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How You Can Improve Your Gut (and Overall) Health

By Andy Scott, DHEd, MS, FDN-P, Pn1, NASM-CPT, CCWS

Gut health continues to be a hot topic within health and fitness circles. This week’s post is another post from Andy Scott on the topic. If you missed the first post, be sure to check out What Blood Tests Tell You About Gut Health.

The gut, plays an influential role in overall health as it is exposed to the daily onslaught of hidden stressors. These internal stressors and dysfunctions are, for the most part, often overlooked while external stressors are easy to focus attention on. The hidden stressors are at the root of most common health problems today. Common hidden stressors include:

  • Poor food choices, food sensitivities, and food additives
  • Toxic exposure and overload
  • Medications/drugs such as corticosteroids, antibiotics, and antacids
  • Emotional stress
  • Pathogenic infections such as parasites, bacteria, viruses, and fungus/yeast

Chronic exposure to antigenic, pathogenic, and inflammatory particles and microorganisms are hidden because you or I don’t think about, feel, or see them on a daily basis, but they can irritate the gut and affect function leading to an inflamed state. But how?

Gut Function

Your gut has small, finger-like projections known as villi. The purpose of villi is to increase the surface area of the intestines to absorb nutrients. Villi are covered with hairlike projections known as microvilli which increase the surface area of the gut even more to enhance nutrient absorption.

Between the villi are areas known as the Crypt of Lieberkuhn which help with mucosal secretions aiding in absorption. As exposure to particles and microorganisms irritate the gut, the lining and hairlike projections become impacted.


Inflammation can destroy the tiny hairlike projections affecting absorption of nutrients. Most dysfunction in a compromised gut is due to damaged microvilli, otherwise known as blunted brush border.

Individuals with a blunted brush border tend to produce fewer enzymes, maltase, lactase, sucrose, dextrinase, and glucoamylase. Without these enzymes, they develop many absorption issues including lactose intolerance and difficulties breaking down fats and oils.

Even while eating a healthy diet, those with gut dysfunction may not be absorb the appropriate nutrients which can impact overall health. 

Villus Atrophy/Crypt Hyperplasia

Eventually, the villi  shrink, and the area between the villi known as the Crypt of Lieberkuhn become inflamed. This results in malnourishment and other deficiencies, compromised immune function, and neurotransmitter imbalances.

When the gut has a difficult time overcoming bacteria, bugs and other particles, it can loosen the lining of the GI tract, making it permeable and letting antigenic or toxic loads to “leak” into the general circulation and lymphatic system. This is known as “leaky gut.” This creates an immune response. These once hidden stressors can lead to very noticeable symptoms in various areas of the body that would appear completely unrelated to gut dysfunction.

Autoimmune Disorders

There is a very high correlation between leaky gut and autoimmune disorders. Individuals with various autoimmune conditions have common factors regardless of the type of autoimmune disorder: increased antigen exposure and increased intestinal permeability (Fasano, 2012).

When large particles and bugs (antigens) get through the gut and meet up the antibodies, they form immune complexes. When these immune complexes get into general circulation, it can cause an auto-immune response, as well as congest the liver. This humoral immune response can lead to auto-immune disorders because the body has difficulties identifying what is an actual antigen or immune complex…so it starts attacking itself.

Fibromyalgia is a good example of when the body becomes inflamed. This is often food allergy-related, and can be worsened by secondary nutritional and neurological imbalances (Fasano, 2012). When the gut is compromised, nutrients won’t be properly absorbed. Also, because the gut is the primary place for development and storage of the neurotransmitters serotonin, melatonin, dopamine, and GABA, this can impact pain sensitivity.

A leaky gut is also seen as a potential cause of multiple sclerosis (Nouri, Bredberg, Westrom, Lavasani, 2014). Intestinal dysfunction supports the disease progression by allowing pathogens and particles to cause an increased immune response which reacts against the myelin sheath surrounding the nerves in the brain.

