Digestive Health

The microbiome, dysbiosis, "leaky" gut and what it means for you.

Your Digestive Health

A lot of people suffer from issues that are obviously caused from issues in their digestive systems like: 

✔️ Bloating and gas

✔️ Stomach pain

✔️ Acid reflux

✔️ IBS, IBD, Diarrhea and Constipation

✔️ Crohn's, Colitis and Celiac Disease

Unfortunately many people aren’t told what is causing these symptoms and are simply given medications that don’t address the cause of their problems.  But poor digestive health doesn’t just lead to symptoms in the digestive system. New research is now showing us how issues that are often undetected and secretly lurking in the digestive system can be causing not only our digestive problems but 100’s of other seemingly unrelated health problems like: 

✔️ Acne

✔️ Eczema

✔️ Asthma

✔️ Chronic Inflammation (headaches/migraines, achy joints, swollen and puffy hands, face and feet) 

✔️ Fibromyalgia

✔️ Chronic fatigue

✔️ Weakened immune system, allergies and worsening food sensitivities

✔️ Thyroid disease

✔️ Autoimmune disease

✔️ Weight gain and diabetes

✔️ Heart disease

✔️ PCOS, Endometriosis and other hormonal issues

✔️ Depression, anxiety, ADD, ADHD, Brain Fog

✔️ Parkinson’s and Alzheimer’s

It’s quite an extensive list right?  You may be wondering, how exactly is our gut involved in all of these different types of problems?  Well let me explain.

Every single tissue, gland, organ, hormone and brain cell in your body is made from the food you eat, and your body is constantly reforming, rebuilding and replenishing itself. Your stomach lining replenishes itself every six hours. Your hormones can last in your body anywhere from 20 minutes to a couple of months. Your skin rejuvenates every 27 days. Your bones transform every two years.

These regenerative cycles depend on amino acids (the building blocks for your cells) and other nutrients from the foods you eat to provide your body with the necessary vitamins, minerals, fats and glucose it needs to rejuvenate. Your liver stores a lot of these nutrients, while your fat cells store fat-soluble vitamins such as A, E, K and D. Since your body also releases water-soluble vitamins, such as vitamin C and B vitamins, it’s vital that you replenish it with foods rich in these important nutrients.

To repair your tissues, organs and glands, your immune system, digestive system and liver have to work together. Think of it like an orchestra playing a symphony. Each instrument has to be in tune with the other instruments or the music will be off key. In the same way, your liver, and immune and digestive systems must be working in harmony for your body to regenerate properly. 

The “conductor” in this whole process is your digestive system and within that digestive system is the all important and essential microbiome. Just as a musical conductor is vital to the pieces of an orchestra coming together to make beautiful music, the tissues, glands, organs, and hormones in your body rely on a proper microbiome and healthy digestive system to assist them in performing at their best. If “your body has an 1) insufficient or imbalanced microbiome, 2) an overgrowth of bad bacteria called dysbiosis, or 3) a condition called “leaky” gut the rest of the body will become out of sync playing a dysfunctional tune.   

What is the microbiome?

Your body contains trillions of bacteria, viruses and fungi, commonly known as “microbes,” most of which are located inside your intestinal tract. Their collective processes are known as your microbiome.  While there are about 30 trillion human cells in your body, there are about 40 trillion bacterial cells, which begs the question are we more bacteria than human? These microbes include about a thousand species, each assigned a different job. Some examples of these normal healthy bacteria are E. coli, escherichia, streptomyces, enterococcus, lactobacillus, clostridia and bifidobacterium.  A common issue we see, on stool tests, is many patients don’t have enough of these normal healthy bacteria, that they are insufficient or deficient.  These microbiome all have their different roles in the function of the body and when missing or imbalanced it can lead to several issues. 

For example, to have a healthy immune system, you need a healthy diverse microbiome. The microbiome contributes to the production of antibodies, which help your immune system to fight infection. New research is also showing how the gut microbiome plays a major role in brain health. The bacteria in the microbiome help make neurotransmitters like serotonin, dopamine, GABA and acetylcholine, which are all critical to normal brain function. These bacteria are so important to our mood that researchers have coined the term “psychobiotics” to explain the importance of the microbiome to mental health.

