• Siri DeMarche

What is the Microbiome? Leaky Gut? In Plain Jane ol' English

Updated: Jul 23

The Brief of It

I suppose the most appropriate place to start is at the root of a vast slew of health issues. We’re talking preventable diseases, allergies, brain fog, chronic lethargy, gastrointestinal discomfort, stress, sleep irregularities..etc. Also known as your second brain, I’m talking about your gut. Get your head out of the gutter. Your gut health should be treated with respect and intentionality. Not only does the gut house the greatest concentration and largest diversity of microbes in our bodies, the gut and its microbiota are unique to every individual. How we feed this little monster is everything. The brain and the gut are intimately connected by a network of physical and biochemical interactions and systems conveniently known as the Gut-Brain Axis.


There are 500 million neurons in our gut and they communicate with the brain through the nervous system, via the Gut-Brain Axis. One of the largest nerves connecting your gut to your brain is the Vagus Nerve. The Vagus Nerve (also known as cranial nerve x) is a two-lane highway transmitting essential information to and from your brain and gut. While the Vagus Nerve has several important functions, for brevity's sake we will focus on the connection between the gut and the brain. Our gut contains trillions of microorganisms that affect the nutritional and chemical makeup of our bodies. The microorganisms (microbes) make small molecules that travel throughout the bloodstream. Amongst their many biological activities, these molecules affect how we use sugar, metabolize nutrients, and regulate appetite. In fact, the gut microbe affects everything from how our bodies use the food we consume to how our moods are expressed to how good we are at fighting off an infection. Clearly, it is in our best interest to take care of it and give it the fuel that it needs.


Not only does the gut microbe affect how we absorb nutrients, the nutrients that we give it affect its composition. Ever heard the saying, “you are what you eat?” Well, it’s true. Except it's more like "you are what you digest." The stuff that makes up your molecules and cells is created from the microorganisms inside you. These microorganisms compete for access to the nutrients we feed our bodies. For example, while simple carbohydrates (such as glucose) are digested and absorbed in our GI tract, more complex carbohydrates pass through undigested. Many of the enzymes necessary to digest these carbohydrate substrates are found in the gut microbiome. Similarly, the gut microbiota is needed for the proper digestion and absorption of proteins. While conventional wisdom says that human-required essential amino acids must be supplied by the diet, emerging studies are showing that gut microbes can greatly impact nitrogen (an essential component of amino acids) balance in humans by de novo synthesis of amino acids and intestinal urea recycling (peep some research HERE). De novo synthesis refers to the creation of complex molecules from simple molecules, rather than the recycling of molecules after partial degradation. Urea is the main nitrogenous product derived from protein metabolism in mammals and excreted in the urine. Urea recycling refers to the constant osmotic transfer of urea between the renal tubule and the interstitial fluid of the medulla. The details of this process are outside the scope of this post. The important bit is that the microbes in our gut contain enzymes able to digest and synthesize nitrogenous molecules necessary for optimum human health. Many more complex molecules in your body are synthesized in a similar way by using simpler molecules extracted from the foods we eat. Remember, you are what you digest.


Not only are important molecules created in the gut, many neurotransmitters are also produced in the gut. Your gut and brain are connected through chemicals that communicate along the Vagus Nerve. While many of these neurotransmitters are made in the brain, many are also produced by the gut cells and the microorganisms living there. Neurotransmitters made in the brain control feelings and emotions. One such neurotransmitter is serotonin. Serotonin contributes to feelings of joy and also helps to regulate your body clock. Interestingly, a large portion of our serotonin is produced in the gut. Another neurotransmitter produced in the gut is GABA (gamma-aminobutyric acid). GABA helps to control anxiety and fear. A deficit of GABA contributes heavily to depression. Starting to see the importance of the gut microbiome and overall well-being? The gut also produces other chemicals that affect brain function. For example SCFAs or short-chain fatty acids, are produced by the gut microbiomes and affect appetite. SCFAs, such as butyrate, propionate, and acetate, are made through the digestion of fiber. Propionate has been shown to reduce food intake and reduce the activity in the brain related to the reward from high-energy foods (check it out HERE). Butyrate and the responsible microbes are necessary to the formation of the blood-brain barrier.


The term “Leaky Gut” refers to intestinal permeability. For all the reasons stated above, we want to keep our intestinal permeability to a minimum. One of the most common causes of leaky gut is an imbalance in gut microbiota, or dysbiosis. Hence, a balanced gut microbiome leads to a stronger gut barrier.


From the book, "Life at the Edge of Sight: A Photographic Exploration of the Microbial World"- by Roberto Kolter and Scott Chimileski

Why Pay Attention to a Leaky Gut?

