The strength of your immune system depends on your gut health

I'm Anindita!

I am a Functional Medicine certified Health Coach and AFMC Practitioner. I help women with autoimmune conditions I help women with autoimmune conditions reverse their symptoms with their body as their guide

hey there

Get the free
shopping guide for groceries and snacks

I want it

TOp categories

Reading Time: 5 minutes

More than 70% of your entire immune system resides in your gut.

Gut health and the strength of your immune system are intricately connected. In addition, your gut is also host to trillions of microbes of several hundred species. These microbes play an important role in maintaining optimal health through various mechanisms. More importantly, it acts as a controller of how the immune system in your gut operates.

“All disease begins in the gut”


Hippocrates had said more than 2000 years ago, it was true then and it’s certainly true now! In a way, the gut is like a tunnel that works as an exchange corridor and is actually separate from the rest of the body. It is highly regulated and well guarded to protect us from the outside world.

A symbiotic relationship

At the same time, in order to ensure that nutrients pass through and can be transported to the rest of our body, our gut lining is semi permeable. Any damage to this internal lining can lead to a cascade of health issues. The cells that line the gut wall keep bacteria, undigested or partially digested food and toxins from entering our blood stream. This selectively permeable gut lining only allows digested food particles to enter the body under normal circumstances. 

This exchange corridor is protected not only by our immune system but also by our gut microbes. This is in fact a symbiotic relationship.

Above all, we feed and nourish our microbiome and they keep us healthy in various ways such as

  • breaking down complex carbohydrates
  • producing short chain fatty acids which are necessary for regulating immune function, maintaining integrity of our gut lining, healing
  • producing vitamins and nutrients like vitamin K, B12 and others
  • protecting against pathogens
  • training our immune system to differentiate between friend and foe
  • supporting detoxification

As you can see now, your microbiome has a profound effect on your overall health!

Woman hands making a heart shape on her stomach, healthy bowel digestion, probiotics for gut health

When things go wrong

Any imbalances can cause pathogenic and opportunistic bacteria and fungi to take over. More importantly, this can cause chronic inflammation and intestinal permeability and eventually lead to chronic illnesses like an autoimmune disease. There are many ways that you can end up with poor gut health.

Some of these factors are

  • medications and other medications like antacids and NSAID (Non steroidal anti inflammatory drugs)
  • chronic stress which impairs digestive secretions like stomach acid
  • poor eating hygiene
  • chronic infections
  • poor diet which comprises refined carbohydrates, sugar and processed foods
  • a low fibre diet
  • high toxin exposure from household products and environment

An unhealthy gut can eventually lead to a leaky gut due to a reduction in biodiversity. This often leads to gut dysbiosis where there is an overgrowth of an opportunistic species of microbes. In addition, there can also be ongoing infections that can become chronic due to a weak immune system.

A balanced, diverse community of bacteria helps to keep our immune system balanced and not overreact. When this fails to happen, our immune system can become dysregulated. It can start reacting to food that looks a little like a foreign invader or a pathogen.

In other words, if this is not addressed, our body can become hypervigilant to foods that it should have otherwise tolerated well. This leads to chronic inflammation as the immune system becomes weak and imbalanced over time. You can read more about this here.

Vector illustration set of intestinal bacteria (good bacteria, bad bacteria, opportunistic bacteria)

Gut health and break down of barrier function

70% of our immune system resides in our gut. We have a single cell thick gut lining and underneath that layer lies our gut’s immune system or the “police station”. This is called gut associated lymphoid tissue (GALT) and it is one of the places where our immune cells mature and grow.

We bring the entire outside world into your system through your mouth, it makes sense to have this front line of defense located in your gut. At the same time, when activated, these immune cells release inflammatory chemicals causing inflammation in all parts of our body. This includes our joints, heart, blood vessels, brain and everywhere else! This is why in a root cause, Functional Medicine approach we focus on gut health first.

If we have a breakdown in this lining (barrier function) then we allow toxins, pathogens, highly processed foods, artificial colours, and preservatives to pass through this lining. This causes our immune system to become activated and respond to this threat. This would challenge our ability to have a healthy and balanced immune system.

Immune dysregulation

Source: The School of Applied Functional Medicine

A good healthy immune system is about balance.

When we are faced with any kind of threat, an inflammatory response is helpful initially. But if it goes on long enough, then what should have been a temporary attack leads to chronic inflammation. This chronic intestinal inflammation can lead to breaches at critical junctions in the gut lining leading to enhanced “intestinal permeability” aka “leaky gut“.

Enhanced intestinal permeability (aka leaky gut) is one of the three contributors to autoimmune disease progression. The other two factors are genetics and a weak and imbalanced immune function. This is part of the disease process where we deal with an over-reactive or a hyper vigilant immune system. This leads to ongoing, chronic and rampant inflammation making it difficult to turn off this pro-inflammatory process.

One thing that is important to note at this point is: 

you do not have to necessarily suffer from digestive symptoms to have a leaky gut. 

Enhanced intestinal permeability can also manifest as other conditions like

  • skin disorders like eczema, psoriasis
  • asthma
  • arthritis
  • autism
  • food sensitivities
  • thyroid issues
  • weight loss resistance
  • type 1 and type 2 diabetes and many more

You may understand well by now why a good barrier function is essential for gut health. As disease usually begins in the gut, resilient health also begins in the gut.

As Hippocrates had said,

Everyone has a doctor in him or her; we just have to help it in its work. The natural healing force within each one of us is the greatest force in getting well.


A carefully curated and comprehensive collection of carefully selected books, podcasts, websites, blogs, and other resources from the field of Functional Medicine with a focus on autoimmune diseases

If have been looking to get ANSWERS to questions like

-Why do I have this disease?
-Will I get any better?
-Can anyone help me? Nothing is working
-Is there any hope for me to get my life back?
-I am still waiting for a diagnosis, which direction do I need to move towards?

 then this GUIDE would a game changer for you!

“Autoimmune Disease 101” is a carefully curated and comprehensive collection of carefully selected books, podcasts, websites, blogs, and other resources from the field of Functional Medicine with a focus on autoimmune diseases.

The Functional Medicine model of care for chronic diseases seeks to answer the question “Why do you have this disease” so that you can get personalised and effective care for your unique condition.

+ show Comments

- Hide Comments

add a comment

Notify of

Inline Feedbacks
View all comments

Leave a Reply

Your email address will not be published. Required fields are marked *

Health Coach, author, blogger, podcaster, mom of two and avid reader

Before you get any further....
Hi, I'm Anindita!

I am a Functional Medicine certified Health Coach and AFMC practitioner. I help women with autoimmune conditions reverse their symptoms with their body as their guide

I work with women who want to go beyond symptom management, reconnect with their bodies and learn how to get well and stay well by tuning into their body's wisdom 

Learn more


“Autoimmune healing toolkit for women”

This toolkit will be focusing on the different kinds of tools you can use to create a healing environment like mindfulness, self compassion, journaling, stress management by reconnecting to your body's wisdom.
Sign up for the WAITLIST to receive the ebook when it is published!

Click HERE to sign up!


© Paper Plane 2020. All rights reserved. | Legal | Design by TONIC

Would love your thoughts, please comment.x