The Microbiome:The Epicenter of Innate Immunity and Immune System Regulation

The human gut microbiome—home to more than 100 trillion microorganisms—is one of the most influential ecosystems in our bodies. In fact, the genes within this community outnumber our own by at least 10-fold, and they aren’t just passive residents. They actively impact key functions like our circadian rhythm, metabolism, how we respond to nutrients, and most importantly, our immune system.

About 90% of the cells in our body are microbial, with the majority living in the gut – if you think about it, we are more microbial than human. These microbes form a self-regulating community that thrives on balance, and this equilibrium is vital for optimal health. As practitioners, it's essential to understand that supporting gut health means supporting the foundation of the immune system.

The idea that microbes are important to human health isn't new—it was first proposed back in 1892 by Albert Doderlein. But it’s only in the last decade that we've truly begun to grasp the immense influence the microbiome has on how our immune system develops and functions. This has huge implications not just for how we help our clients manage their health, but also for our own health journey.

How the Gut Microbiome Develops

It turns out that a person’s systemic immune response throughout their entire life may depend heavily on the gut microbiota and microbes they're exposed to during those first crucial moments of life. Studies have shown that babies born via C-section are more likely to develop asthma and food allergies by the age of three. Why? They miss out on the “gut microbiome seeding” that occurs when a baby passes through the birth canal, which is a natural way to transfer beneficial microbes from mother to child.

Even more fascinating is research showing that babies born at home have a different intestinal microbiota composition compared to those born in hospitals, especially via C-section. The first contact a newborn has—whether it’s with a caregiver’s skin or a sterile hospital environment—can directly affect the kinds of microbes they are exposed to, and this has been linked to later cases of asthma, eczema, and food sensitivities.

Recent findings show that first microbial contact may actually happen in utero. The placenta, once thought to be sterile, harbors its own small but diverse community of bacteria in healthy pregnancies. This early exposure likely plays a role in how a baby’s adaptive immunity and protective immune response develop.

For practitioners, this is incredibly valuable information. It is crucial to support intestinal homeostasis and microbiome health from the very beginning—whether that’s through birthing practices, breastfeeding, or offering probiotic support for both mom and baby.

The Microbiome Educates the Immune System

What’s even more impressive is how the microbiome actually trains our immune system. It’s like the microbiome is a teacher, showing our defense system how to respond appropriately to different challenges. This happens through something called pattern recognition receptors (PRRs), which help the immune system identify what’s foreign and what’s friendly.

Certain gut microbes, as they colonize the gut, produce PRRs that teach immature T-cells to become regulatory T-cells, which are important for immune tolerance. For example, Bacteroides fragilis produces a metabolite called Polysaccharide A (PSA), which has been shown to encourage the immune system to recognize it as a friend, not a foe. PSA even helps trigger the expression of anti-inflammatory genes, promoting balance and reducing the risk of inflammation-related diseases.

While Bacteroides fragilis is usually beneficial in maintaining immune balance, it's important to keep it in check. In the right amounts, it does great things for the immune system, but when the gut microbiome becomes imbalanced or the immune system is weakened, Bacteroides fragilis can turn problematic.

If intestinal bacteria overgrows or moves to places it shouldn’t, it can cause infections or fuel inflammation, even leading to issues like abscesses or systemic inflammation. There is a delicate balance needed in the gut, where commensal bacteria like Bacteroides fragilis support health without becoming a problem.

This is just one example, but it demonstrates why having a diverse microbiome is so important. The more diverse our microbes along the gastrointestinal tract, the more likely our natural defense system will learn to differentiate between harmful invaders and harmless bystanders.

As practitioners, understanding this connection allows us to guide clients toward improving gut diversity through diet and lifestyle changes, knowing it can have a powerful impact on their immune health.

Understanding Gut Health and Immune Function

The commensal microbiota in the gut support and regulate our innate and adaptive immune system, with an incredible 70% of it located in this complex organ. Gut health is important for overall immune function, as the gut serves as the body’s first line of defense against pathogens and harmful substances. A healthy. human gut microbiota allows for adequate nutrition absorption, protection from invaders, and the immune system's constitutive function.

