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Gut microbiome: An essential guide to your gut tribe

What is the microbiome?

The 'human microbiome' (also referred to as ‘microbiota’ or ‘flora’) is the tribe of microbes (microorganisms including bacteria, viruses and fungi) that inhabit the human body.

It’s made up of trillions of microbes that live in harmony with us in a symbiotic relationship, meaning that we depend on each other for survival. They live all over your skin, in your mouth, up your nose, in your lungs, on your face, but mostly, in your gut.  

The ‘gut microbiome’ refers to the same community of microbes, but the ones that live in your gut, mainly in your large intestine, or colon.

There are thousands of different species of bacteria that make up the gut microbiota, each requiring different nutrients and environments for growth and each carrying out different jobs in order to keep you healthy.

Gut microbiome

‘All disease starts in the gut’. Hippocrates said this more than 2,000 years ago, but we are only now beginning to understand just how right he was. 

Over the past two decades, research has found that gut health is critical to overall health, and an unhealthy gut microbiome can contribute to a wide range of diseases including obesity, diabetes, rheumatoid arthritis, autism, depression, and skin conditions such as eczema and psoriasis, just to name a few. Many researchers now believe that supporting intestinal health and restoring the integrity of the gut barrier will be one of the most important goals of medicine in the 21st century.

There are said to be two closely related variables that determine our gut health: the gut microbiome - also known as the gut microbiota or gut flora -  and the gut barrier. 

Why is the gut microbiome important?

Your gut microbiome affects so many aspects of your body, but it can be broken down into three root fundamentals:

Immune system

Poor gut health (including bacterial imbalance) can lead to an overactive immune response. This is partly because most of the immune cells in your entire body live in your small intestine, meaning your gut microbiota  has a major impact on your immune system. 

When we lack the  good gut bacteria to regulate our immune system, it becomes overactive and attacks when it shouldn’t. Inflammation is the weapon our immune system uses to attack things it doesn’t like.


An overactive immune system produces high levels of inflammation, which can cause numerous problems as most diseases are linked to inflammation of some sort. Inflammation in the body is also poisonous to good gut bacteria, damaging it and the gut lining. 

Modern-day inflammatory conditions and symptoms include:

  • Fatigue
  • Depression or anxiety
  • Brain fog
  • Insomnia 
  • Acne or other skin conditions
  • Female hormone imbalances
  • Male hormone imbalances 
  • Hypothyroid symptoms
  • Immune system dysregulation and autoimmunity

Nutrient absorption

This inflammation can also damage the gut lining, which then impacts nutrient absorption. If you’re eating a healthy diet but not adequately absorbing the nutrients, the effects can be similar to eating an unhealthy diet. 

Another important role of your gut microbiome is to digest complex dietary fibre. So, the health of your gut microbiota is dependent on you eating enough fibre! The fibre you eat makes its way down to the large intestine, providing food for your good gut bacteria to feast on. When your good gut bacteria  eat fibre, they break it down into chemicals such as short-chain fatty acids which keep your gut happy and healthy.

Gut bacteria

Our gut is home to approximately 100 trillion microorganisms and this constitutes the gut microbiome. These gut bacteria have been living with us all of our lives, and we have only recently begun to understand the extent of their role in human health and disease.

Good gut bacteria

Most people think of bacteria within the body as a cause of getting sick or developing certain diseases, but not all bacteria are bad. You actually have billions of beneficial bacteria living within you at all times. Not only do you live in harmony with these beneficial bacteria, but they are actually essential to your survival and play many important roles in human health.   

One of the main roles good bacteria play in the body is in supporting healthy digestion. Good gut bacteria help your body to digest food and absorb nutrients, and they produce several vitamins in the intestinal tract, including folic acid, niacin, and vitamins B6 and B12. 

They also play a role in supporting the immune system. Good gut bacteria account for roughly 80% of the body’s immune response and help to modulate inflammation. They protect the lining of your intestines, provide a strong barrier against invading “bad” bacteria and toxins and produce acids that inhibit bad bacteria growth and stimulate the immune system to fight them off.

Additionally, they activate neural pathways that travel directly between the gut and the brain, and they produce neurotransmitters like serotonin.

Bad gut bacteria

Bad bacteria can exist in your body at low levels without causing much harm. However, an imbalance between the good and bad bacteria, known as dysbiosis, may contribute to many negative health consequences. This imbalance can be caused by many factors, including age, diet, medications, and presence of an infection or illness.

Bad gut bacteria produce toxins that cause unpleasant symptoms affecting digestion, such as diarrhoea, stomach cramps and bloating. They are also behind a number of serious diseases including pneumonia, meningitis, strep throat, food poisoning, and a variety of other infections when present in high numbers. 

Dysbiosis has been linked to diseases ranging from autism and depression to autoimmune conditions like Hashimoto’s, inflammatory bowel disease, skin conditions such as eczema and psoriasis, and metabolic conditions like type 2 diabetes.  

What is dysbiosis?

