend on other microbes to clean up after them and make sure they don’t create problems.

One example many of us may have experienced is acne, associated with the bacteria C. acnes. Healthy skin has both commensal (beneficial) and pathogenic (harmful) strains of C. acnes. The commensal strains protect the skin against other unwanted visitors by regulating the pH, while the pathogenic strains are inhibited by another bacteria called S. epidermidis. Although patients with acne do not harbor more C. acnes on the whole than those with healthy skin, disturbances in the skin microbiome can interrupt the equilibrium between C. acnes and other skin bacteria (like S. epidermidis). As a result, pathogenic strains of C. acnes can be activated, growing and causing red bumps and zits by promoting sebaceous gland inflammation (citation).

Another unpleasant example is Clostridioides difficile (C. diff), a culprit behind intestinal infection, gut inflammation, and diarrhea, among other things. Although this bacteria is very common and many people are naturally exposed to it, its proliferation and toxicity in the gut are suppressed by a healthy microbiome (citation).

When the diversity in our gut is disrupted – say, because of antibiotics or an unhealthy diet – it gives C. diff room to grow and wreak havoc. Today, the recurrence of C. diff infections is considered evidence of an unhealthy microbiome, but it is still not clear what specific bacteria are required to inhibit C. diff activity.


The effect of an unhealthy microbiome on C. diff infections, as well as our lack of understanding, becomes much more apparent in the clinical approach to this disease. Transferring a healthy gut microbiome sample into a patient suffering from C. diff results in that patient developing resistance from future C. diff infections. This is done in a crude (and kind of gross) way called a fecal transplant, by taking a fecal sample (and in essence, the entire microbiome) from the healthy person and implanting it directly into the colon of the patient (citation).

It demonstrates the importance of a healthy microbiome, while also showing how little we know about its specifics. If we had more insight, we could have just isolated the key protective bacteria, and delivered it as a pill. Instead, since we don’t, we just take the whole thing and transfer it over! This is similar to selecting 100 people randomly from a popular flea market – some of which are the folks who pick up litter – into your litter-covered market. Because you didn’t know which ones were the cleaners, you had to bring in as many people as possible to make sure you get the right folks that address the problem.

Acne and gut inflammation are only two examples of a long list of cases. If you look at the disease mechanisms of diabetes, obesity, and depression, you are going to encounter similar stories.


The microbiome is central to human health, with its impact reaching nearly every system of the body in some way. For the past decade, the scientific community has made rapid progress in understanding the microbiome, and that progress isn't slowing down. But while the microbiome is absolutely the next frontier of health and performance, we are still just scratching the surface of what there is to be known. And currently, there are no universal "silver bullets" that reliably move your microbiome in a way that benefits your body. But as our understanding grows, the microbiome will doubtless become an incredible lever for improving human health.

In part two of our microbiome series, we are going to give actionable insights into what you can do to protect the integrity and diversity of your microbiome.

This article is for informational purposes only and does not constitute medical advice. The information contained herein is not a substitute for and should never be relied upon for professional medical advice.