Personalizing Healthcare From The Inside Out: Learning From The Gut Microbiome

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Illustration of a person's profile with their head and upper neck depicted as transparent, revealing the brain and intricate network of nerves. Surrounding the head are vibrant, abstract representations of neural pathways radiating outward, symbolizing functional lab ranges in neurological studies.

What if the chronic conditions your clients face—from heart disease to type 2 diabetes to autoimmune diseases—are not just rooted in their symptoms but deep within their gut. What if the key to unlocking true wellness isn’t just following another protocol or another treatment plan but is understanding the relationship between the gut microbiome and gene expression?

As a practitioner committed to personalized healthcare, it's essential to grasp how this internal ecosystem influences everything from metabolic disorders to mental health. A vibrant, diverse microbiome is no longer just a wellness buzzword. The science is clear: gut health is not just a part of the equation; it is the equation.

The Microbiome's Role in Chronic Disease

Your client’s health is intricately tied to the state of their gut microbiome. When the balance of beneficial and harmful bacteria is disrupted—whether by diet, stress, lack of sleep, or environmental toxins—it can set off a cascade of health challenges. This imbalance, or dysbiosis, doesn’t just stay in the gut. It often slowly manifests as chronic diseases that your clients struggle to overcome.

One of the most significant consequences of dysbiosis is increased intestinal permeability, commonly known as “leaky gut.” When this barrier is compromised, toxins, undigested food particles, and harmful microbes can escape into the bloodstream, triggering systemic inflammation. This inflammation isn’t just a symptom; it’s the beginning of a host of chronic conditions, including autoimmune diseases, cardiovascular problems, and even metabolic disorders like type 2 diabetes.

But the microbiome's influence goes even deeper. It influences immune system modulation. A balanced microbiome helps maintain immune tolerance, so that the immune system doesn’t overreact to harmless substances—a common pathway to allergies, asthma, and autoimmune conditions.

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Take action now—use tighter lab ranges to significantly enhance patient outcomes. Early detection of imbalances, identification of potential nutritional deficiencies, and personalized care will guide your patients towards optimal health, not just disease management. Choose proactive care today!

The Microbiome and Brain Health

The connection between the gut microbiome and brain is one of the most exciting areas of research, revealing just how much the microbiome influences brain function and mental health. The gut and brain are in constant communication through the gut-brain axis—a network of nerves, hormones, and biochemical signals that bridge these two vital systems.

Your client’s gut bacteria influence the production of neurotransmitters like serotonin, dopamine, and GABA (gamma-aminobutyric acid) which regulate mood, anxiety, and cognitive function.

About 90% of serotonin—often referred to as the “feel-good” neurotransmitter—is produced in the gut. When the balance of gut bacteria is off, it can disrupt the levels of these neurotransmitters and increase the likelihood of depression, anxiety, and other mood disorders.

The microbiome also affects brain health through its impact on inflammation. Chronic low-grade inflammation, usually from gut dysbiosis, is increasingly linked to neurodegenerative diseases like Alzheimer's and Parkinson's. Promoting and maintaining a healthy, balanced microbiome supports gut health and helps to modulate the immune system, reduce inflammation, and protect brain health.

Mood and Mental Health

The link between gut health and mental well-being is so profound that the gut is often called the “second brain.” This connection is largely mediated by the vagus nerve, a nerve that runs from the brainstem to the abdomen and acts as a communication highway between the gut and the brain.

The vagus nerve transmits signals from the gut to the brain and vice versa. A well-functioning vagus nerve helps maintain this communication, so that the brain receives accurate signals about the body’s internal state. This connection influences not just mood, but also stress response, anxiety levels, and overall mental health.

The vagus nerve helps in regulating the parasympathetic nervous system, responsible for the body's “rest and digest” functions. When the vagus nerve is functioning optimally, it promotes a state of calm and relaxation, aiding digestion and reducing inflammation.

If the vagus nerve's function is impaired— due to chronic stress, poor diet, or other factors—the communication between the gut and brain becomes disrupted. This can lead to an exaggerated stress response, increased anxiety, and even depressive symptoms. Strengthening vagal tone, through practices like deep breathing, meditation, and regular physical activity, can help restore balance.

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The Impact of Diet on the Microbiome

Diet is arguably the most influential factor in shaping the gut microbiome. The foods we choose to consume either nourish the beneficial bacteria that support our health or fuel the harmful microbes that can lead to dysbiosis—a state of imbalance within the gut microbiome. Depending on the state of your client's health, you may need to customize your approach to changing their diet.