A dysfuncgtional gut allows unwanted food particles into the blood stream, creating a hypersensitive reaction (and antibodies) to foods leading to rheumatoid arthritis (Hvatum, Kanerud, Hallgren, Brandtzaeg, 2006). This increased immune response has been shown to provide an added effect of an autoimmune reaction against the joints causing pain, discomfort, and stiffness.


Not only is a healthy gut important for digestion and absorption of nutrients, but it is also a key factor in a healthy brain. Outside of the central nervous system, the GI tract is the highest concentration of nerve tissue in the body, which has a direct affect on how the brain functions. Changes in the gut can lead to anxiety and depression, perceived pain, learning, and memory (Cryan & Dinan, 2012). As addressed in my first article, roughly 95 percent of serotonin is created and stored the gut. Serotonin facilitates the communication between the gut and rest of the body. Consequently, if the gut is irritated, brain health and function decline similar to the rest of the body.

There is a strong relationship between poor gut function and depression.

Researchers have found that antibodies against toxins from pathogenic microorganisms are higher in individuals with depression, compared to those who do not have depression (Maes, Kubera, & Leunis, 2008). In fact,

major depression and anxiety can be seen in up to 94 percent of people with gut dysfunction.

Oftentimes, migraines and headaches are caused by an imbalance in neurotransmitters like serotonin (Li & Misiewicz, 2003). Serotonin controls the size of blood vessels in your head. When neurotransmitters are low, as occurs in those with gut dysfunction, blood vessels enlarge, creating a tremendous amount of pain, or what we know as migraine headaches.

There is also a significant link between the gut and chronic fatigue syndrome (CFS). Researchers have found a marked difference in the amount of good bacteria in individuals with CFS compared to healthy individuals; there are less good bacteria in those with CFS (Rao, Bested, Beaulne, et al., 2009). The pathogens in the gut communicate through the central nervous system increasing cognitive dysfunction, headaches, muscle tension, and fatigue.


Poor gut health not only limits the quantity of nutrients absorbed which is necessary for optimal, but affects heart health as increased permeability allows for an immune response (Rogler & Rosan, 2013). An elevated immune response can clog arteries increasing the risk for heart disease, induce muscle wasting affecting the heart leading to congestive heart failure, and promoting thromboembolic events which could result in a stroke.

Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Diseases (IBD)

Roughly 20% of Americans will experience bowel disorders within their lifetime (Arrieta, Bistritz, & Meddings, 2006). They are typically characterized by pain in the abdomen, discomfort, bloating, constipation and diarrhea, etc. Although the causes are idiopathic, or not entirely understood, IBS and IBD are often associated with autoimmune conditions, food allergies, and abnormal bacterial overgrowth.

If you have found that you react more to foods, you might want to check your gut. Because your gut is more permeable, more food particles can penetrate the gut and lead to and increased amount of food sensitivities (Arrieta, Bistritz, & Meddings, 2006). This alarms the body’s immune system to rid the undigested food particles, as they are unwanted waste in your blood.


Poor gut health leads to liver congestion. A leaky gut allows for bigger particles, toxins, and antigens to cross into the general circulatory and lymphatic systems placing a greater load on the liver to detoxify the body (Arrieta, Bistritz, & Meddings, 2006). In most cases, the liver is unable to keep up with the constant flow of intruders in the body causing the congestion.


Hormone levels are closely associated with age. As we age, we experience a decline in our sex hormones and thyroid; however, some are experiencing hormone imbalances in their early 20’s. Hormone imbalances seem to be occurring in younger individuals. A poor gut can affect nutrient digestion and absorption, depriving the cells of nutrients needed for daily functions.

Nutrients such as vitamins and minerals, along with fats, proteins and carbohydrates are influential in how the thyroid, adrenal glands, testes, and ovaries function. So when we are deficient in nutrients, we can expect to have potential hormonal imbalances.

