The Many Microbiomes and How They Work Together for Total Health

many microbiomes connected

Looking at the whole Earth, we notice an abundance of variety: a variety in landscapes, climates, wildlife, and in people and cultures. Each region has its own challenges, its own benefits and helps shape the living organisms that thrive there. And as the landscape changes, its inhabitants adapt with it - ebbing and flowing as the environment shifts.

To the microbes that call our bodies their home, it’s very much the same. Each part of our body is vastly different than its other parts, like different countries around the world. From our skin to our organs, our mouths to our toes, each section of our body has its own ‘climate’ and ecosystem. To thrive, our microscopic companions must adapt to their environment, and just like the people of Earth, they too, vary from region to region.

But like all of the inhabitants of Earth, no matter their location - everything is connected. In many ways, it is part of the beauty of viewing a system as a whole. Though it may be tough to see how they interact and communicate on such a small scale, many of the things that occur beneath the surface of our body have a ‘butterfly effect.’ What happens in one place can be felt in the far reaches of another.

Though that may seem sort of scary, especially in the case of something bad, it also means good news can travel just as fast.

The (Very) Different Microbiomes of the Human Body

The word microbiome literally translates to ‘microscopic ecosystem’ and a number of them can be found all over your body. With over 11 microbiomes identified, researchers have become convinced that humans - and life as we know it - have evolved alongside the microbes living on and inside us.1

Just to name a few, microbiomes exist in our gut, mouth, skin, kidneys, and sex organs (such as the vagina and testes). Not to mention, our bodies have adapted to life with microbial friends by keeping a stockpile of spare colonies in case of emergency (we’re looking at you, appendix).2

Each environment is unique to each microbiome, including the type of microbial populations that live there. Some are shared, like many oral microbes that travel through to the far reaches of our digestive system and settle into colonies in our gut.3 Others vary significantly due to drastic changes in our internal and external ‘environments.’ Much as you would expect to find cactus-species plants in the desert and palm trees in the tropics, the microbes that live within us vary greatly based on what region of our body they live in. 

Despite their differences, there are still a number of ways in which they can ‘communicate’ signaling to each other when changes to the environment are hostile and threatening, or calm and supportive.

Playing Telephone

If we are trying to communicate with someone across the world, we have a number of ways to do so. We may send an email, text, or phone call - all the way down to more traditional avenues like old-fashioned snail mail. Similarly, the microbes inside us have different ways of sending messages - some ways are quick like a phone call, and other ways require a little more travel.

For those quick, direct calls, microbes use what scientists call quorum sensing to send out immediate messages to surrounding microbes.4 Likewise, sometimes they’re quick to interrupt other conversations by halting or even talking over them. Called quorum sensing inhibition, this allows microbes in proximity to each other (like all within the same microbiome) to alert each other to important changes. This could be in the form of beneficial opportunities in nutrients, down to warning signals of incoming pathogens.

But when changes in a local environment - like the mouth or the gut - could have significant effects on the whole system, there are other ways microbes can connect with other regional microbiomes.

The Butterfly Effect

We see this often when it comes to the impact of gut health on skin health. Just like our gut, our skin has its own colonies of microbes that help protect us from foreign pathogens and support the health of our own cells. However, if our diet is negatively influencing the health of our gut, our gut microbiome may alter patterns in our immune system that penetrate the far reaches of our body. This can disrupt signals sent to the skin, influence our skin’s acidity levels, and make it easier for pathogens to thrive.


Disruptions to the gut can also impact our ability to regulate hormones (as many hormones in our body are actually produced by gut microbes).5 Changes in these patterns can also alert our skin microbes of negative changes - but these signals can also be sent directly to our own human cells too. Let’s face it, our body is very smart and in tune with its surroundings. If our internal balance starts to shift and affects our gut microbes, signals can be sent up our central nervous system through the enteric nervous system that directly links the gut to the brain.6

The Key is Balance

No one is perfect. We all have our good days and our bad days - just like the Earth. Our global weather patterns are constantly changing with storms brewing but also calm, sunny days ahead.

It’s all about balance: balance in our diet, balance in our activity, balance in our lives.

And that balance over time can support balance inside us as well. It can lead to more communication between our microbiomes in positive ways. It can support better communication in times of stress (like the presence of a pathogen) as well as help our body adapt to our ever-changing environment.

Ultimately, the balance we see in the world reflects how important balance can be within us all. Maybe that’s the key to total health: learning to balance the pros and cons of our biology and being just a little more resilient all around.


1 Rosenberg, E., Zilber-Rosenberg, I. (2016). mBio. ASM Journals,

2 [Digestive tools and resources center]. (n.d.).

3 Schmidt, T. SB, Hayward, M.R., et al. (2019). Computational and Systems Biology, Microbiology and Infectious Disease. eLife,

4 Otti, O., Deines, P., et al. (2019). Frontiers for Young Minds. Frontiers, kids.

5 Martin, A.M., Sun, E.W., et al. (2019). Frontiers in Physiology. PubMed Central.

6 Carabotti, M., Scirocco, A., et al. (2015). Annals of Gastroenterology. PubMed Central.