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The Gut & The Immune System

Updated: Sep 22, 2023

From the desk of Dr. Brkich


What is the Immune System?


Immunology research articles from the NIH National Library of Medicine define the immune system as a collection of cells, chemicals and processes that function to protect the skin, respiratory passages, intestinal tract and other areas from foreign antigens, such as microbes (organisms such as bacteria, fungi, and parasites), viruses, cancer cells, and toxins.

A simple way of understanding the immune system is an arsenal of specialized cells that act as security guards, monitoring and guarding a border, keeping bad stuff out and allowing good stuff in. Bad stuff are things like microorganisms or microbes. Good stuff are things like water, electrolytes, minerals, vitamins, and other essential nutrients in food. A healthy immune system is able to recognize and distinguish good from bad, allowing free passage to everything good, denying entry to microbes and disabling and disarming anything bad such as viruses, cancer cells, and toxins.

Given the explosion of research on the microbiome over the last few years, we are beginning to understand just how complex the immune system really is. Although much still remains to be understood, what is now known is that the function of the immune system is inextricably intertwined with the microbiome in ways that we could never have imagined.

What is the Microbiome?


The NIH National Human Genome Research Institute defines the microbiome as the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment. The microbiome environment in humans is found in places like the gastrointestinal tract, sinuses, ears, nose, throat, vaginal mucosa, and lungs.

The Immune System and the Microbiome

The relationship between the immune system and the microbiome, on the surface, appears to be of an antagonistic and adversarial nature. The immune system and microbiome are separated everywhere by a mucus barrier demarcating the boundary between their separate territories. We tend to think of the immune system as the good guys and the microbiome, teeming with bacteria, viruses, and fungi, as the bad guys. However, the exact opposite is true.

Studies have shown that the immune system cannot function without the microbiome. Immunity ceases completely when the microbiome is removed in animal studies. Human studies have shown that immunity declines when the microbiome is damaged by antibiotics. It is now clear that the immune system is co-dependent on the microbiome. The immune system and microbiome are not separate entities. They function together, in concert, symbiotically and synergistically, as one unified whole, a holobiome.

We have more microorganisms (microbes) living in us and on us than we have cells that make up our body. The microbes along our mucosal surfaces outnumber our immune cells by about two hundred thousand to one. That means that each immune cell is responsible for governing and regulating the activity of two hundred thousand microbes along its border. The immune cells, so hopelessly outnumbered, don’t stand a chance.

Imagine if a lone security guard was in charge of a crowd of two hundred thousand people at a gathering, not all of them having good intentions. An impossible task. The only way that the lone security guard could possibly maintain peace and order in such a large crowd would be if the members of the crowd acted as the neighbourhood watch, sending information to the security guard, identifying the troublemakers, and specifying their location. That is exactly what happens between the immune system and the microbiome. The microbiome is the eyes and ears of the immune system.

The Gut Microbiome Controls the Immune System

The gut microbiome is the master headquarters of all immune functions everywhere in the body, even outside the gut itself. Local immune systems away from the gut, such as the skin, nasal passages, sinuses, and lungs are unable to mount an immune response independently on their own without information and direction from the gut microbiome. Upper respiratory infections and inflammatory conditions can become chronic when a dysfunctional gut microbiome is unable to maintain long distance cell signaling service to these areas.

The Gut Microbiome is an Immune System

The interrelationship between the gut and the immune system goes far beyond the gut microbiome acting as the eyes and ears of the immune system. A healthy, balanced gut microbiome has commensal microbes (friendly bacteria) which have immune properties of their own, just like the immune system does. These friendly bacterial strains, when present, can produce antimicrobial substances that can inhibit the growth of pathogens. One particular commensal bacterial strain has been shown in vitro (in a petri dish) to produce antimicrobial substances that are effective against even the most recent methicillin-resistant Staphylococcus aureus (MRSA) which is resistant to all antibiotics. The antimicrobial compounds produced by these highly potent commensal bacteria do not destroy good bacteria. They instead produce substances that encourage the growth and survival of good bacteria, unlike antibiotics, which kill all bacteria, good and bad.

Other microbes in a healthy, balanced microbiome can do the same with viruses, either destroying the viruses directly, or producing compounds that make it harder for viruses to penetrate the mucus barrier. A commensal bacteria found in a healthy microbiome, Akkermansia muciniphila, restores and regenerates the mucus layer, making it more impenetrable for pathogens and toxins. Other commensal bacteria produce compounds that initiate the healing and recovery phase for repair of damage caused by viral infections.

To summarize, the gut microbiome not only instructs and orchestrates immune system functions, it is an immune organ itself, functioning separately and independently of the immune system. Optimal immunity is not possible in the absence of a healthy, balanced gut microbiome. Optimizing the immune system goes hand in hand with optimizing gut function and correcting microbiome imbalance. The good news is that no matter how imbalanced the gut microbiome, there are ways of bringing it back into balance with appropriate dietary and lifestyle modifications along with targeted supplementation of missing keystone commensal strains that are able to selectively kill the bad guys and encourage the growth of the good guys.

Immune Boosting Remedies

There are many well researched and effective natural immune modulating natural remedies that can be used to improve immune function. However, they cannot overcome an attenuated state of a weakened immune system caused by a dysfunctional gut. Natural immune boosting remedies work more effectively when the gut microbiome is in balance. Correcting a gut microbiome imbalance (called dysbiosis) is too often neglected in the pursuit of improved immune function.

Microbiome Testing

How can we tell if our gut microbiome is compromised? We can make assumptions and inferences based on symptoms, or we can test. I believe it is always best to test rather than to guess. Common gut symptoms like heartburn, indigestion, heaviness after meals, gas, bloating, constipation, or diarrhea are surrogate markers of dysbiosis, or microbiome imbalance. However, an imbalanced gut microbiome may also have no gut symptoms at all. There may be neurological or dermatological symptoms instead, such as anxiety, depression, or insomnia, or skin issues such as eczema, psoriasis, acne, hives, rashes, or itchiness (pruritis). All of these symptoms are correlated with an imbalanced gut microbiome.

A sure sign of dysbiosis is inflammation, which can be measured by a CRP (C-Reactive Protein) blood test. However, dysbiosis can be present even with a normal CRP. The CRP may not begin to elevate until the inflammation reaches a significant threshold level. If you have chronic pain that is relieved by anti-inflammatory medication, you can be sure that you have systemic inflammation, which is highly correlated with gut microbiome disfunction. A major driver of morbidity and mortality worldwide is inflammation caused by a condition called metabolic endotoxemia which is strongly associated with an imbalanced microbiome. Some researchers believe that metabolic endotoxemia is caused by an imbalanced microbiome.

Microbiome Stool Test

New generation genomic sequencing stool testing is now available which uses whole genome sequencing to quantify the composition and diversity of the microbiome of the colon, which is where the majority of the gut microbiome is found. Whole genome stool testing measures the ratios between the various functional groups of good and bad bacteria, overgrowth of pathogenic bacteria, fungi (yeast), and viruses, and most importantly, the diversity and abundance of key health promoting bacteria that produce butyrate, propionate, and acetate, which are short chain fatty acids essential for a host of metabolic processes that promote health and prevent disease. Individualized treatment options can be implemented based on the test results. Everyone is different, with a different microbiome that is unique to them.

For more information about the immune system, the microbiome, or microbiome testing, please give us a call.

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