Our bodies are remarkable feats of evolution. While we may think of ourselves as one living organism – with one head, one heart, one digestive system and one mind – we are actually galaxies of living creatures united toward one purpose – our continued existence. Our bodies each have completely unique and individual microbiomes that will change and grow with us from birth until death. These communities of bacteria, fungi and biotics living on and within us have profound impacts on our health, even beyond the reach of science’s current understanding. Much like we’re only beginning to define the depths of space as we know it, similarly DNA-sequencing tools are beginning to help us see our microbiomes more clearly now than we ever could before, giving us new respect for all that it does for us.

So why should we care about the tiniest members of our body-communities? Because they matter! In ways we never could have guessed. Our ancestors were able to fight some of the most dangerous and damaging illnesses, parasites, viruses and bacteria to walk the Earth without the benefit of antibiotics because of their strong microbiomes. Some of those microbes have been passed down to us for generations, from mother to child. Unfortunately our modern lifestyles have weakened our microbiomes to a dangerous level. Humans have spent the last 80 years trying to clean “germs” from our bodies and our homes. Antibiotics have saved countless lives – but with unintended consequences to our microbiomes that we are only beginning to understand.

Disrupting our microbial ecosystems can cause disease, and some diseases disrupt our microbial ecosystems. Manipulating these interactions may help doctors understand and manage diseases. Understanding, nourishing and sustaining our microbiomes is the future of modern medicine.

Due to the collateral damage our modern society has done to our microbiomes by things like cesarean sections, poor diet and high antibiotic usage, generations of microbial data has been lost forever. As a result, medical science has begun collecting microbiome data from primitive cultures around the world to try to save some of that information that has been lost. That’s how important of a role we are beginning to understand microbiomes play in our health and vitality.

So let’s take a closer look together, and learn better ways to keep our WHOLE selves healthy, including our tiniest partners in health.

We know we aren’t just single individuals, we’re walking ecosystems. We’re a walking cosmos of ecosystems. Our bodies have many different environments and each of them has a unique set of biotic factors. The microbes on our skin are different than the microbes in our intestines, which are different from the microbes in our ears, and so on. While they’re vastly different, each and every member of our microbiome serves an integral purpose to our health.


Our microbiomes and the rest of our body function together as a symbiosis, much like plants and animals on Earth do. It is becoming clear to science that a healthy microbiome is integral to life itself.

The genes of the microbes that live inside and on our bodies outnumber our own genes by 100 to 1. Think about that for a second. One hundred to one! Most of these genes simply help the microbes survive. But many help us. Microbial genes code for enzymes that break down food that we can’t digest on our own. Some code for proteins that build vital nutrients or make molecules that keep harmful bacteria away. We’re just beginning to understand our relationship with microbes, but we do know that without them, we wouldn’t be here.

Our microbiome act on our body’s nutrition, immunity to illness, protection from infection, maintenance of protective barriers, and organ development. Some of the health conditions that involve our microbes include: acne, antibiotic associated diarrhea, asthma/allergies, autism, autoimmune disease, cancer, dental cavities, depression and anxiety, diabetes, eczema, gastric ulcers, hardening of the arteries, IBS, malnutrition, and obesity.

Our microbiome can even control our blood pressure. Bacteria in the large intestine help break down complex carbohydrate molecules. One of the breakdown products they produce, as they digest the fiber found in rice and grains, is formate. Formate diffuses out of the intestine into the blood stream. In the kidneys, it effects salt processing. People with formate in their blood tend to have lower blood pressure.

Our microbiome also protect us from toxins. Eating a healthy diet high in fiber and low in sugar and fat supports a healthy community of befidobacteria. Bifidobacteria keep toxins made by other bacteria (specifically lipopolysaccharides) from passing through the intestinal wall and into the blood stream. Harmful strains of E.Coli bacteria release toxins that can damage the kidneys and destroy red blood cells. Certain species of beneficial gut bacteria can prevent these toxins from entering the blood stream. Some microbes even inactivate toxic molecules that we ingest along with our food, as well as toxins made by other microbes.


Our DNA never changes (unless you’re an astronaut in space), but our microbiomes are constantly changing. As we grow up, our microbial profiles change along with us, adapting to the foods we eat, the contaminants we expose ourselves to and the ways we treat our bodies.