Identifying Gut Health

If you haven’t had a Longevity and Vitality Panel, there are other methods to provide insight to potential gut issues. If you have had a comprehensive lab panel, the additional methods will help validate the findings.

Cortisol Testing

The Stress & Resilience test assesses the health of your adrenal glands which are at the center of a stress response. By evaluating the impact of chronic stress on the body, it can provide additional insight on potential stress, hormone balance, along with clues about the location/nature of additional hidden stressors such as gut dysfunction. Typically, an elevated nighttime cortisol is indicative of gut dysfunction.

Basic questions

Another simple, cost-effective method to assess gut health is to reflect on your health. Do you have abdominal pain? Bloating? Constipation? Diarrhea? Gas? Excessiv sweet cravings? Indigestion or heartburn? Headaches after meals? Mood swings? On (or been on) antibiotics? Have a stressful life? These are common questions to shed some light on digestion and gut issues. If you answered yes to any of these, you could potentially have an unhealthy gut.

Stool Testing

Although when a bug is present many health providers will run a stool test (which may or may not reveal a bug), it is important to understand in most cases bugs are the result of a compromised gut. A healthy gut will thwart bacteria through the immune function. If bacteria are thriving, then the gut is not working well and the immune system is likely compromised. You need to address the bug AND heal the gut.

Healing the Gut

Healthy function of the gut is essential to prevent disease and achieve optimal health. The GI tract is one of our first lines of defense against the onslaught of stressors. Healing the gut should be one of your primary focuses.


When you experience gut issues, it is important to remove inflammatory type of foods. In general, avoid alcohol, gluten, corn, soy, dairy, sugar, fast foods, and processed foods as they can be very irritating on the intestinal lining. Food sensitivity testing is another important step in healing the gut. Identifying specific foods that are inflammatory can help eliminate additional stressors. Your food should be organic, free-range, and grass-fed.


Reduced variation of bacteria in the gut is associated with the aforementioned health-related issues. The good news is that research nows shows that exercise is beneficial beyond just burning calories. It can also boost the diversity of bacteria in your gut (Clarke, et al., 2014). People that are more active tend to have better gut flora which helps combat dysfunction and disease.

Stress Management

Controlling stress is a must when trying to heal the gut. When you become stressed the body increases the stress hormone, cortisol, and catecholamines. These can wreak havoc on your gut lining.

Check your environment for relative exposures to chemicals such as cleaning products, insecticides, pesticides, etc. Ideally, eliminate unnatural personal care products such as perfume, hair dye, toothpaste, mouthwash, shaving cream, aftershave, shampoo, conditioner, deodorant, hand cream, lotion, etc. 

Check your hormones

A hormone imbalance can point a finger at potential gut dysfunction. Poor thyroid function can be due to an unhealthy gut as some of the less active thyroid hormone,T4, is converted to the more active thyroid hormone, T3, in the GI tract along with a required enzyme for the conversion called intestinal sulfate. The stress hormone, cortisol, increases as more and more pathogens penetrate the gut lining. This increased stress directly impacts important hormones such as pregnenolone, progesterone, and DHEA which leads to a decreased production of estradiol and testosterone. Lastly, melatonin is a hormone that is produced in the gut. If an individual has an unhealthy, more than likely, their melatonin levels will be decreased.


Because a compromised gut allows food particles, toxins and pathogens to enter the body easily. It’s important to determine if any parasites, yeast/fungus, or bacteria are present. Specific protocols should be followed to rid the bugs. Often times when people have gut issues, they have a difficult time making hydrochloric acid (HCL) so they start to supplement HCL to help with digestion. It is important to make sure you DO NOT have H.Pylori before taking HCL as it helps the bug thrive leading to more serious stomach and GI issues.


Many people take medications today to alleviate other ailments. Unfortunately, antibiotics and other medications can be harmful to the good bacteria in the gut. Antibiotics are very harmful to the healthy gut bacteria. In fact, antibiotic use greatly reduces the diversity of bacteria in the gut and is not recovered after the antibiotics are discontinued (Dethlefsen & Relman, 2011). Antacids are commonly used to fight heartburn. Sadly, they significantly raise the pH in the stomach by reducing stomach acid secretion allowing bad bacteria thrive increasing the risk of infections (Leonard, Marshall, Moayyedi, 2007).


