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microbiome and the immune system

May 2024


The Microbiome

  • Microbiome 101
  • The Microbiome & The Immune System
  • Microbiome, Digestion & Metabolism
  • The Microbiome & Your Mood

Rather watch and listen?

Gut bacteria and the immune system

It was 1875 when Louis Pasteur while researching alcohol fermentation, discovered these little critters we now call bacteria. Pasteur, now considered the father of immunology, deduced that microbes would deplete the host of vital trace nutrients essential for their vitality and growth.

Pasteur’s discovery was followed by decades of research to fight the threat of bacteria with vaccination and antibiotics. At the time, the future of the health of the human race was looking very promising. We found the enemy. Now, all that was left was to find a way to eliminate it. 

In 1681, Antonie van Leeuwenhoek examined his stool under a microscope and found “more than 1000 living animals.” 

gut bacteria and immune system

Two years later, he could observe the “animals” living on his teeth. Despite this observation, the research into the human microbiome didn’t take off.


A mystery

I find it intriguing that we have a host of bacteria, viruses, and fungi living in our bodies, yet the body, or rather our immune system, does not attack them. 

The microbiome developed with the human body from the primordial swamp. We live with these critters in a symbiotic relationship. Research shows that the strains, number, and diversity of your biome can predict how resilient your immune system is and how healthy you are. 


How does the microbiome promote immune resiliency?

The microbiome “bought much of the real estate” in your body. When foreign bacteria try to invade their “hood,” the microbiome outcompetes them, meaning it prevents them from invading and settling in the tissue. 

Your immune system superpower – the mucus

Your microbiome plays a vital role in developing the mucus layer, the body’s first frontier. The mucus is a physical boundary that traps pathogens and eliminates them from the body. It also contains immune cells that are trained by your microbiome and that communicate with it.

Feeding your bacteria is in your best interest

The microbiome snacks on the fiber and resistant starch in your food and produces short-chain fatty acids, an anti-inflammatory compound.

Calm down your horses – microbiome taming the immune system

Your adaptive immune system contains pro-inflammatory and anti-inflammatory cells. Inflammation, although a healing mechanism, can get out of hand and damage tissue. We got a reminder of how inflammation can wreak havoc on tissue in 2020 when people who got sick with COVID passed because of a cytokine storm, which is inflammation that gets out of hand. The role of anti-inflammatory adaptive immune cells is to keep inflammation at bay. Your microbiome reduces the immune response in order to prevent the body from attacking it. The microbiome does so by stimulating the production of anti-inflammatory, immune cells.

A balancing act

You might want to think about your microbiome as a second immune system that keeps your immune system on its toes. Your immune system can’t go into a complete relax mode because there are proteins in the body that are not “self,” yet the immune system learned to live with these “not self” proteins under an agreement that benefits both the body and the microbiome.

The epidemic of absence

In his book “The Epidemic Of Absence,” Author Moises Valasquez Manoof documents the reduction in infectious disease and the steep rise in autoimmune diseases and allergies in places where cultures moved from frequent exposure to soil and farm animals to city life. 

He explains how hygiene awareness and practices help reduce mortality due to infectious diseases. At the same time, less exposure to microbial life leads to a “lazy” immune system. 

Modern medicine throws the baby with the bathwater by pushing vaccination for non-life-altering diseases or antibiotics for conditions the body could overcome with rest and hydration. Research shows that the number and variety of microbiomes reduce the closer you get to modern Western culture, especially big cities. 

The seeds for science as we know it today were planted in the 17th and 18th centuries. At the time, the mindset was that nature was given to man to tame and control. It might be time for us to see ourselves as equal participants in the miracle that is nature. We are dependent on a healthy ecosystem in and outside of our bodies. 


To sum it all up, your microbiome increases your immune resiliency by:

  • Preventing pathogens from “settling down” in your tissue
  • Producing short-chain fatty acids that are anti-inflammatory.
  • Stimulating the production of anti-inflammatory immune cells.
  • Increasing mucus production
  • Keeping your immune system on her toes. 

A holistic approach to allergies and autoimmune conditions takes into account the role that the microbiome plays in modulating the immune system. Feeding the microbiome is an essential part of a care plan that supports people who struggle with these conditions.


Struggling with an inflammatory condition?

I can help!


Now that you are convinced that a balanced microbiome is important for reducing inflammation, what can you do about it? The Epidemic Of Absence is a 6-week program that teaches a four-step protocol for rebooting your microbiome.

It’s a lot!
But that is why I am here.
Need help to figure out the details? Do you need support while implementing an inflammation-free lifestyle?
Let’s chat!
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Disclaimer: This document is for educational and informational purposes only and solely as a self-help tool for your own use. I am not providing medical, psychological, or nutrition therapy advice. You should not use this information to diagnose or treat any health problems or illnesses without consulting your own medical practitioner. Always seek the advice of your own medical practitioner and/or mental health provider about your specific health situation. You can view my full disclaimer here.
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