Before birth, we’re all more or less sterile – we have no microbes. We acquire our microbiomes from the environment at birth.  The moment we enter the world, microbes colonize our bodies. And depending on how and where we’re born, we’re colonized by different types of microbes.

Our first dose of microbes comes from our mother. Babies delivered vaginally are covered in a film of microbes as they pass through the birth canal. Included in the mix are bacteria that help babies digest their first meals. Babies delivered by cesarean section are colonized mainly by skin microbes – a very different set of species.

Babies pick up microbes not only from their mothers, but also from every person and thing they touch. So babies who are born at home are exposed to different of microbes than babies born in hospitals.

These very first differences – vaginal vs cesarean section birth, home versus hospital birth – are still measurable months and possibly even years after birth. And they may have even longer-lasting impacts on health that we aren’t aware of.

Regardless of how we come into the world, within a few years we’re covered in thousands of different species of microbes. They colonize every millimeter of the body that’s exposed to the outside world. By the time we enter kindergarten, we have vastly different populations living in the different habitats around our bodies. Even as adults and into old age, our microbiota continue to shift.


Ecosystems are constantly changing. We see it all around us all of the time. Forests are burned by fires. Species introduced from outside ecosystems compete for resources. Climate change turns wetlands into deserts. Ecologists study these phenomena, and they come up with strategies for understanding and managing them. It turns out that some of these strategies apply to the body’s ecosystems as well.

While science is only beginning to understand some of these strategies, explore and understand the various communities in our bodies, their interactions on our health, and how to improve the health of our microbes we can apply similar strategies to these microbiota that we do to our gardens, our wilderness, and the creatures living there.

If you’re trying to increase the number of frogs living in a swamp, you’re going to make sure the swamp water is free of contaminants – pesticides, garbage, and predators that would eat your frogs. We can view the microbes in our guts similarly. In the gut, one important abiotic (meaning not alive) factor is food. Changing our diet influences the balance of microbes living in our guts. Eating a healthy diet high in fiber and low in sugar and fat supports a healthy community of microbes that are beneficial to our health, enabling them to fight the bacteria, virus or fungi we might have inside of us that would seek to do us harm. We can drink plenty of healthy fluids to keep our swamp water clean. We can eat organic foods to minimize the pesticides our microbes are exposed to. We can eat whole healthy foods to keep garbage out of the swamp. You know who eats garbage (meaning additive, preservatives, dyes and etc.)? Viruses, E.coli, and damaging bacteria.

Things like the acidity of the digestive tract, and through variations in proteins on our cells effect how our microbes communicate with those cells. Eating a diet rich in fruits and vegetables, and minimum of grains and animal proteins supports all of these systems to run optimally and that means the microbes we need to thrive can run optimally as well.

Something else to consider would be decreasing your exposure to harmful microbes (like the predators in the swamp). If you’re someone who eats out a lot, you might want to avoid the buffet. Those trays of food just sitting there unsupervised are subject to untold numbers of gross microbes from the people passing by. If you’re ordering food from a restaurant, try to order food that’s extremely hot. You have a better chance of the bad microbes being killed. How many news stories have we heard of people contracting Hepatitis or worse from restaurants?

Wash your hands often and well. If you use a gas pump, use hand sanitizer until you can get to soap and water. Don’t share drinks or utensils with others. Don’t swim in stagnant water. One time I contracted camplyobacteriosis. The CDC called me to ask some questions (seriously). The first question they asked was if I’d swum in stagnant water. In the end it was undercooked chicken that made me sick. The meat we buy from grocery stores is almost guaranteed to have bad microbes on it. Be mindful of what food you’re buying, where you’re buying it, that you’re cleaning it well, and that you’re cooking it appropriately.

Do your microbiome a service, and do you best to keep out bad invaders.

The world of microbiomes is vast and mostly unknown. It is, however, a vital part of our lives and worthy of being understood. I hope I’ve done a small part to dispel some of the mystery and bring your microbiome to the forefront of your mind as you’re working so hard to fight for your whole health.

For Further Research Check Out:

Human Microbiome Project

The Human Microbiome

Mental Health May Depend on Creatures in the Gut

Breast-feeding the Microbiome


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