Dysbiosis is when there is an imbalance in the number and diversity of bacteria in the digestive tract, and bad gut bacteria outnumber good gut bacteria. Your digestive system contains trillions of bacteria with over 500 different species all playing vital roles in gut health. Ideally, you want most of your gut bacteria to be beneficial types, with fewer of the less beneficial types of bacteria which tend to produce gas and unpleasant digestive issues. When the balance of bacteria becomes disordered, so the less desirable bacteria outnumber the good, then you have dysbiosis. 

Dysbiosis can result in negative effects on your immune system and is associated with many health problems and diseases including Inflammatory Bowel Diseases (IBD), Irritable Bowel Syndrome (IBS), diabetes, obesity, cancer, cardiovascular and central nervous system disorders.

What causes dysbiosis?

Communities that still live hunter-gatherer or rural agrarian lifestyles today have bigger, more diverse gut microbiotas than those living the more common, Western lifestyle.

Some features of the modern lifestyle that directly contribute to an unhealthy gut microbiome include: 

  • Poor diet: Diets high in refined carbohydrates, sugar and processed foods and low in fermentable fibres and diversity
  • Dietary and environmental toxins: BPAs in plastic, heavy metals, etc.
  • Chronic stress or infections
  • Over-exercising
  • Sedentary lifestyle
  • Poor sleep hygiene
  • Hormonal imbalances
  • Medications such as antibiotics, NSAIDs, steroids, antacids, etc.
  • Lack of breastfeeding as a baby
  • Caesarean section (C-section) birth
  • Overuse of antibacterial soap
  • An overly clean environment 

Antibiotics are extremely necessary in some circumstances, and when used correctly are life saving. However, they do have huge implications on gut health. If you do require antibiotics, we can help to restore the balance of your gut flora with probiotics, which are essential when taking antibiotics. The diversity of your gut microbiome following antibiotic use is not recoverable without these interventions.

Research also shows that babies that aren’t breastfed, born by caesarean section or born to mothers with impaired gut flora are more likely to develop bad gut bacteria, and that these early compromises in gut microbiome  may predict a person’s chances of being overweight and developing eczema, psoriasis, diabetes, depression and other health problems in the future.

Understandably, some of these things are out of our control, as we can’t change our own births or how we were fed as infants. Similarly, breastfeeding is not always possible for many women and c-sections have their place in ensuring the safety of both mothers and babies during childbirth. In these situations, it is helpful to understand gut health can be compromised, but equally there are many things you can do to account for these situations. 

What is the gut barrier? 

The gut barrier is like the gatekeeper between our intestines and bloodstream, and controls what is allowed to pass into the bloodstream from our digestive system, and what stays out. This barrier protecting our intestines is only one cell thick and linked together by tight junction proteins. 

When our digestive system is in optimal health, it should be a sealed passageway from our mouths to our back passage. Anything that goes in the mouth and is not digested will pass out the other end. This is actually one of the most important functions of the gut: to prevent foreign substances from entering the body.

When the gut barrier becomes damaged and compromised, gaps begin to form between the tight junctions, resulting in it becoming permeable and leading to a condition known as ‘leaky gut syndrome’ (aka ‘intestinal hyperpermeability’). When you have a ‘leaky gut’, certain particles that should never be able to enter your bloodstream start to make their way through. Since these particles don’t belong outside of the gut (i.e. inside the body), the body’s protective immune system mounts an immune response and attacks them, causing inflammation. This inflammation may cause ‘IBS’ type symptoms such as diarrhoea, stomach cramps and bloating, and even the prescription of medication which may further perpetuate the problem.

What compromises the gut barrier?

Being that the gut barrier is made up of only a single layer of epithelial cells, it is quite delicate and can be easily compromised. 

Some foods can be quite difficult to digest and irritating to the gut, causing damage to the intestinal lining. This can be due to the way the food has been processed or manufactured over the years. Gluten is the main one of these. Gluten contains a protein called gliadin which is quite difficult for us to digest. Undigested gluten can cause an array of digestive problems, and can lead to leaky gut. Gluten can cause an immune response and contribute to inflammation, which affects not only the gut itself, but also other vital organs such as your skeletal system, pancreas, kidney, liver, and brain. Therefore eliminating or reducing gluten in the diet may improve symptoms.

The breach of the intestinal barrier, aka leaky gut, can also be caused by: 

  • Allergens and inflammatory foods including added sugar, GMO foods,  food additives and gluten
  • Chronic stress
  • Toxin overload: drugs, alcohol, antibiotics, pesticides, NSAIDS, BPA
  • Gut dysbiosis

Leaky gut and an unhealthy gut flora are common because of our modern lifestyle. If you have a leaky gut, you are likely to have an unhealthy gut flora, and vice versa. And when your gut microbiome and gut barrier are impaired, you will feel less than 100%.

