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What is the gut microbiota? An essential guide to your gut tribe

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

It’s made up of trillions of microbes that live in harmony with you in a symbiotic relationship, meaning you 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 microbiota’ 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 your gut microbiota, each requiring different nutrients and environments for growth and each carrying out different jobs in order to keep you healthy.

The gut microbiota

‘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 microbiota can contribute to a wide range of diseases, including obesity, diabetes, rheumatoid arthritis, autism, depression, and skin conditions such as eczema and psoriasis, to name just 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 your gut health: your gut microbiota and your gut barrier. 

Why is the gut microbiota important?

Your gut microbiota affects many aspects of your body, but it can be broken down into three key roles:

Gut microbiota regulating your immune system

Poor gut health (including bacterial imbalance) can lead to your immune system becoming overactive! Most of the immune cells in your entire body live in your small intestine, so your gut microbiota has a major impact on your immune system

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

Gut microbiota helping to control inflammation

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

Gut microbiota supporting nutrient absorption

The damage this inflammation can do to your gut lining also impacts your ability to absorb nutrients properly. If you’re eating a healthy diet without adequately absorbing the nutrients, the effects can be similar to eating an unhealthy diet. 

Another important role of your gut microbiota is to digest complex dietary 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 like short-chain fatty acids which keep your gut happy and healthy. So, the health of your gut microbiota is dependent on you eating enough fibre! 

Improving your gut microbiota

It’s not always possible to maintain a healthy gut microbiota, especially in cases 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 microbiota

The average person is said to eat only around 20 different foods per week, far less than the 150 our ancestors are thought to have eaten. Gut microbiota 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 

Your good gut bacteria love to feast on fibre-rich, fermented foods, so try to eat as many different types of fruits and vegetables, wholegrains, nuts, seeds, legumes and beans as possible.

Foods like yoghurt, 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 your intake of these foods is critical to your gut microbiota 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 affecting your gut microbiota are gluten, wheat, dairy, eggs and soy. You can also test for food intolerances and sensitivities.

Adopt a gut-friendly lifestyle

It’s crucial to first cut out or minimise the things that are irritating your gut and preventing your gut microbiota working effectively. 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 microbiota. 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 microbiota

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

Support your gut microbiota with supplements

Certain probiotic strains and nutrients like collagen and omega 3 can help to support the proper function of your gut microbiota.

In your 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 good for your gut.

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. 

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 lower (1).  Amino acids in collagen build the tissue that lines the colon and GI tract, so supplementing with collagen can support gut health and help maintain a healthy gut microbiota

Omega 3 also supports the gut-immune system and inflammation levels (2).  

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

There is a lot you can do to improve your gut microbiota and prevent many of the 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 microbiota and improve many aspects of your health. 

In one way or another, poor gut health is tied to nearly every disease there is, because this is where much of our immune system lives and where inflammation often begins. 

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


  1. Serum laminin and collagen IV in inflammatory bowel disease

  2. Associations among Dietary Omega-3 Polyunsaturated Fatty Acids, the Gut Microbiota, and Intestinal Immunity




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