Supplements can be a great holistic way to improve gut health. A basic repair protocol should include:

Digestive Enzymes

Amylase, protease, and lipase aid in digestion of food and improving nutrient absorption. These will help prevent damage to the intestinal lining by reducing the number of undigested food particles passing through the GI tract.

Hydrochloric Acid

HCL helps with digestion of the food. Without sufficient HCL, digestion of food is not as efficient affecting absorption of nutrients. Remember, you must determine if H.Pylori is present. If so, DO NOT use HCL.


Glutamine is an amino acid that has been found to be the primary energy source of the healing intestinal cells.


The men’s and women’s AM/PM multivitamin contains vitamins and minerals that are beneficial in gut repair. Zinc is essential for growth and wound healing, especially in cells that turn over rapidly as those found within the GI tract. Vitamin A is required to maintain the GI tract and also helps in the production of antibodies that protect the gut lining.


N-acetyl-l-cysteine plays an important role in boosting the immune system by helping to replenish glutathione, a powerful antioxidant.


Soothing herbs like deglycerrhizinated licorice and anti-inflammatory herbs such as boswellia and peppermint can help promote gut healing. Curcumin has also been shown to improve gut health.


Probiotics help with the “good” bacteria by crowding out the unwanted, harmful bacteria and yeasts.

Arrieta, M.C., Bistritz, L., Meddings, J.B. (2006). Alterations in intestinal permeability. Gut, 55(10).

Clarke, S.F., Murphy, E.F., O’Sullivan, O., Lucey, A.J., Humphreys, M., Hogan, A. et al. 92014). Exercise and associated dietary extremes impact on gut microbial diversity. Gut, 63(12).

Cryan, J.F. & Dinan, T.G. (2012). Mind-altering microorganisms: The impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience, 13(10).

Dethlefen, L. & Relman, D. A. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS, 108(1).

Fasano, A. (2012). Leaky gut and autoimmune diseases. Clinical Reviews in Allergy & Immunology, 42(1).

Hvatum, M., Kanerud, L., Hallgren, R., & Brandtzaeg, P. (2006). The gut-joint axis: Cross reactive food antibodies in rheumatoid arthritis. Gut, 55(9).

Leonard, J., Marshall, J.K., Moayyedi, P. (2007). Systematic review of the risk of enteric infection in patients taking acid suppression. American Journal of Gastroenterology, 102(9).

Li, B. & Misiewicz, L. (2003). Cyclic vomiting syndrome: A brain-gut disorder. Gastroenterology Clinics of North America, 32(3).

Maes, M., Kubera, M., & Leunis, J.C. (2008). The gut-brain barrier in major depression: Intestinal mucosal dysfunction with an increased translocation of LPS from gram negative enterobacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression. Neuroendocrinology Letters, 29(1).

Nouri, M., Bredberg, A., Westrom, B., & Lavasani, S. (2014). Intestinal barrier dysfunction develops at the onset of experimental autoimmune encephalomyelitis, and can be induced by adoptive transfer of auto-reactive T cells. PLoS One, 9(9).

Rao, A.V., Bested, A.C., Beaulne, T.M., et al. (2009). A randomized, double-blind, placebo-controlled pilot study of a probiotic in emotional symptoms of chronic fatigue syndrome. Gut Pathogens, 1(1).

Rogler, G. & Rosano, G. (2013). The heart and the gut. European Heart Journal, 35(7).

The posts on this blog are not intended to suggest or recommend the diagnosis, treatment, cure, or prevention of any disease, nor to substitute for medical treatment, nor to be an alternative to medical advice. The use of the suggestions and recommendations on this blog post is at the choice and risk of the reader.
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