Nourishing the Microbiome with Fiber and Plant-Based Nutrients

Fiber is the key to a healthy microbiome. It acts as a prebiotic that feeds beneficial bacteria. Instead of being absorbed early in the digestive process, fiber travels to the colon, where it is fermented by gut bacteria. This fermentation process produces short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate, which have powerful anti-inflammatory properties and help maintain the integrity of the gut lining.

Encourage clients to eat a variety of plant foods for different types of fiber—soluble, insoluble, and resistant starch. Each support the growth of different bacterial species.

For example, soluble fiber in foods like chia seeds, oats, beans, and apples, dissolves in water and is easily fermented by gut bacteria. Insoluble fiber in leafy greens and vegetables, adds bulk to the stool and promotes regular bowel movements, increasing bowel transit time which decreases the likelihood of fermentation of other non-fiber substances.

Focusing on Resistant Starch

Resistant starch (RS) in foods like green bananas, legumes, and cooked and cooled rice and potatoes, escapes digestion in the small intestine and instead undergoes fermentation in the colon. This fermentation process supports the growth of beneficial bacteria, including Bifidobacteria and Lactobacillus, needed for maintaining a balanced gut environment.

Bacteroidetes phylum in RS fermentation are not only efficient at breaking down resistant starch but are also important in maintaining gut barrier integrity, modulating immune responses, and synthesizing essential vitamins.

Ruminococcus bromii, another vital bacterium, is a keystone species in RS degradation. It initiates the breakdown of resistant starch making it indispensable. Higher levels of Ruminococcus are associated with an improved gut health profile.

Bifidobacteria also thrive on resistant starch. As they ferment RS, they produce SCFAs which lower the pH of the gut. This creates an environment that is less favorable for pathogenic bacteria and reduces the risk of infections.

Enhancing Microbial Diversity with Fermented Foods

Fermented foods can be very healing for the gut microbiome. Foods like sauerkraut, kimchi, yogurt, and kefir are rich in live beneficial bacteria, probiotics. These foods can help to repopulate the gut microbiome with good bacteria to enhance microbial diversity and stability. A diverse microbiome is more resilient to disruptions, such as illness or antibiotic use, and is better equipped to support overall health.

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Try new recipes like this Kraut and Sprout Salad. Better yet, lead a food demo to teach your community how to prepare fermented food dishes like this one.

The Detrimental Effects of Processed Foods and Sugar

Diets that include processed foods, sugar, and unhealthy fats can have the opposite effect. These foods lack the nutrients that beneficial bacteria need to thrive and instead promote the growth of harmful bacteria. For instance, a diet that includes refined sugar can lead to an overgrowth of yeast and pathogenic bacteria which outcompete the beneficial microbes and disrupt the balance of the gut microbiome.

Artificial sweeteners are not a healthier alternative. They have also been shown to negatively impact the microbiome. They can alter the composition of gut bacteria and even lead to glucose intolerance and metabolic disorders. Processed foods, with their high levels of additives, preservatives, and unhealthy fats, further contribute to gut dysbiosis, promote inflammation, and impair immune function.

Flours, even most gluten-free flours, increase inflammation and can spike blood sugar levels which also creates imbalance in the gut. These flours are often refined and stripped of essential nutrients and fiber that are beneficial for feeding beneficial bacteria. Without these nutrients, the gut environment becomes less hospitable to good bacteria and more prone to harboring harmful ones.

The additives and preservatives found in processed foods can have a detrimental impact on the microbiome. These substances can disrupt the delicate balance of gut bacteria by killing off beneficial strains and allowing harmful ones to proliferate.

The unhealthy fats in these foods, particularly trans fats, heated oils, and excessive saturated fats, have been linked to increased gut inflammation. This inflammation can weaken the gut barrier integrity.

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Epigenetics: How the Microbiome Influences Gene Expression

Epigenetics refers to changes in gene activity that do not involve alterations to the underlying DNA sequence. This is one of the most fascinating aspects of the microbiome. These changes can be influenced by environmental factors.

For example, gut bacteria produce SCFAs like butyrate which modify gene expression by influencing DNA methylation and histone acetylation. These epigenetic modifications can influence gene expression, affecting processes such as inflammation, metabolism, and immune function.

The ability of the microbiome to influence gene expression means that it has a direct impact on your risk for diseases like cancer, diabetes, and autoimmune conditions. Maintaining a healthy microbiome, allows you to potentially modulate gene expression in ways that promote health and prevent disease.

Practical Dietary Interventions for a Healthy Microbiome

To support a thriving microbiome, guide your clients toward a diet rich in whole, plant-based foods, as unadulterated as possible. Some clients do well on raw foods while others need softened and lightly steamed foods.

Encourage a variety of colorful, fiber-rich vegetables, leafy greens, fruits, seeds, nuts, and sprouted legumes and whole grains to promote a diverse and resilient gut microbiome. Daily fermented foods further enhance microbial diversity and stability. On the other hand, eliminating processed foods, added sugars, and heated and unhealthy fats is crucial for maintaining a healthy gut environment.