Innate Immunity and the Gut

Innate immunity is closely tied to gut health through the gut-associated lymphoid tissue (GALT), which plays a key role in regulating the gut microbiota. GALT acts as an immune surveillance system within the gut, essential for recognizing harmful invaders such as bacteria, viruses, and toxins that enter the gut and maintaining immune tolerance to harmless substances.

Spread throughout the intestinal mucosa, GALT includes structures like Peyer's patches, isolated lymphoid follicles, and the lamina propria. These components are critical for monitoring and responding to threats. Peyer's patches are clusters of lymphoid tissue found in the small intestine that serve as immune “outposts,” constantly surveying for pathogens and triggering systemic immune responses when necessary.

The isolated lymphoid follicles serve a similar role, detecting foreign substances throughout the intestines. The lamina propria, a layer of connective tissue beneath the gut lining, contains immune cells like macrophages and dendritic cells, which rapidly respond to infections or harmful agents.

Together, these structures help the innate immune system maintain intestinal homeostasis by detecting and addressing potential threats in the gut. By protecting the gut from pathogens and controlling intestinal inflammation, GALT supports the overall function of the innate immune system, ensuring a healthy and responsive immune environment.

Healing and Harmful Factors for the Gut and Immune System

Everything we eat and are exposed to either promotes healing or contributes to harm affecting both gut health and immune function.  Environmental factors from toxins in the air and water to beauty products and fuels can easily disrupt normal gut microbiota composition and create inflammation.

Foods to increase short-chain fatty acids (SCFAs): Fiber-rich foods, including fruits, vegetables, legumes, and sprouted whole grains, are essential for nourishing beneficial gut bacteria. These fibers ferment into SCFAs, which have anti-inflammatory properties and support gut barrier function. Consuming a variety of plant foods helps increase SCFAs needed to reduce inflammation and enhance immune reactions.

Fermented Foods: Fermented foods, such as yogurt, kefir, sauerkraut, and kimchi, provide beneficial microorganisms that help maintain a balanced gut microbiome. These probiotics support immune function by enhancing the gut's defense mechanisms and protecting against pathogenic bacteria.

Anti-Inflammatory Foods: Foods rich in antioxidants, omega-3 fatty acids, and phytonutrients help reduce inflammation and promote a healthy gut environment. Add rainbow foods, leafy greens, and omega 3-rich sources like walnuts, chia seeds, hemp seeds, and flax seeds into your diet. These foods help modulate inflammatory responses, support gut integrity, and enhance immune function.

Teach your clients to make foods like homemade Sauerkraut to feed beneficial microbes and boost their immune system.

Processed Foods: Eating processed foods can negatively alter the gut microbiome and lead to a microbial imbalance or dysbiosis that can trigger inflammation and immune dysfunction. These foods often contain additives and preservatives that injure the cut lining and disrupt the health of the gut. By eliminating processed foods and focusing on whole, nutrient-dense foods, you can help restore microbial balance and support a healthier immune system.

Sugars: Sugar disrupts the balance of your gut microbiota, creating an environment where harmful microbes can flourish. These harmful bacteria feed on sugar, fueling intestinal inflammation and weakening your immune system. Cutting out added sugar helps restore balance in your gut microbiome, promoting better gut health and strengthening your immune response.

Alcohol: Alcohol consumption can damage the gut lining, leading to increased permeability (leaky gut) and systemic inflammation. Eliminating alcohol allows the gut lining to repair and maintain its integrity, reduce inflammation, and support immune function.

Toxins, Plastics, and Chemicals: Exposure to environmental toxins, plastics, and chemicals can disrupt gut health and immune function. These substances can interfere with normal cellular processes and contribute to systemic inflammation. Minimizing exposure to these toxins by choosing organic and toxin-free products helps support gut health and immune system resilience.

Chronic Stress: Persistent stress can impact gut microbial balance and function, exacerbating inflammation and impairing immune responses. Many people do not realize the extent of their daily stress, which can significantly affect gut health. By learning and implementing stress management techniques such as mindfulness, yoga, and deep breathing, we can improve gut health and overall immune function.

Symbiosis Between the Gut Microbiome and Immune System Regulation

The relationship between the immune system regulation and gut microbiome is a symbiotic one. A healthy gut microbiome supports immune function.