Why is Leaky Gut an issue? Why address it in the first place? Well the answer is obvious, but often overlooked because of the necessary due diligence. AKA it’s not a cute little pill that you can just pop into your mouth with the instant gratification that you did “something” to address the issue. No. My friends, the cute little pill is like taking Novocaine to fix a terrible toothache; it makes it feel better in the short term, but eventually the pain comes back. Now, a sensible person rips the bandaid off, bites the bullet, and gets a root canal. Why? Because a sensible person wants to fix the problem, not prolong it indefinitely. Everyone knows what a root canal is. Why don’t more people know what Leaky Gut is? Part of the reason is Big Pharma and an industry that makes billions off selling pill-form bandaids to sort larger problems (thereby perpetuating these problems and leading the consumer to buy more “bandaids”).


Another piece of the puzzle is a prevalent unwillingness and impatience to understand the necessary steps needed to address the fundamental problem. Life is not a quick fix and it is not about instant gratification. If you’re about that take-the-pill-and-call-it-a-day life, then Habitually Holistic is not for you. While I will outline easy steps to implement into a daily routine, it is not a one-stop shop by any means. No buying a single pill to mask your problems! It’s time to address the root issue and get on with living your best life (and creating a better one for your future self)!


So….how does Leaky Gut happen in the first place? Clearly it’s important or I haven’t done a good job at explaining anything. Leaky Gut is another name for the condition “Hyperpermeable Intestines.” Essentially, the intestinal lining has become too porous with larger than normal holes developing because the filter system between the intestinal lining and blood stream is not properly functioning. This allows things such as undigested food particles, toxins, yeast, and other forms of waste to flow freely in the bloodstream. These things should not be in our blood and consequently our liver and immune system react as if they are foreign bodies, resulting in inflammation and the accumulation of toxins and pathogens in our bodies. The liver begins working overtime to filter these displaced "foreign" particles. Very rarely is the liver able to keep up with the continual flow of undigested food particles, yeast, toxins, and pathogens. Consequently, this waste accumulates in the body and the immune system ramps up to aid in the cleanup.


The immune system kicks it up a notch and gets in on the action, but the body is not able to cope with the continual influx of waste. The result is wide spread inflammation because the absorption of these foreign bodies into body tissue. Inflammation is an immune response and adds more stress to the system. While the body focuses its efforts on fighting these foreign invaders, smaller (but necessary) systems and mechanisms begin to degrade. These include blood filtration systems, processes for calming inflamed areas, fighting bacterial infections, regulating the gut...etc. All this accumulates to your body fighting itself and causing a whole array of issues, such as autoimmune diseases like MS, IBS, Chronic Fatigue, Fibromyalgia, and others.


Bacterium sampled and measured at 1-micron in length


To fight these foreign invaders, the body produces antibodies. Antibodies are blood proteins produced in response to a specific antigen. They chemically combine with alien substances such as bacteria, foreign materials in the blood, and viruses to combat a specific antigen. Antigens are toxins or foreign substances that cause an immune response in the body and spark the production of antibodies. The antibody soldiers produced by the body can be things like the protein in eggs and grains, the Casein protein from dairy, and even chemicals normally found in foods. All of a sudden, foods that you are eating start triggering an immune response in your body and you begin experiencing food sensitivities. If you have food sensitivities to more than a few foods, Leaky Gut is highly suspect. Any undigested foods are now sparking a strong immune response in the body because they are being absorbed into the blood.


Consequently, food intolerances develop because of the immune system’s reaction to the undigested food particles. This happens because a Leaky Gut has damaged microvilli (microscopic cellular protrusions on the tips of the tight junctions that connect the outer layer of intestinal epithelial cells, they absorb properly digested nutrients and transport them through the epithelial cell and into the bloodstream). These damaged microvilli along the intestinal lining cannot create the digestive enzymes needed to break down food for proper digestion. Consequently, this allows undigested food particles to flow into the bloodstream.


Normally, the tight junctions with the microvilli remain closed, forcing all particles to be filtered and allowed only to pass into the bloodstream through the mucosa cells. When these tight junctions become open, un-filtered particles flow directly into the bloodstream and wreck havoc. QED, your food intolerance problems are not the foods that you are eating, but rather the leaky gut allowing the food particles into the bloodstream. While there are foods that can promote leaky gut syndrome, it is not the food itself that is at the center of food intolerance.


My advice? Get your blood tested and find out what is really going on. You are only as good as your digestion and absorption of nutrients. It does not matter the noble intention behind eating high quality foods if you are not absorbing the nutrients from them. Find out the current status of your blood. It could be the single best thing you do for your health moving forward.




Statements made on this website have not been evaluated by the U.S. Food and Drug Administration or any other medical body. I do not aim to diagnose, treat, cure, or prevent any illness or disease. Information is shared for educational purposes only. You must consult your doctor before acting on any content on this website, especially if you are pregnant, nursing, taking medication, or have a medical condition.

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