Practical Steps for Practitioners: Harnessing the Power of the Microbiome

As a practitioner, integrating microbiome-focused strategies into your practice can make a big shift in your clients' health. These simple steps can have an impact on gene expression, brain health, mood, and chronic diseases.

1. Incorporate Gut Health Assessments into Your Practice

Begin by making gut health a routine part of your client assessments. Ask about digestive symptoms, dietary habits, stress levels, previous antibiotic use, and even their birth, as these can provide clues about the state of your client's microbiome.

Consider using a detailed questionnaire to gather more information about your client's digestive health, food intolerances, and lifestyle factors that may be affecting their gut microbiome. This initial assessment can guide your recommendations for diet, lifestyle changes, and targeted supplements.

2. Dietary Recommendations to Support a Healthy Microbiome

Encourage clients to adopt a diet that supports a diverse and balanced microbiome.

Increase Fiber Intake: Only plants have fiber. Emphasize the importance of consuming a variety of fiber-rich, plant foods, such as leafy greens, vegetables, fruits, nuts and seeds, and sprouted legumes and whole grains. These act as prebiotics and nourish  beneficial gut bacteria.

Incorporate Fermented Foods: Recommend slowly adding fermented foods like sauerkraut, kimchi, yogurt, kefir, and miso to their diet. These foods contain live bacteria that can enhance gut microbial diversity. Introduce slowly while also creating a daily habit of including a variety of these foods.

Eliminate Ultra Processed Foods and Sugars: Teach clients to read labels and reduce their intake of processed foods, added sugars, and artificial sweeteners which disrupt the balance of the microbiome, promote the growth of harmful bacteria, and damage the intestinal lining.

Promote a Whole Food Plant-Based Diet: A diet rich in colorful plant-based foods is naturally anti-inflammatory and provides the fiber and phytonutrients that support a healthy microbiome. Encourage clients to eat a wide variety of plant foods to maximize their intake of different types of fiber and beneficial compounds.

A colorful assortment of fresh and healthy foods arranged on a table, including blueberries, carrots, broccoli, avocado, onion, tomatoes, bell peppers, eggs, and various grains and nuts. The variety showcases a balanced diet that aligns with functional lab ranges for optimal health.

3. Stress Management and Lifestyle Interventions

Helping clients understand the connection between stress and gut health is important. Clients want to know why it is important before they make a change. Chronic stress can have a significant negative impact on the gut microbiome by disrupting the balance of beneficial and harmful bacteria contributing to chronic illnesses.

Stress and the Gut-Brain Axis: Stress affects the gut through the gut-brain axis. When you're stressed, your body releases stress hormones like cortisol which alters gut function. This can lead to symptoms like bloating, discomfort, and changes in bowel movements.

Impact on Gut Bacteria: Chronic stress decreases the diversity of gut bacteria, reducing the population of beneficial microbes and allowing harmful bacteria to thrive. This imbalance can weaken the gut barrier integrity.

Stress-Induced Inflammation: Stress can also contribute to inflammation in the gut, which exacerbates dysbiosis and can lead to chronic conditions like irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD) or maybe no noticeable bowel symptoms.

Daily Stress Management: To protect gut health, it's important to incorporate stress management techniques into regular, daily routines. Teach your clients about HeartMath and the importance of taking breaks throughout each and every day. Encourage your clients to practice mindfulness, deep breathing exercises, stretches, journaling, playing in the dirt, what ever feels good to them and allows them to get grounded and reset their mindset.

4. Use of Functional Testing to Assess Microbiome Health

Functional lab testing can be a valuable tool for assessing your client's health and getting a deeper look at their gut health. These tests can help identify imbalances, dysbiosis, and other gut-related issues that may be contributing to chronic illness and affecting overall health.

Comprehensive Stool Analysis

This test provides detailed information about the composition of the gut microbiome, including the presence of beneficial bacteria, pathogenic bacteria, yeast, and parasites. It also assesses digestive function, inflammation, and immune markers. This test is particularly useful when clients present with gastrointestinal symptoms, unexplained fatigue, mental health conditions, or chronic health conditions.

Gut Permeability (Leaky Gut) Testing

If you suspect your client has increased intestinal permeability, this test can confirm it. It measures the levels of zonulin, a protein that regulates intestinal barrier function, and other markers that indicate gut permeability. This test is appropriate for clients with autoimmune conditions, food sensitivities, or chronic inflammation.

Organic Acids Test (OAT)

This test measures metabolites in the urine that provide information about the metabolic activity of gut bacteria and yeast. It can help identify dysbiosis, yeast overgrowth, and other metabolic imbalances. The OAT is particularly useful for clients with mood disorders, neurological symptoms, or chronic fatigue.

