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The Gut Microbiome And Its Role In Immune Health Explained

The Gut Microbiome And Its Role In Immune Health Explained

The Gut Microbiome And Its Role In Immune Health Explained

We now know that the health of our gut microbiome is linked to our overall health and more and more research is revealing the extent of its importance for our immune system. In fact, about 70% of the body’s immune system is actually located in the gut, meaning that taking care of the good bacteria in your gut is vital to staying well.

How do you know if you have a weakened immune system?

There are several signs that tell us that our immune system is not where it should be. These include:

  • You always have a cold.
  • Your stress levels are high.
  • You’re always tired.
  • Your wounds heal slowly.
  • You have frequent infections.


  • You have gut problems. If your gut microbiome isn’t balance and healthy, neither will your immune system. More bad than good bacteria can leave you vulnerable to viruses, chronic inflammation and even autoimmune disorders.

So, what exactly is the gut microbiome?

The gut microbiota is the population of bacteria, viruses, and fungi living all along our intestines. The composition of this population is determined by our DNA. We first encounter microorganisms when we are born as we travel through the birth canal and through the ingestion of breast milk. Whichever microbes our mother has, is initially what we will have. As we grow and get older, being exposed to the environment and the type of diet we have will change our microbiome to be one that keeps us healthy or put us at risk of disease.

As we know, there are good bacteria and bad bacteria. There are also some that are both helpful and potentially harmful. The good bacteria crowds out potentially harmful bacteria by competing for space and food and producing bacteriocins, which are antimicrobial molecules that kill harmful bacteria. [1]

When we are healthy, the good and bad microbes coexist without problems. But if there is a disturbance in that balance brought on by infectious illnesses, poor diet or the prolonged use of antibiotics or other bacteria-destroying medications, dysbiosis occurs, stopping these normal interactions. As a result, the body may become more susceptible to disease. [2]

Dysbiosis of gut microbiota has been closely linked to several diseases, such as obesity, type 2 diabetes, hypertension, necrotizing enterocolitis, and inflammatory bowel diseases. [3]

The contents of your intestinal microbiome are either pathogenic, beneficial and both pathogenic and beneficial. In the microbiome, you will find:

  • Bacteria – single-celled organisms with a unique internal structure. Humans and other multicellular organisms are eukaryotes, which means our cells have distinct nuclei bound with a membrane. Bacteria are prokaryotes which means they don’t have organised nuclei or any other membrane-bound organelles. [4]
  • Yeast – Candida is a type of fungus or yeast which grows all over the human body, especially in warm and moist areas like the mouth, stomach and vagina.
  • Fungi – capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). [5]
  • Viruses – More than 140,000 different viruses live in the gut, one of which is bacteriophages, which are a type of virus that infects bacteria. They play a vital role in regulating gut bacteria, which have a wide range of effects on our health.
  • Archaea – these are microbiota responsible for methane production, which can be measured in clinical methane breath analyses
  • Helminths –endo-parasites that are classified into 2 major groups: the nematodes (round worms) and platyhelminths (flatworms), with the later subdivided into trematodes (flukes) and cestodes (tapeworms) [6]
  • Protists – Also known as eukaryotic microbes, protists in the gut influence health and disease. They are usually considered parasites, but some are beneficial.

The composition of your gut microbiome

The gut is made up of three components – the mucosal layer, the epithelium and the lamina propria – these are the three main hurdles pathogens need to overcome to reach the gut itself and regulate the immune response.

Mucosal layer

The mucosal layer is the first in line for physical defence. This mucus barrier coats the inside of the gastrointestinal tract, providing a physical and biochemical barrier that prevents harmful microorganisms, digestive enzymes and acids, microbial by-products, digestive food particles and toxic substances from entering the gut and allowing beneficial nutrients to pass through.

Research shows that if you don’t get enough fibre in your diet, this mucous barrier will be eroded, making you more susceptible to disease-causing bacteria.


In addition to the mucosal layer, the epithelium, a network of tight junctions, also provides a physical protective barrier for the gut. The epithelium is regulated by a meshwork of proteins that orchestrate complex biological function such as permeability, transepithelial electrical resistance, and movement of various macromolecules. [7] It transports fluid and senses and responds to microbial signals. Most of the cells are enterocytes, which transport fluid and absorb molecules from the gut.

