The Gut Microbiome – What is it and why should we care?

Why is it good to ‘eat the rainbow’ and look after your gut microbiome?  

Our knowledge of the ecosystem living inside us is increasing rapidly, albeit, we may only have revealed the tip of the iceberg.  There are separate microbial landscapes all over the body; on the skin, in the nose, mouth, lungs etc, but today I’m talking about the ecosystem in your large intestine.  Research demonstrates the remarkable connectedness between us, our gut microbiome, and our health outcomes.  My aim, here, is to share a little about what the gut microbiome is, what it does, what happens when it goes wrong and what we can do to look after it.

What is the gut microbiome?

The gut microbiome is often compared to a forest.  An ecosystem with trillions of microbes (bacteria, fungi, protozoa, viruses, parasites) that live within it and communicate with our human cells.  

Although inside our bodies, the contents of the colon (including up to 2kg of microbiome inhabitants, is considered outside, separated from our blood stream and organs by an intestinal barrier 1 cell thick, lined with protective mucus.

The microbiome is partly inherited through natural birth and breast feeding but is largely shaped by your environment and food choices, especially in the first few years of life.  The residents of your microbiome are not permanent but, just a like a city, inhabitants will come and go over your lifetime and according to your dietary and lifestyle habits.  Using stool testing, research has identified some cornerstone species, in recognizable patterns, which may shift slightly on a daily basis but are likely to remain in known ratios to each other in a healthy gut.  Looking at these patterns provides an insight into the health of your ecosystem.

A healthy gut is associated with a diverse, balanced, stable, well-functioning microbial ecosystem within. 

What role is it thought to play in our bodies and why is it beneficial?

The microbiome is thought to influence, for example:

  • Your responses to fats and sugars (the way you break them down).
  • Your weight.  Twin studies reveal that the environmental and microbiome component to weight control is much greater than was believed1.
  • how our genes work (a process called epigenetics)2
  • the functioning of our vital organs3.

No small feat!!  How does it have such an impact?

Through our diet and environment, we feed these organisms and they allow us to thrive by:

  • Producing important biological chemicals like serotonin and dopamine (needed for brain function and to feel good).
  • Synthesizing vitamins (B Vitamins and Vitamin K) to produce energy for our intestinal cells.
  • Protecting us from harmful chemicals (such as chemical substances that are foreign to humans (xenobiotics) including: plant constituents, drugs, pesticides, cosmetics, flavourings, fragrances, food additives, industrial chemicals and environmental pollutants4.
  • Helping support stool consistency and regularity.
  • Inhibiting and killing off harmful bacteria and other nasty bugs.
  • Maintaining a healthy immune system.
  • Providing anti-inflammatory effects through the chemicals they produce. 
  • Supporting the protective mucus coating on the gut walls.
  • Promoting normal peristaltic action in the bowel to keep us regular

When the microbiome is in balance, we call it SYMBIOSIS: a mutually beneficial relationship allowing the gut, brain, and the rest of the body to function healthily – free from disease. 

What happens when the balance is off and what does that mean?

Disturbances or imbalances in gut microorganism communities are frequently referred to as “DYSBIOSIS”.  Here are three scenarios of what that might look like in practice?

  • Too much of the “less beneficial” microbes

A larger presence of these in the gut is the most common imbalance.  An overabundance of typically inflammatory bacteria, or too much yeast (candida albicans is a particularly common and unwelcome yeast in large amounts), are two examples of overgrowth that cause dysbiosis.  An unwelcome virus or parasite can also cause overgrowth imbalance. 

  • Microbial undergrowth can be the culprit. 

It is rarer than the situation above, but sometimes a stool test result shows an under-abundance of all bacteria – good and otherwise.  An under-abundance indicates we need to work on improving the terrain (the gut lining) where the microbes take residence, as well as supporting the growth of the flora we want to encourage. 

  • Your microbiome settles in the wrong place. 

Living microbes are wanted, but we need them to live where they belong, and not take up residence in places where they cause problems. Most frequently, this type of dysbiosis is SIBO (Small Intestinal Bacterial Overgrowth). SIBO occurs when the gastrointestinal microbiome has shifted from primarily growing and thriving in the large intestines (the colon) to taking up residence in the small intestine in too great a number. This tends to cause digestive problems and bloating, but can be silent as well. 

It is now widely understood that disturbance of the complex equilibrium of the gut microbiota is associated with the development of various disorders, including:

  • metabolic disorders (like weight gain or weight loss resistance), 
  • immune disorders (such as autoimmunity)
  • digestive disorders (IBS, ulcerative colitis, Crohn’s disease)
  • psychological/behavioral disorders (depression, anxiety)
  • Asthma
  • Diabetes
  • Arthritis
  • Fibromyalgia
  • Eczema, psoriasis, rosacea
  • Cardiovascular diseases
  • Food allergies

Why might this be happening?

Here are some examples of factors that may disturb this ecosystem and contribute to Dysbiosis4,5.

  • Antibiotics (prescribed medications as well as antibiotics fed to animals we eat)
  • A nutrient deficient diet
  • Prolonged stress
  • Chronic illness
  • Intense, or low levels of exercise
  • Birth control pills/ hormone replacement therapy
  • Age
  • Other pharmaceuticals

What can we do to look after our individual ecosystems?