This systemic inflammatory response can then lead to the development of autoimmunity. While leaky gut and a bad gut flora may manifest as digestive trouble, in many people it doesn’t. It can instead show up as problems as diverse as heart failure, depression, brain fog, eczema/psoriasis and other skin conditions, metabolic problems like obesity and diabetes and allergies such as asthma.

To properly address these conditions, it is important to rebuild a healthy gut microbiome and restore the integrity of your intestinal barrier. This is especially important if you have any kind of autoimmune disease, whether you experience digestive issues or not.

Improving gut microbiome

The first step in maintaining a healthy gut microbiome is to try to avoid all of the things listed above that destroy the gut flora and damage the intestinal barrier.

But that is not always possible, especially in the case of chronic stress and infections. Nor were we able to control whether we were breast-fed or whether our mothers had healthy guts when they gave birth to us.

If you have been exposed to some of these factors, there are still steps you can take to restore your gut microbiota:

Diversify your gut microbiome

The average person is said to only eat around 20 different foods per week, which is far less than the 150 our ancestors are thought to have eaten. Gut microbiome health requires many different types of good gut bacteria because they’re needed to carry out lots of important jobs. To make your tribe of good gut bacteria more diverse, mix up your meals and ingredients daily and fill your plates with as many colours (from fresh whole foods) as possible.

Feed your good gut bacteria

As you have learned, your good gut bacteria love to feast on fibre-rich, fermented foods, so try to eat as many different types of fruits and vegetables, whole grains, nuts, seeds, legumes and beans as possible.

Foods like yogurt, sauerkraut, kombucha, kimchi, miso, kefir and microalgae such as spirulina and chlorella are all high in prebiotics which will give your microbes an extra dose of nutrients.

Address food sensitivities and intolerances

Food sensitivities and intolerances can cause an inflammatory response in your body, so reducing these foods is critical to your gut microbiome health. An elimination diet is pretty simple. All you have to do is eliminate one thing at a time - so you know what it is that bothers you! - and after two to four weeks, bring it back in to see how you feel. The most common food sensitivities and intolerances are to gluten, wheat, dairy, eggs and soy. You also test for food intolerances and sensitivities.

Adopt a gut-friendly lifestyle

It’s key to first cut out or minimise the things that are irritating your gut in the first place. These include sugar, processed foods, GMOs, alcohol, gluten and dairy in some cases, NSAIDs and pesticides.

Beyond poor diet, many other lifestyle factors can greatly increase your level of stress, which can contribute to an unhealthy gut flora. These include overtraining, not sleeping enough, or not including enough relaxation time in your daily life. Focus on healthy daily practices like  gentle exercise such as walking, jogging, yoga and Pilates, mindful practices like meditation, journaling, qigong, yin yoga and breathing techniques and getting enough good quality sleep.

Test your gut microbiome

Doing a stool test can be an accurate way to understand what is causing your gut problems by giving you insight into the health of your gut microbiome. Stool tests can test for things including gut dysbiosis, leaky gut, inflammation and parasites.

Support your gut microbiome with supplements

Certain probiotic strains and gut supporting nutrients like collagen, omega 3 and L-Glutamine can support a healthy gut flora. 

In the gut, probiotics work by inhibiting the growth of bad gut bacteria and encouraging the growth of natural friendly bacteria. They also produce certain vitamins and short chain fatty acids which are known to be beneficial for your health.

Not all probiotics are the same and some strains have been shown to be more effective than others for treating certain conditions. The most common probiotics that have been found to provide health benefits belong to groups called Lactobacillus and Bifidobacterium. Other bacteria may also be used as probiotics, as well as some yeasts such as Saccharomyces Boulardii.

Collagen helps form connective tissue and therefore “seals and heals” the protective lining of the gastrointestinal tract. Studies have found that in people with inflammatory bowel disease, serum concentrations of collagen are decreased (1). Because the amino acids in collagen build the tissue that lines the colon and GI tract, supplementing with collagen can help with gastrointestinal symptoms and disorders, such as leaky gut syndrome, IBS, acid reflux, Crohn’s disease and ulcerative colitis.

Omega 3 can modulate the gut-immune system thanks to the nourishing properties of essential fatty acids (PUFAs). Omega 3 supplementation can be used to prevent and alleviate intestinal diseases and reduce inflammation (2).  

L-Glutamine is an essential amino acid supplement that has anti-inflammatory properties and is necessary for the growth and repair of your intestinal lining, therefore important for digestive health. L-glutamine acts as a protector, coating your cell walls and acting as a repellent to irritants (3).


Your gut microbiota is malleable and changes day to day, so can be affected, positively as well as negatively, by so many factors. 

Poor gut health is tied to nearly every disease there is in some way, because this is where much of our immune system lives and where inflammation often begins. 

There is also a lot you can do to improve your gut microbiome and prevent a lot of chronic conditions we are seeing today. By improving your diet, eating plenty of anti-inflammatory foods and probiotics, lowering stress, and exercising regularly, you can support your body’s microbiome and improve many aspects of your health. 

Take good care of your gut now and you will reap the benefits for years to come.






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