Lamina propria

The lamina propria lies beneath the epithelium and connects the epithelium to the muscularis mucosa. Much like the mucosa layer and the epithelium, the lamina propria provides an important barrier for unwanted microorganisms and pathogens. Most of the intestinal immune cells are found here. These cells orchestrate gut immune system by communicating with one another through cytokine production or cell-cell contact. There are numerous CD4+ T cells in the lamina propria, most of which are effector or memory T cells. [8]

How does the gut microbiome impact your immune health?

The gut microbiome interacts with and affects our immune cells in the lamina propria. So, if the bacteria in your gut is healthy and diverse, your gut’s immune cells will be supported. They produce substances called short chain fatty acids (SCFAs), primarily butyrate, propionate and acetate which reduce inflammation and in turn, support and boost our immune systems.

Additionally, when the tight junctions in your intestinal wall break apart, toxins and unwanted microbes pass through the mucosa layer, epithelium, and lamina propria and into your bloodstream. This is called leaky gut and can be caused by poor diet, stress, infections and toxins.

Your immune system identifies these as pathogens and attacks them, causing the following symptoms:

  • Digestive issues, such as gas, bloating, diarrhea, or irritable bowel syndrome (IBS)
  • Brain fog, difficulty concentrating, or ADD/ADHD
  • Skin issues, such as acne, eczema, or rosacea
  • Food allergies or intolerances
  • Mood imbalances, such as anxiety or depression
  • Diagnosis of chronic fatigue or fibromyalgia
  • Diagnosis of autoimmune disease, including Hashimoto’s thyroiditis, lupus, celiac disease, psoriasis, or rheumatoid arthritis [9]

How you can keep your immune system healthy through your gut

Eating a nutritious diet will keep your gut microbiome healthy and your immune system strong. Some of the ways you can eat well for your gut include:

Eat fibre – fibre stimulates the growth and diversity of good bacteria in the gut. Fruits, vegetables and wholegrains are a great source of fibre.

Eat probiotics – probiotic foods include fermented foods like yogurt, kimchi, sauerkraut and kombucha are key in increasing healthy gut bacteria.

Eat prebiotics – probiotic foods also encourage good bacteria to flourish. These include onions, garlic, dandelion leaves, chicory root, asparagus and Jerusalem artichokes.

Eat lots of plants – eat a wide variety of colourful fruits and vegetables to keep your fibre and nutrient intake high.

Eat healthy fats – olive and avocado oil are good options.

Eat wild-caught fish – aim to eat fish three times a week to increase your Vitamin D intake.

Eat protein at every meal – plant and animal sources are great for your immune system, especially free-range and organic where possible.

Use natural spices and herbs – these are high in phytochemicals.

Avoid processed foods

Chronic inflammation also negatively impacts the health of your gut. Underlying infections, stress, or allergies can trigger leaky gut, cause damage to healthy tissues, impact nutrient absorption and create gut dysbiosis.

With the help of a functional medicine health practitioner, you can take steps to reduce inflammation and restore balance in the body by:

  • Identifying food allergies or sensitivities and taking steps to remove those foods from your diet
  • Avoiding inflammatory foods such as gluten or overly processed foods
  • Identifying and healing underlying infections such as sinus infections or yeast infections [10]

There are also some lifestyle changes you can make to ensure you are maintaining a healthy gut. These include:

  • Exercise often
  • Limit your alcohol intake
  • Get plenty of sleep
  • Consider a probiotic supplement
  • Avoid antibiotics where possible and not necessary

How we can help

As you can see, the health of your gut is directly influenced by your diet and lifestyle. This, in turn, impacts the strength of your immune system. If you are struggling with a poor immunity, it may be time to investigate the state of your gut – you may have imbalances in the microbiome caused by overgrowth of bacteria, yeast, fungus or parasites.

Get in touch with our functional health experts at Advanced Functional Medicine today to find out more about how we can restore the balance of your gut microbiome and strengthen your immune system.

The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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