Get to Know Your Gut Microbiome


How much do you know about your gut microbiome? If you’re like most people, you don’t know much. But knowing more about the world inside your gut and how to keep it healthy is vital to your overall health.

As human beings, we are composed of approximately ten trillion cells that make up our tissues, organs, and bodies. However, each one of us is so much more than that. Your body is a habitat, a complex ecosystem, housing a vast and expansive myriad of tiny residents.

Each of us plays host to a hundred trillion non-human micro-organisms. They outnumber our human cells 10 to 1. These creatures inhabit our bodies and live in distinct communities with a variety of different environments. Some species live on our skin, some live in our mouths, and the biggest population lives inside our gut.

The “gut microbiome” is the colony of bacteria, fungi, and viruses that live in our digestive tract. It has been co-existing and evolving with us throughout human history. But only recently have we begun to understand how these tiny, unicellular organisms can affect so many aspects of our health.

This virtual menagerie of microbes has a huge impact on our immune system, digestion, hormones, mood, and overall health. In turn, our lifestyle also has a major impact on microbes. Everything from the food we eat, to the way we think, and the way we are born, influence the creatures that take up residence in our gut.

Who’s in there?

The diverse population of residents living inside your intestine is often referred to as the “gut flora” or gut microbiota. It is comprised of at least 1000 different species. It is believed that about one-third of the microbes are common across the board in most people. The remaining two-thirds are completely unique to each individual. The leaders of this microbial metropolis are known as the “essential flora.” They keep the peace by controlling unfriendly and unproductive members of the bacterial community, while also performing some very important functions necessary for human health.

Where did they come from?

How in the world did tens of trillions of non-human creatures get inside your gut? 

It all started at birth. When you were a baby inside your mother’s uterus, you started out 100% human. You were sterile and microbe-free, but very quickly began transforming. While still inside your mother’s belly, embryonic fluid delivered microbes to your system. Then, as you traveled through the birth canal and entered the world, your body was quickly colonized with microorganisms passed on from your mother. They came from her vagina and skin, the air, and the environment in which the delivery took place. This is when the first residents “moved in” and made your gut their home.

From then on, you likely picked up microbes all over the place. You picked them up from family members, household surfaces, dirt, pets, food, and medicines. Your gut ecosystem remained in a flexible developmental state until about age three when it became more stable. This means that the events from birth to age three played a significant role in determining who is living in your gut microbiome today.  Since one of the largest contributors is breast milk, the health of a mother has a significant impact on the future health of her child.

A Bounty of Busy Bacteria – Friendly Flora or Bad Bugs

Why do we need the gut microbiota?

The community in your gut microbiome is a very productive one. In fact, microbiota’s role in human function is so significant that many scientists view this collection of tiny creatures as an “acquired organ”. Scientists recognize that without their existence, long-term human survival would be unlikely.

How does it work?

Many of the complexities of the gut microbiome still remain a mystery. But we have been able to identify some key roles that gut flora plays in our health. We also have seen how these microbes interact with one another. To better understand this diverse and intricate collection of organisms, gut flora can be divided into three distinct classes.

Essential Flora:

These are the leaders of your community, the movers and the shakers, the army, the police, and the factory workers. The essential flora gets things done and doesn’t let anyone get in their way. This means controlling any revolts or uprising from “bad bugs” and conducting numerous roles that keep your body healthy, such as digestion and immune function.

Opportunistic Flora:

This group of misbehaving microbes are the rebels, troublemakers, and party animals of the community. They are harmless in small numbers, but without proper supervision, can easily get out of hand and are capable of causing disease and dysfunction. The essential flora does a great job of keeping these guys in line. However, if the essential flora becomes compromised and unable to control them, opportunistic flora can multiply and make a real toxic mess.

Transitional Flora:

These are the tourists and visitors to your community. They are various microorganisms that are introduced into the body through eating, drinking, and contact with your external environment. This type of flora, in a healthy person, does not present a threat. Your essential flora has some pretty good immigration and homeland security measures in place to assure that these foreigners don’t overstay their welcome or travel to any unauthorized locations. Typically, they come for a visit, then pass through the digestive tract without causing harm. However, if the essential flora is damaged and security is breached, transitional flora can cause disease and dysfunction.

Fabulous Functions of Your Friendly Flora

Not only does the essential flora work to control the population of unhealthy flora, but it also does some pretty fabulous work to help nourish and protect your body. It promotes normal gastrointestinal function, provides protection from infection, regulates metabolism, and protects the integrity of the gut which is responsible for approximately 70% of our immune system. An imbalance in gut flora has been linked to conditions ranging from colic in babies to autism, anxiety, and depression, to inflammatory bowel disease, obesity, and autoimmunity, to diseases like type 1 diabetes and cancer.

Two of the key roles we will look at here are nourishment and immune function.


Essential flora helps with the digestion and absorption of food by producing enzymes that aid in the breakdown of proteins, carbohydrates, and fats. Certain types of essential flora are capable of manufacturing nutrients such as vitamins K2, B1, B2, B3, B6, B12, folic acid, pantothenic acid, and various amino acids. Without the hard work of these busy little bugs, we could easily become malnourished, intolerant to certain foods, and have multiple nutritional deficiencies that could lead to dysfunction and disease throughout the body.