Here are some areas to focus on to keep your microbiome in balance (please note, at no point do I suggest removing foods or stopping consuming something you enjoy, just don’t forget to feed your microbes with something they like too!!):

  • Fill up on prebiotic foods. This is the fuel to help your beneficial microbes bloom.  These include apples, asparagus, bananas, cocoa, aubergine, flaxseed, garlic, honey, artichokes, legumes, onions, peas, and whole grains. 
  • Don’t forget probiotic foods. These include yoghurt, kefir, kimchi, sauerkraut, tempeh, miso.  These contain live beneficial bacteria, which are not thought to colonize the intestine themselves or change the diversity but have been shown to have other beneficial effects along their digestive journey6.  
  • Think Diversity.  Shop for different colours and varieties of vegetables, fruit, wholegrains and legumes.  Combine a mix at each meal to improve diversity of phytonutrients (plant chemicals shown to support a healthy human body).  Increasing the variety of whole foods you’re eating results in a more diverse microbial colony.  Foods high in fibre will get further down the gastrointestinal tract and interact with your microbes.  Fibre is food for them not for you.  Your microbes extract nutrients and create chemicals from fibrous food which are beneficial for you.  The polyphenols (chemicals found in colourful produce including coffee and cocoa powder) act like rocket fuel, energizing the existing microbes to produce chemicals and vitamins, to support our body and immune system7.  
  • Buy local and in season. Remember that fresh, unprocessed food, that hasn’t travelled the globe is generally higher in nutrient content.  Check out your local market. 
  • Reduce the ultra-processed foods.  Processing can be an important part in the preparation of food to make it edible (think fermenting, canning, drying, freezing, cooking), unless you just want to eat broccoli!  However, there are foods that have been entirely altered, which are usually high in fat and sugar and have undergone industrial processes like hydrogenation (margarine) and contain dyes, stabilizers, flavour enhancers and emulsifiers (some sliced bread, cookies, chips and fast food).  These foods have been shown to support growth of the unbeneficial bacteria who thrive in this environment and contribute to systemic inflammation8. The best meals are those you prepare yourself – keep it simple. When packaged or processed foods are unavoidable (we all live busy lives), look for those with the fewest ingredients, ones that you recognise.  Own brand options often have fewer added extras.
  • Reduce added sugar.  Sugar (glucose) is rapidly absorbed through the small intestine.  Regularly consuming food and drink high in sugar and low in fibre (sweet treats, fizzy drinks) mean no food for your large colon inhabitants and risks encouraging the movement of microbiota to the wrong place.
  • Reduce Alcohol. Consumed in excess, changes microbial composition and affects the integrity of your protective gut wall9.
  • Don’t be so clean!  Look at your lifestyle.  Do you use powerful chemicals around the home to kill everything, including your gut bugs.  Do you get exposure to beneficial bacteria in your local outdoor environment (walking/exercising in nature, gardening, playing with the kids, pets)
  • Find some calm. Ongoing stress is shown to have a detrimental effect on the microbial population.  It is more important than ever to prioritize some time for calm every day.  Reassess your routine, take a digital detox, nurture positive relationships and remember to breathe10.


  1. Zoe. (2022) The more the merrier: why diversity matters for your gut microbiome. project
  2. Manvi, S., Yuanyuan, Li., Matthew, L, Stoll., Trygve, O, Tollesfsbol. (2020) The Epigenetic Connection Between the Gut Microbiome in Obesity and Diabetes, Frontiers in Genetics, 10, DOI=10.3389/fgene.2019.01329
  3. Altveş, S., Yildiz, H. K., & Vural, H. C. (2020). Interaction of the microbiota with the human body in health and diseases. Bioscience of microbiota, food and health39(2), 23–32.
  4. Bajinka, O., Tan, Y., Abdelhalim, K.A. et al. Extrinsic factors influencing gut microbes, the immediate consequences and restoring eubiosis. AMB Expr 10, 130 (2020).
  5. Madison, A., & Kiecolt-Glaser, J. K. (2019). Stress, depression, diet, and the gut microbiota: human-bacteria interactions at the core of psychoneuroimmunology and nutrition. Current opinion in behavioral sciences28, 105–110.
  6. Grazul, H., Kanda, L. L., & Gondek, D. (2016). Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. Gut microbes7(2), 101–114.
  7. Kumar Singh, A., Cabral, C., Kumar, R., Ganguly, R., Kumar Rana, H., Gupta, A., Rosaria Lauro, M., Carbone, C., Reis, F., & Pandey, A. K. (2019). Beneficial Effects of Dietary Polyphenols on Gut Microbiota and Strategies to Improve Delivery Efficiency. Nutrients11(9), 2216.
  8. Zoe. (January 2022) How to identify ultra-processed food and what to eat instead.
  9. Eunjung Lee, E. & Lee, J-E. (2021) Impact of drinking alcohol on gut microbiota: recent perspectives on ethanol and alcoholic beverage, Current Opinion in Food Science, 37: 91-97. 
  10. Dr R Chatterjee. (2018) The Stress Solution. Penguin Random House UK 

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