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Understanding the Microbiome and Whole Body Health

Understanding the Microbiome and Whole Body Health

Experiencing joint pain or having trouble finding your words?

Joint pain and brain fog can be symptoms of microbial imbalance (dysbiosis) in the gut. In fact, many health issues begin in the gut and affect health throughout the whole body.

Your gut microbiome contains trillions of microorganisms, both beneficial and harmful. That’s why understanding your gut and how to keep those microorganisms in balance is critical to good health.

Who’s in Charge of Who?

To understand the gut microbiome, we have to start with the big picture.

Did you know human cells make up only 43% of your body's total cell count, while microorganisms comprise the remaining 57%?1 Yes, that’s right! Your skin and mucosa (a membrane that lines various cavities in the body) are covered by a wide range of microorganisms that include:

  • Bacteria
  • Fungi
  • Viruses
  • Parasites

The majority of these microbes colonize the gastrointestinal (GI) tract. Collectively they are known as the gut microbiome. From within your GI tract, these microorganisms are in constant communication with your immune system.2 As your immune system encounters foreign threats, this crosstalk becomes critically important to your health.

The Role of our Gut Barrier

How does this work? Let’s talk about your gut barrier.

The gut barrier is a multi-layer system consisting of three major components

  • Mucosa
  • Epithelial cells
  • Immune cells3

(Fun Fact: According to a 2014 study, the total surface area of the mucosa in your GI tract is about half the size of a badminton court! )4

The mucosal layer acts as a barrier to prevent harmful, pathogenic organisms from coming into contact with the intestinal epithelial cells (IEC). The role of the IEC is to keep microorganisms, toxins, and undigested food from entering the bloodstream. That third component – your immune cells – discriminates between harmful (pathogenic) and beneficial microorganisms and mounts an appropriate immune response.

Gut Barrier Function – Keeping the Bad Guys at Bay

When it comes to balancing the microorganisms in your gut, your intestinal epithelial cells (IEC) play a critical role. Think of your IEC as panels with tight junctions that make up a fence. Their primary role is to detect what is friend or foe and control what enters the body from the GI tract.

In addition to surveillance and security, this barrier has a semi-permeable quality that aids in the digestion and fermentation of food. This is important for production of essential vitamins, nutrients, and short-chain fatty acids.

When your epithelial cells are damaged, there is a breach in your gut barrier (known as intestinal permeability or leaky gut), allowing undigested proteins, microorganisms, antigens, and toxins to sneak through the tight junctions and circulate in the bloodstream.

Fortunately, immediately beyond this first line of defense is an army of immune cells. The immune cells mount an attack (immune response) against anything harmful that has passed through the damaged barrier.

The downside of this is that if this immune response happens repeatedly, it can result in a vicious cycle of chronic inflammation leading to:

  • Food allergies
  • Joint pain
  • Brain fog
  • Mood disorders
  • Autoimmune disease5

Good Microbiome, Good Gut, Good You

So how do you keep the gut microbiome and your epithelium barrier healthy? Balance is the key!

When your gut microbiome is in balance, it promotes strong epithelial cells with tight junctions that will reliably act as a semi-permeable barrier to shield the inside of your body from the invasion of pathogenic organisms.

A thriving microbiome is vital for the health and well-being of your gut and your body as a whole. Many factors contribute to dysbiosis and the breakdown of the gut barrier including:

  • Chronic stress
  • A diet high in processed foods
  • Microbial infections
  • Overuse of antibiotics and some prescription drugs.

In addition to avoiding processed foods and managing stress, probiotics and botanicals can support microbial balance in the gastrointestinal tract.

Here’s to a balanced gut microbiome and a healthier you!


  1. Gallagher, James.  “More Than Half of Your Body is not Human.”  BBC News, 10 Apr. 2018,


Author Bio:

Alia Khan-Elhady, MSW, FNTP, is Biocidin’s Lead Clinical Consultant. A licensed Social Worker and certified Functional Nutritional Therapist, she brings 15+ years of clinical experience to her role. Fueled by her own health journey, Alia is passionate about microbial balance and getting to the root cause of complex cases. She lives in Calgary, Canada, where she enjoys cooking whole foods from various cultures, inspired by her extensive travels.


This content was originally published on website (March 28th 2022):

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