Gut Microbiome: How our digestive system plays an important role in overall health and immunity

February 10, 2022

The father of modern medicine, Hippocrates, said, “All disease begins in the gut.”

What happens inside your gut has everything to do with your overall health. Did you know that 70 to 80% of your immune system lives in your gut? Because our intestines are inside our bodies, many people don’t realize they form a protective barrier between the bloodstream and the outside world. So, what’s inside your gut is actually “outside” your body!

Have you heard of the gut microbiome? This is the name given to the tens of trillions of microorganisms that live in our gut. Every day new research is showing us the necessity of a healthy gut microbiome and how that’s connected to anxiety, depression, Alzheimer’s, and autoimmune disease. Your gut microbiome can even dictate what food cravings you have, to name just a few recent studies!

The microbiome includes at least 1000 different species of known bacteria with over 3 million genes. A healthy gut microbiome controls gut health by communicating with cells in the intestines, digesting certain foods, and preventing disease-causing bacteria from sticking to intestinal walls.

Have you heard of the term “leaky gut?” Have you been wondering what it means to have a leaky gut? Do you know what symptoms are experienced with leaky gut, and how it relates to developing disease?

If you experience bloating, food insensitivities, fatigue, digestive issues like constipation or diarrhea, “irritable bowel syndrome,” joint pain, depression/anxiety, and skin problems, and dozens more – you may have leaky gut.

As more Americans are affected by poor dietary choices, toxic overload, chronic stress, and bacterial imbalance in the gut, it seems that the prevalence of leaky gut has reached pretty impressive proportions. There’s been some debate in mainstream medicine about whether this term even exists, but “intestinal permeability” (another name for leaky gut), has been discussed in medical literature for over a hundred years!

Today, let’s have a better understanding about how important it is to maintain gut integrity because this is one of the major first lines of defense for your body. You will also learn what conditions may be associated with a leaky gut, and most importantly, what you can do to restore your gut health.

As a functional & integrative physician, I champion the inborn potential in every person. Our bodies are beautifully and intricately designed to support our health and well-being. Using a systems oriented approach, we aim to give the body the right environment to heal itself, thereby restoring energy and vitality. We absolutely have the power to improve our health, folks.

The human digestive system is made up of many parts: our mind, mouth, esophagus, stomach, small intestine, liver, gallbladder, pancreas, and large intestine (colon). In the small intestine, 90% of digestion and absorption of food occurs. The lining of the small bowel is a single cell layer thick and serves additionally as a strong barrier to toxins, pathogens and large undigested food particles.

The walls of the intestines act as barriers, controlling what enters the bloodstream to be transported to your organs. This cell layer is held together very securely with intercellular tight junctions which prevent anything from passing through other than thoroughly digested food and nutrients. When the tight junctions of the intestinal walls become loose, the gut becomes more permeable, which may allow bacteria and toxins to pass from the gut to the bloodstream. This is the phenomenon referred to as “leaky gut.”

Then what happens when things enter through these normally “tight” junctions, that shouldn’t be entering? Well, our immune system, which is highly trained to recognize things that belong in our bodies vs. those that don’t belong, will mount a defensive antibody reaction against what has inappropriately crossed this gut barrier. Simply put, a normal part of your immune response that serves to fight infections and diseases winds up over-performing, leading to chronic inflammation, which is at the root of most diseases.

Some of the causes of leaky gut include 1) poor diets, laden with added sugars, simple carbohydrates, processed foods, GMOs, and synthetic food additives; 2) chronic stress which is the root cause of all illness; 3) overexposure to toxins – including antibiotics, pesticides, tap water, excessive alcohol intake; 4) bacterial dysbiosis – an imbalance between beneficial and harmful types of bacteria in your gut. When the numbers of good bacteria are reduced, this gives an opportunity for harmful bacteria, yeast, viruses, and parasites to take hold and cause problems in the gut. Unfortunately, we see these results all the time when reviewing comprehensive GI testing.

Maybe you have also heard of the gut-brain connection. Those butterflies in your gut before a presentation, or the pit in your stomach after a stressful situation.  Anxiety, fear, sadness or elation, all of these feelings can trigger symptoms in the gut. An occasional stressful situation, is not going to cause any harm to the gut. However, chronic stress may have an impact on your gut microbiota. This connection goes both ways, a troubled intestinal tract can be the cause or at least a factor in mental distress such as anxiety, stress or depression. The brain and the gut are intimately connected.

It’s important to understand that when the normal defenses of the body (of which the gut is primary) are compromised, exposures which wouldn’t normally affect us can take root and cause illness. Not every exposure causes disease in every individual. When we take care to regain and maintain the natural balance within our body, we support the natural defenses of the body and prevent illness. So, how do we get there?

A solid program we use all the time in our practice is the 5R gut healing protocol. The R’s stand for: Remove, Replace, Restore, Repair, Rebalance.

First, you want to remove what is causing inflammation in the gut – such as food insensitivities which can be identified by an elimination diet or food insensitivity testing. The big categories of inflammatory foods are: gluten, soy, eggs, dairy, sugar. You also want to remove infections – identified by a comprehensive stool analysis - and toxins and medications.

Then you want to replace what the gut needs for optimal performance such as digestive enzymes (if you’re low). Next, restore the balance of healthy gut bacteria with pre and probiotic foods as well as fiber. A comprehensive stool analysis can tell you if you need digestive enzymes, if you’re having maldigestion, if your fiber levels are low, and what types of bacteria you have too little and too much of.

It’s essential to repair the gut with important nutrients it needs to heal and function property such as collagen, glutamine, zinc, fish oils, and vitamins A, C, E.

The last R stands for rebalance – addressing the lack of balance and relaxation that can lead to poor gut health. This means relaxing the mind and body and reducing stress.

Here are some tips to optimize your gut health: 1) Plenty of plants, vegetables, fruits and fiber rich foods 2) cut down on animal fat in your diet. 3) avoid mass-produced and processed foods, eat only real, whole food 4) eat fermented foods and probiotics, such as plain yogurt, kimchi, sauerkraut and kimbucha, 5) eat smaller portions, 6) periodically fast, research reveals this has a profound effect on the gut microbiome and possibly the brain 7) Take steps to manage stress; meditation, mindfulness, yoga. 8) Eat slowly and minfully without distractions. This will help engage the full digestive process.


So, now we understand how gut health is fundamental to your overall health and well-being. A healthy gut means a healthy immune system. When this basic compartment of our bodies is compromised, as have seen with leaky gut, all kinds of illnesses can result. It’s also vital that you know you have the power to heal your gut, and reduce the inflammation associated with a poorly functioning gut.

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