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Gut health: a dive into the microbiome

“All disease begins in the gut”.Hippocrates said this more than 2,000 years ago, but we’re only now starting to understand just how right he was. In the last decade, diabetes, obesity, autoimmunity, depression and chronic fatigue syndrome have all been linked to an unhealthy gut. You may have heard the term ‘microbiome’ when reading about gut health, but what exactly does it mean and why is it so important?

What is the microbiome?

The 'human microbiome' (also referred to as ‘microbiota’ or ‘flora’) is the community 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 our skin, in our mouth, up our nose, in our lungs, on our face, but mostly, in our gut.  

The ‘gut microbiome’(‘microbiota’ or ‘gut flora’) refers to the same community of microbes, but the ones that reside in our gut, mainly in our large intestine, or colon.

There are thousands of different species that make up the microbiome, each requiring different nutrients and conditions for growth and each carrying out different jobs in order to keep us healthy.

What is the role of the gut microbiome?

These gut microbes affect hormone production and regulation, make vitamins, influence our immune system, regulate our appetite, metabolism, mood and sleep and even communicate with our brain and nervous system.

The health of our microbiome and its ability to carry out the tasks our body needs, depends on our diet. One of the most important roles of our gut microbiome is to digest complex dietary fiber. The fiber we eat makes its way down to the large intestine, providing food for all of our gut microbes to feast on. When gut microbes eat fiber, they break it down into chemicals such as short-chain fatty acids, which keep our gut happy and healthy.

What can disrupt a healthy gut microbiome?

Communities today that still live hunter-gatherer lifestyles or rural agrarian lifestyles, have a bigger, more diverse microbiota, many of which are completely missing in today’s Western population.

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

  • Poor diet: Diets high in refined carbohydrates, sugar and processed foods
  • Diets low in fermentable fibers
  • Dietary and environmental toxins: Refined vegetable and seed oils, BPA, heavy metals etc.
  • Chronic stress or infections
  • Over training/exercising
  • Poor sleep
  • Hormone imbalances
  • Even some medications such as antibiotics, NSAIDs, steroids, antacids, etc.

What are the consequences of a disrupted gut microbiome?

If our microbiome becomes imbalanced, the consequences can extend well beyond the gut. People with lower gut diversity tend to have worse metabolic health and higher levels of inflammation. There’s a strong connection between the health of our gut microbiota and inflammation, and inflammation is what drives many of these chronic diseases and conditions such as allergies, diabetes, inflammatory bowel disease, metabolic diseases, autoimmune conditions, mental health and obesity.

How to maintain and restore a healthy gut

Our gut microbiota is malleable and changes day to day, so can be affected by everything we consume. This means we have incredible power over many aspects of our health, including gut health, immune health and so much more.

Here are some ways you can improve your gut health: 

Focus on diversity

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. We want as many different types of ‘good bacteria’ in our gut to carry out all of their important jobs so mix up your meals and add a few new ingredients each week, focusing on fresh, colourful wholefoods.

Fibre rich and fermented (prebiotic) foods

As you have learned, our friendly gut bacteria love to feast on fiber, so try to eat as many different types of fruits and vegetables, whole grains, nuts, seeds and beans as possible to help grow a healthy ecosystem. 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 supply of nutrients.

Food sensitivities and intolerances

Food sensitivities and intolerances can cause an inflammatory response in the body, so reducing these foods is critical to healing your gut microbiome. These include foods you are sensitive or intolerant to, as well as alcohol, sugar and some processed foods so try to limit your intake of these. If you feel you are sensitive to any particular foods, you can try an elimination diet yourself. Start by eliminating those which you feel you are reacting to (some of the most common foods are gluten, wheat, dairy, eggs, and  soy), and after two to four weeks, you can bring them back in one at a time and see how you feel.


Beyond poor diet, many other lifestyle factors can greatly increase your level of stress, which can contribute to poor gut health. These include overtraining, not sleeping enough, or not including enough pleasure in your daily life. Focus on healthy daily practices like gentle exercise, yoga, mindfulness getting, good quality sleep, relaxation and breathing exercises.

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