The microbiome also assists in regulating hormones. The importance of these friendly bacteria to hormone regulation has been gaining attention as researchers have discovered that particular bacteria are responsible for the regulation of estrogen and have named this part of the microbiome the “estrobolome.” An imbalanced estrobolome leads to faulty metabolism of estrogen and therefore the risk of developing estrogen-related diseases such as endometriosis, breast cancer and prostate cancer.

Medical researchers are also finding strong links between what is occurring in the microbiome and the development of autoimmune disease, leaky gut, IBS or IBD, metabolic disease and weight gain, inflammation, depression, anxiety, Parkinson’s and Alzheimer’s diseases, autism and even chronic pain. And other research has shown an unbalanced microbiome contributes to infectious diseases, liver diseases, gastrointestinal cancers, metabolic diseases, respiratory diseases, mental or psychological diseases, hormonal issues and autoimmune diseases.

Dysbiosis: When things get ugly!

In general, bad bacteria, viruses and fungi aren’t a problem. In fact, they work hand in hand with the rest of the body’s bacteria to digest food and produce vitamins. If these bad bacteria didn't exist, we couldn't exist. We need both good and bad bacteria to thrive. The problem happens when the good bacteria become outnumbered by the bad bacteria, a condition known as “dysbiosis.” When the bad bacteria start to outnumber the good bacteria or grow in numbers beyond what is considered normal, it creates an unhealthy environment not only in the gut, but in the entire body, which can lead to a wide array of illnesses. 

The bad guys taking over and creating an environment that’s considered dysbiotic is linked to intestinal inflammation that can damage the gut lining. As a result, digestive symptoms such as indigestion, diarrhea, gas, constipation and bloating can emerge. Dysbiosis can lead to damage of the intestinal wall and has been associated with leaky gut syndrome, which is explained more later. A dysbiotic environment is also linked to other GI conditions including, but not limited to, gastritis, peptic ulcer disease, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and even colon cancer. 

Dysbiosis can also adversely affect digestive processes, leading to nutritional deficiencies which can affect energy levels and lead to fatigue, poor skin and nail health, and hair loss. Dysbiosis has also been linked to asthma and allergy issues and heart disease. Since about 80% of immune system cells are located in the gut, dysbiosis has been linked to a weakened immune defense against disease and illness, and is seen as a major contributor to autoimmune disease and patients who experience frequent recurring infections.

What can lead to dysbiosis occurring, you might ask? Dysbiosis has been linked to excessive use of antibiotics, alcohol intake, exposure to pesticides, poor dental hygiene, stress, and dietary changes that increase the intake of sugar, protein or food additives.

‍What is “leaky” gut?

Although the condition known as “leaky” gut can cause an array of symptoms, many of which take place outside of the digestive system, most mainstream medical practitioners still aren’t familiar with this condition.

So, what is leaky gut?  In scientific terms it's referred to as “increased intestinal permeability” and if you do a PubMed search there are over 8,870 articles written to date on the topic of increased intestinal permeability. The term itself is actually a pretty accurate description of what occurs in the body. Your digestive system is masterfully designed to keep harmful substances such as undigested food, toxins, allergens, microbes, viruses, parasites, bacteria and metabolic wastes confined to the digestive tract. However, when the digestive system develops gaps between the cells of its membrane lining – hence the term “leaky gut” – the substances which should be confined to your digestive tract can escape from your intestines and enter your bloodstream.

What happens then? Because these harmful substances aren’t normally in your blood, your immune system recognizes them as foreign invaders and begins to attack by releasing antibodies, much like an army of soldiers trying to clear out the enemy. Because these foreign substances are continually leaking into the bloodstream, where they don’t belong, the antibodies become confused, go rogue and literally attack your own body as if it were the enemy. When these antibodies start attacking the body, it is called “autoimmune disease.” The continued release of antibodies causes inflammation (swelling), which accumulates over time, causing the digestive system to not work properly and leading to an array of unpleasant symptoms like depression, weight gain and type 2 diabetes. Many of our patients who suffer from leaky gut or autoimmune disease report a chronic feeling of unwellness, almost like they have a low-grade infection every day of their lives because of this overactivation of their immune systems.