SIBO (Small Intestinal Bacterial Overgrowth) Testing

For clients with bloating, gas, or IBS-like symptoms, a SIBO breath test can determine whether an overgrowth of bacteria in the small intestine is the underlying cause. SIBO can contribute to a range of symptoms and is often missed in traditional assessments.

Food Sensitivity Testing

Food sensitivities can contribute to gut inflammation and dysbiosis. Testing for food sensitivities can help identify problematic foods that may need to be temporarily removed from the diet while working to restore gut health. If a client knows or suspects that they are sensitive to many foods, it would be more appropriate to do a well-planned elimination diet like the one we teach in our Nutritional Endocrinology Practitioner Training.  It is important to remove the suspects, clean up the environment, repair the damage, and then add foods back as appropriate.

Personalized Supplementation

Based on the results of functional testing and client assessments, you may consider recommending specific supplements temporarily to support gut health.

  • Probiotics: Targeted probiotic supplementation can help restore a healthy balance of gut bacteria along with other diet and lifestyle changes, especially after antibiotic use or in cases of dysbiosis. Choosing the right strain is important for addressing specific health concerns, such as supporting immune function or alleviating symptoms.
  • Prebiotics: Prebiotic supplements, such as inulin, fructooligosaccharides (FOS), and resistant starch, can support the growth of beneficial bacteria. Adding these into the diet can enhance microbiome diversity to promote long-term gut health and reduce the risk of chronic disease.
  • Digestive Enzymes: For clients with digestive insufficiency, enzymes can improve nutrient absorption and reduce the burden on the gut. These supplements can be particularly beneficial for those dealing with conditions like SIBO or leaky gut, helping to heal the gut lining while optimizing digestion.
  • L-Glutamine: This amino acid supports the integrity of the gut lining and is particularly useful for clients with leaky gut or intestinal inflammation. Use caution with clients with a history of bipolar disorder or severe depression. L-Glutamine can potentially convert to glutamate, an excitatory neurotransmitter, which might exacerbate symptoms of anxiety or mood disorders in sensitive individuals.
  • Herbal Antimicrobials: In cases of SIBO or dysbiosis, herbal antimicrobials like oregano oil, berberine, and garlic can help reduce pathogenic bacteria. However, these should be avoided in clients who are pregnant, breastfeeding, or have a history of sensitive gastrointestinal conditions, as they may cause irritation. These should also not be used longterm.

6. Continuous Education and Client Empowerment

Empower your clients by teaching them about the importance of gut health and how it influences various aspects of their health. Provide them with resources, handouts, articles, or even workshops, to deepen their understanding and encourage them to take an active role in their health.

Stay up to date on the latest research and developments in microbiome science. Consider enrolling in continuing education programs, attending webinars, and participating in professional networks focused on functional nutrition and gut health.

By integrating these strategies into your practice, you can help your clients achieve better health outcomes by addressing the root causes of their health issues. Caring for the microbiome is a powerful tool in your practitioner's toolbox—harness it to create personalized, effective care plans that truly make a difference.

For practitioners, this means that understanding and addressing the microbiome is becoming increasingly essential in achieving optimal health outcomes for clients. By incorporating microbiome-focused strategies into your practice, you can offer more personalized and effective care that addresses the root cause.

Empowering You: The Nutritional Endocrinology Mastery and Certification Program

As the connection between the microbiome and health becomes clearer, the need for practitioners who can navigate this complex landscape is growing. My Nutritional Endocrinology Practitioner Training (NEPT) program is designed to equip you with the knowledge and skills you need to understand the microbiome's role in health and disease, and to leverage this understanding in your practice.

Through this program, you'll learn how to use functional nutrition to support the microbiome, how to interpret and apply the latest research, and how to create personalized plans that address the unique needs of each client. You'll also gain access to a community of like-minded practitioners who are dedicated to transforming health care from the ground up.

If you're looking to deepen your understanding of the microbiome or to expand your practice with cutting-edge strategies, the NEPT program offers the education and support you need to succeed. Together, we can empower clients. Go to inemethod.com to learn more..

Understanding the microbiome is ongoing, but with the right knowledge and tools, you can make a profound difference in the lives of your clients. Join me in the Nutritional Endocrinology Practitioner Training program and be part of the movement to create a healthier future for all.

Thyroid-gland-stethoscope-blood-tube-and-hematology-test-result

Take action now—use tighter lab ranges to significantly enhance patient outcomes. Early detection of imbalances, identification of potential nutritional deficiencies, and personalized care will guide your patients towards optimal health, not just disease management. Choose proactive care today!

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