Immune Function:

We’ve established that approximately 70 percent of the immune system is located in the digestive tract. In healthy individuals, the essential gut flora acts as a bacterial blanket that covers the entire intestinal wall protecting against parasites, toxins, viruses, undigested food particles, and transitional flora.

One of the essential flora’s most fabulous immune functions is its ability to mobilize tiny armies of cellular troops that not only protect the gut but the entire body. In the gut, essential flora can stimulate the tissues of the lymphatic system to produce infection-fighting white blood cells which destroy foreign invaders as they enter the body through food and drink. Systemically, essential gut flora is on the front lines in the development and balance of regulatory T cells, which are necessary to regulate the immune system, maintain tolerance to self-antigens, and prevent autoimmune disease.

Whose Team are You On?

It’s pretty clear that you need your essential gut flora to keep you healthy. But you may not realize how much it needs you as well. Your tiny teammates depend on you, their host, to make their job easier, support their efforts, and keep their environment clean and balanced.

Unfortunately, many of us eating the Standard American Diet, taking medications and antibiotics, using antibacterial soaps and cleaners, and living a fast-paced, high-stress lifestyle are creating a difficult time for our friendly flora and, instead, are giving the bacterial bad boys in our gut the upper hand.

When the gut flora is balanced, our digestive system runs efficiently. But when it’s not, we may begin to feel vaguely out of sorts. This is the first sign that your essential flora is in trouble.

If you suspect that you may have unknowingly been batting for the wrong team, you may be experiencing symptoms like bloating, constipation, diarrhea, brain fog, depression, weight gain, or autoimmune conditions like Hashimoto’s. Luckily, friendly flora is forgiving. These guys will welcome your goodwill and hospitality, and graciously accept your help in supporting their triumphant takeover of your gut microbiota.

Enlist Help to Manage the Microbial Mayhem

To help you understand the best course of action, you can enlist the help of an FDNThrive health detective. Your FDNThrive practitioner can test you for gut dysbiosis, which is an imbalance of good and bad bacteria in your gut. They can also test you for leaky gut or hyperpermeability of the gut lining, SIBO (small intestinal bacterial overgrowth), and parasite infestations. All of these issues occur when the opportunistic and transitional flora get the upper hand on our essential flora. With the proper guidance, you will be able to stop the microbial mayhem caused by an overgrowth of unfriendly flora.

Once you have evened the score by eradicating any unwelcome guests and reestablishing balance and order in your microbial community, you can show your support for your friendly flora by providing a happy and healthy environment where they can flourish.

How to be a Healthy Host to Your Friendly Gut Flora

Our essential gut flora plays a particularly important role in our health and well-being. It is important that we treat them with respect and give them the proper care and feeding that they deserve. Doing so will help the gut microbiome to thrive!

Don’t Feed the Animals

In this case, we are talking about the less civilized, bad bacteria. These less beneficial florae thrive with a diet high in sugar, certain fats, and processed food. As a result, they can cause gas, discomfort, bloating, and inflammation. This flora can also emit chemicals that compromise the intestinal lining. By cutting sweets and processed foods out of your diet, you make it easier for your friendly flora to keep the bad seeds in line.

Curtail Killing Sprees 

Avoid overuse of antibiotic medications and antibacterial products. These kill bacteria but do not differentiate between the good and the bad. With continued use, you may kill off enough of your good guys to allow the bad bacteria to take over.

Go Pro

Probiotic that is. The good bacteria in fermented foods and supplements can bolster the number of friendly bacteria in the gut. For relatively healthy people, it’s always a good idea to start with real food before taking supplements. Bifidobacteria, found in most yogurt and kefir, release chemicals that create an acidic environment. It is this environment in which many harmful bacteria can’t thrive. For those with dairy allergies or intolerances, fermented vegetables like pickles or coconut kefir can be good options. However, fermented foods are not the best choice for everyone. Consult with your health coach to determine the best probiotic methods for you.

Feed your Flora

Prebiotics, which contain non-digestible carbohydrates found in onions, garlic, leeks, artichokes, asparagus, and chicory root nourishes the essential gut flora. Regular intake has been associated with decreases in irritable bowel syndrome and fat storage. It may reduce allergic reactions like skin rashes. Well-fed friendly flora are able to perform their jobs better and tend to increase your overall feeling of well-being.

Stress Less

Stress may change the makeup of your gut flora according to a 2011 study. The study reported that stressed-out mice experienced a significant plunge in beneficial bacteria. They also experienced an increase of inflammatory chemicals in the blood. Chronic stress also appears to alter the functioning of the immune system. It does this by suppressing its response to foreign invaders. So, for the good of your gut microbiome, take measures to eliminate both internal and external stressors.

The world that lives inside your gut microbiome has a powerful influence on your overall health. Taking the time to nourish your gut health will go a long way to helping you feel good!

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