These foreign substances also become toxic in nature once they leave the intestines and can interfere with normal hormone production or trigger allergies and asthma. These toxins can also disrupt normal brain function leading to anxiety, depression, headaches and brain fog.

The results of one study that looked at 30 children and adolescents with thyroid disease to see if they had leaky gut were astonishing. The study found a correlation between the severeness of the subjects’ intestinal permeability and the severity of their thyroid disease, causing those with the more permeable leaky guts to take higher doses of thyroid medication and gain more weight.  

Here are SOME of the most common signs and conditions associated with leaky gut:

 1. Fatigue

2. Anxiety and/or depression

3. Chronic sinus and allergy problems

4. Weight gain, obesity and Type 2 diabetes

 5. Joint pain and fibromyalgia

 6. Autoimmune diseases (including Crohn’s, celiac, lupus, eczema, psoriasis, rheumatoid arthritis and Hashimoto’s)

 7. Skin, hair and nail issues (including acne, hives, dry or oily skin, hair loss and weak or ridged nails)

8. Heart disease and high cholesterol

9. Brain Fog, Headaches, and migraines

10. Hormonal issues such as hypothyroid, PMS, PCOS, endometriosis and low testosterone

It’s important to note that individuals with leaky gut may have no digestive symptoms at all. I've done stool tests on patients with no digestive symptoms and have found disastrous results. I will run a stool test in patients without digestive symptoms if they are experiencing unexplained hormonal issues, acne, hair loss, autoimmune disease, chronic illness and infections, depression, anxiety, allergies and other gut-related issues mentioned above.

What causes “leaky” gut?

The list of causes of leaky gut is about as extensive as the list of symptoms and includes dysbiosis, use of medications such as antibiotics and NSAIDS, toxins, alcohol, stress, excessive weight, pregnancy, food sensitivities, lack of vitamin D and lack of movement or exercise. Another cause of leaky gut is a poor diet full of processed foods. Unfortunately, the Standard American Diet, also known as SAD, really lives up to its initials. It’s the naturally occurring bacteria present in “real” food that keeps our guts healthy. Foods that have been pressed, pulverized, processed, preserved and packaged before being frozen or put in a box or bag are going to lead to an imbalanced ecology in the gut. A growing body of research also indicates grains such as wheat might be culprits in the development of leaky gut because they contain substances that have been shown to damage the intestinal walls.

How do you know if you have “leaky” gut, dysbiosis or a healthy microbiome?

If you think you might have any of the digestive issues that have been mentioned, it is extremely important to find a practitioner who doesn’t just look at basic lab work and use conventional therapies, but instead who looks to find and correct the underlying causes. At our practice, we offer various types of testing to assist in determining if a patient’s problems could be stemming from the digestive system.

We can do a food sensitivity test to see if someone is having multiple food sensitivities to things they commonly eat. Remember, leakage in your intestinal wall leads to undigested food passing into the bloodstream. This test tells us if your immune system is releasing antibodies to “attack” any of the foods. If you test positive for antibodies to a certain percentage of foods, it indicates that undigested particles of these foods are leaking from your gut into your blood. The more antibodies we find, the more your immune system is in overdrive.

I want to stress that positive reactions don’t mean you are “allergic” to these foods. It means that your body is reacting to foods that aren’t where they’re supposed to be. Once your leaky gut is healed, you might be able to reintroduce the foods into your diet.

I want to share with you an example of a patient who came to our clinic in rough shape. She suffered from autoimmune conditions of her skin, causing her to have rosacea, for which she had been prescribed steroids. The steroids led to her gaining weight and contributed to her developing diabetes.

