When we hurt ourselves or contract a virus or a bacteria, our immune system triggers the defense mechanism called inflammation.

Immune System

I think our immune system is amazing. At the slightest sign of danger, it acts promptly by releasing a variety of proteins to fight off invaders. It even gets rid of damaged cells and helps the body heal itself. When we hurt ourselves or contract a virus or a bacteria, the immune system triggers the defense mechanisms called inflammatory processes. In all inflammation, a little redness, swelling, or fever shows up in the first few days. Those physical symptoms are signs that the immune processes are doing their jobs.

Innate System

Our immune system has two sub-systems. One is the innate system (IIS) and the other is the adaptive system (AIM). The innate system is the first-line responder. It is formed by white blood cells including macrophages, which are a special type of leukocytes. The main function of a macrophage is to engulf and digest pathogens, such as cancer cells, microbes, cellular debris, and foreign substances. There are macrophages in all types of tissues.

Adaptive System

The adaptive immune system, also known as acquired immunity, is composed of specialized, systemic cells that eliminate or prevent the growth of specific pathogens. Unlike the innate system, which is pre-programmed to react to a wide array of common pathogens, the adaptive creates antibodies, or immune memory, after an initial response is given to a specific foreign body. Adaptive immunity can provide long-lasting, or even life-lasting, protection, as in cases of measles and rubella, being the basic principle of vaccination.

Inflammatory Markers

When the innate system is triggered, it releases defense molecules in addition to the white blood cells. One of them is the C-reactive protein – CRP. Produced by the liver, the CRP is normally found at low levels in the bloodstream. When there is some inflammation going on, the liver releases more of this protein. The main role of PCR is to activate macrophages. Interleukin-6 (IL6) is another defense molecule. It’s a special cytokine (protein and signal molecule) that is secreted by white blood cells when the innate immune system is activated. Therefore, CRP and IL-6 are good inflammation markers that can be easily tested by blood work.


For our innate immune system to be successful, there needs to be a balance between the amount of pro-inflammatory and anti-inflammatory molecules in the body. When there is an imbalance, a large amount of pro-inflammatory molecules flood the bloodstream, and inflammation becomes chronic. For yet unknown reasons, when chronic inflammation is in place, the immune system begins to attack healthy cells along with the diseased ones. And that’s when trouble can start.

Mental health

In the brain, like in the rest of the body, there are several types of specialized immune cells. When there is some sort of damage to neurons, like infections or injuries, these cells spring into action. As Roger McIntyre, a physician and psychopharmacologist at the University of Toronto says, the inflammatory system is key to keeping the body and brain in top shape. However, if the brain has too many pro-inflammatory molecules, the neural circuits in some regions related to arousal, fear, and emotions may be altered. As Dr. Drew Ramsey MD states in his book Eat to Beat Depression and Anxiety, “Thanks to dozens of groundbreaking studies, we now understand that chronic inflammation has a hand in depression and anxiety disorders”.

Probable Causes

Unfortunately, there are several causes of chronic inflammation. Some indisputable are stress, smoking, pathologies, sleep deprivation, environmental toxins, sedentary lifestyle, social isolation, hormonal imbalance, and obesity. All of that can lead to an imbalance in the release of pro-inflammatory and anti-inflammatory molecules. As all inflammation leads to loss of cells, it endangers key systems and circuitry.

Chronic Diseases

According to functional physician Dr. Tom O’Bryan, inflammation is at the root of practically all diseases. However, the development path of chronic inflammatory diseases has 5 pillars: genetics, environmental triggers, dysbiosis, leaky gut, and inflammation. Chronic inflammatory disease develops over time when all pillars are present. It can take 10 to 20 years for the first symptoms to appear.

Functional Medicine Approach

As we have no control over genetics or inflammation mechanisms, we are left with 3 courses of action to prevent the development of chronic disease: environmental triggers, dysbiosis, and intestinal permeability. Dr. O’Bryan uses a multistep process, referred to as the 5R Framework, to support gut health and help heal leaky gut. The steps are Remove, Replace, Reinoculate, Repair, and Rebalance. It entails removing inflammatory foods, replacing enzymes and prebiotics in the GI tract, reinoculating the gut microbiome with probiotics, soothing and repairing the gut lining, and rebalancing the client’s holistic health.

Leaky Gut

The gut lining is made up of only one layer of cells. The over 2,000 strains of bacteria living inside our gut are the ones protecting that thin barrier. When there is dysbiosis or imbalance of good and bad bacteria, the intestine’s wall becomes exposed and susceptible to damage. Therefore, common environmental factors, such as medication, alcohol, and stress, can cause a cell junction to become loose, creating a condition known as leaky gut. Pathogenic bacteria or partially digested molecules can enter the bloodstream through these gaps. What happens next is the activation of the innate immune system causing inflammation.


Changes in diet can help prevent or reverse chronic inflammation in two ways – rebalancing the innate system and strengthening the gut microbiome. Elimination of gluten and lactose is usually the first step since they are highly inflammatory. Both are long, complex protein chains that when noticed in the bloodstream trigger the IIS. Eliminating sugar is essential as well since, among other harms, sugar feeds bad bacteria. Increasing the intake of anti-inflammatory foods is one way to strengthen the immune system. Foods in this category are those rich in vitamins A, C, and D, in minerals such as zinc, omega-3 fatty acids, and polyphenols. To diversify the gut microbiome, prebiotics and probiotics should also be included in the diet.

Probiotics and Prebiotics

I like Dr. Mark Hyman‘s analogy of the gut as our inner garden. PRObiotics are like the seeds we plant in our gardens, some will grow others won’t, so we must keep planting. PREbiotics are the fertilizer, or what we feed the microbiome. Good probiotics are plain yogurt, kefir, sourdough bread, and all kinds of fermented foods. Fiber is the good bacteria’s favorite food so, it’s the best prebiotic out there. If, eventually, weeds, or pathogenic bacteria, grow in our garden, we will do some weeding using a prescription.

In a Nutshell

Inflammation is the root cause of most chronic diseases. All diseases start in the gut, where 70% of our immunity is, thanks to our microbiome. We can certainly reverse inflammatory conditions and strengthen immunity with changes in diet and lifestyle. Research shows that diets high in processed meats, refined carbohydrates (flour, sugar), and trans fats (refined oils and fried foods) have been consistently associated with high levels of inflammatory markers. Individuals with a diet rich in whole foods, fruits, vegetables, and legumes, have much lower PCR and IL-6 levels. So, prevention is key! 

Remember: Good is what makes you feel well!


Read more about the importance of gut Microbiome in Microbiome and Mental Health.

Anna Resende

Anna Resende

Integrative Nutrition Health Coach
Certified by IIN - Institute for Integrative Nutrition

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