Beneficial gut bacteria help in modulating immune responses. They help in the development and function of immune cells, such as white blood cells, and influence the production of immune-regulating proteins. This modulation ensures that the immune system can effectively respond to pathogens while avoiding overreactions that could lead to chronic inflammation and disease.

SCFAs produced by fermenting dietary fibers are crucial for maintaining the integrity of the gut lining. They help to reinforce the gut barrier which prevents harmful substances from entering the bloodstream and causing systemic inflammation. A robust gut barrier is essential for preventing leaky gut syndrome, which can compromise immune function and contribute to various health issues.

A well-balanced microbiome helps regulate immune responses by producing anti-inflammatory compounds and influencing immune cell activity. This balance prevents excessive inflammation which leads to chronic conditions and affects overall health. By supporting the growth of beneficial microbes through diet, we can promote a state of anti-inflammatory balance.

The gut microbiome promotes immune tolerance and teaches the immune system to differentiate between harmful pathogens and harmless substances. This education helps in reducing the risk of allergies and autoimmune diseases. A diverse and balanced microbiome supports this process, so that the immune system can accurately target threats without overreacting to benign substances.

A Deeper Look at the Problem

Here’s where the real concern lies: autoimmune diseases are projected to rise by 3% to 9% each year, with much of this increase driven by the Western fast-food diet. This is more than just a statistic—it’s a warning. 

The highly processed, nutrient-poor foods so common today are fueling inflammation and disrupting the delicate balance of the gut microbiome. In fact, approximately 70-80% of supermarket offerings consist of highly processed products filled with added sugars, unhealthy fats, and preservatives. The consequences? Widespread immune dysfunction, a surge in chronic illnesses, and a population more vulnerable to disease. Reducing reliance on these processed foods is key to restoring gut health and supporting a resilient immune system.

Here's a chart that illustrates the trend of ultra-processed foods in supermarkets from 1980 to 2020, showing a steady increase over time. While this is a general representation, it highlights the growing dominance of highly processed foods in the market, contributing to widespread health concerns. ??

What’s even more troubling is the way we’re approaching the issue. The conversation frequently revolves around genetic susceptibility, almost as if we’re resigned to the idea that we can’t fight the global spread of unhealthy diets. But why is this passivity accepted? We successfully reduced smoking rates through public awareness campaigns, education, and clear warnings. So why aren’t we applying the same urgency to the fast-food epidemic?

Instead of focusing on prevention, the medical system often emphasizes symptom management—drugs, surgeries, and lifelong injections—as autoimmune cases skyrocket. The bigger picture is often overlooked. One expert bluntly stated, “Growing numbers of people will face surgery or regular injections for the rest of their lives. It’s grim for patients and a massive strain on health services. Hence the urgent need for new, effective treatments.”

But as practitioners, we know that managing symptoms alone won’t fix the root of the problem. The truth is that diet and lifestyle play an undeniable role in immune system regulation, particularly through their effects on the gut microbiome.

The fast-food culture is not only damaging the gut but also crippling the immune system’s ability to function properly. Processed foods, high in sugar and low in fiber, fuel inflammation and strip the body of the nutrients it needs to maintain a healthy immune response.

We need to shift the narrative toward prevention, educating ourselves and our clients about the impact of diet and lifestyle on the immune system. If we can tackle these issues head-on—by promoting real food, gut health, and mindful living—we have a much better chance of not only slowing the rise of autoimmune diseases and other chronic illness but potentially reversing the trend altogether.

Am I Missing Something Here?

We already know the root cause of the current health crisis, yet the focus remains on pouring vast amounts of money, time, and resources into treating symptoms instead of addressing immune system health at its core. This backwards approach is exactly why I launched my podcast, ReInvent Healthcare.

As functional healthcare providers, we can’t afford to be discouraged. In fact, we’re more crucial now than ever before. Graduates of my Nutritional Endocrinology Practitioner Training (NEPT) program are at the forefront of the change we desperately need—working to fix a system that perpetuates illness rather than promotes health.

If you’re a practitioner who wants to be part of the solution, who’s committed to supporting clients on their journey to optimal health, I invite you to join us. You are needed now more than ever. 

Understanding the microbiome and immune health is an ongoing journey, 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 let’s be part of the movement to create a healthier future for all.