Pre-treatment testing

As you can see from all the red in her test results, the patient had a significant number of foods that she was reacting to. Once we worked with her to identify and correct her gut issues – including reducing the overgrowth of the bad bacteria, improving her nutritional deficiencies and re-inoculating her microbiome with more of the good bacteria she was missing -- her leaky gut improved and she saw significant reductions in her food sensitivities:


Post-treatment testing (four months later)

As you can see by the test results, with treatment we were able to heal her gut which reduced her immune response to the common foods she was eating. (Notice the amount of red on the first test versus the second test.) We were also able to help her reverse her high blood sugars and get off the steroids she was taking for her skin conditions. Not only did she lose weight, but her skin cleared up, her energy level sky-rocketed and she felt better than she had in years.

Stool testing

We also use a Comprehensive Stool Analysis to see if patients have parasites, worms, viruses, the proper amount of normal bacteria, dysbiosis, leaky gut, inflammation and more. This test is much more sophisticated than the stool tests most gastroenterologists order – in fact, the results are four pages long. This stool test uses DNA analysis to detect pathogens and imbalances in the digestive system. Traditional testing, ordered by most gastroenterologists or primary care physicians, uses a microscopic and cultural evaluation to look and test for pathogens. This form of testing can miss many of the pathogens and imbalances that exist simply because there aren’t any pathogens in the sample that was collected. It's like calling the police to your house after a robbery. When they arrive, they look around, don't see anyone, and say "Nothing is here, so I guess there was no robbery." The testing we use is comparable to the police coming in and dusting all the surfaces to look for DNA that was left behind by the thieves. This form of analysis has been shown to be much more sensitive than the older types of stool tests. 

Below are the results from a stool test showing the levels for normal flora, or the good bacteria. Remember these good bacteria are critical to support proper immune function, detoxification, metabolism, digestion and assimilation of nutrients, neurotransmitter production and hormone regulation. However, if the firmicutes/bacteroidetes ratio is high it can contribute to weight gain and diabetes. Researchers can actually look at stool tests to predict which patients are having trouble with regulating their blood sugars.

Elevated Firmicutes/Bacteroidetes ratio is linked to Obesity and Diabetes


On this page of the report, we can see how the dysbiotic, or bad, bacteria have taken over. Having these infections present can contribute to intestinal wall damage, leading to increased susceptibility to leaky gut and autoimmune disease. These infections can lead to someone having worsening allergies, asthma, frequent illness and infections, gastritis, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), cancer and metabolic disease. Bloating, diarrhea and constipation are common digestive symptoms of dysbiosis.

Dysbiosis - The Bad Bacteria


On this last page of the report, we can see the patient has enough elastase, the enzymes secreted by the pancreas which assist in breaking down proteins. This patient also has normal levels of b-Glucoronidase, which when elevated has been associated with poor estrogen regulation, and has been researched as a possible causative factor for breast cancer and other hormonal issues. This portion of the stool test also shows the patient has an elevated response to gliadin, a protein found in wheat, and is used with other findings to confirm celiac disease. Calprotectin levels are also shown, which indicate the amount of inflammation present in the colon. High levels have been associated with an increased predisposition to or presence of colon cancer. Finally, we have zonulin levels, which when elevated can indicate leaky gut.

Zonulin is associated with "leaky" gut

Correcting the cause

Lab testing can illuminate what it is you are truly dealing with. All too often patients come in after years of getting colonoscopies, endoscopies and basic stool tests, and being prescribed antacids, antibiotics and other medications, with little to no answers or relief from their symptoms. As these conditions go untreated, people continue to suffer from chronic conditions such as frequent coughs, allergies, sinus infections, acne, hormonal issues, weight gain, headaches and migraines, anxiety, depression, autoimmune disease and much more – all stemming from their gut issues! However, when patients finally get the proper testing, they are able to at last see what is causing their health issues and determine the best course of treatment to help them get their lives back.

Our clinic is here to help end your suffering and put you on the road to wellness. So many of us turn to conventional medicine which just covers the problem and often doesn’t offer any real relief. Because medications fail to address the true causes of health issues, many people continue to suffer and in many cases their conditions worsen, leading to more serious problems.

So, where do I begin?

I recommend you consider an approach that tests for and looks to correct the underlying causes of your health problems. To get started, our clinic offers complimentary consultations. Call us today at 734-779-1650, or click below to request an appointment or take our online health evaluation to discover the causes of your health issues.

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