Gut Microbiota

Of all the complex components of naturopathic and functional medicine, gut health almost always takes centre stage. It’s not hard to see why. Starting at the mouth and extending to the anus, the gut is the main internal interface with the outside world.

Also known as the gastrointestinal system or digestive system, the gut is a series of hollow organs (and accessory organs including the liver, gallbladder and pancreas) that are connected to one another from the mouth down. The main function of this system is to break down the food we eat, absorb our nutrients and eliminate our metabolic waste products. But the role of the gut goes far beyond simply digestion. 

Within the gut, mainly the large intestines, resides the gut microbiota – a complex ecosystem made up of roughly 100 trillion microorganisms, including bacteria, fungi, viruses, parasites and archaea. The gut microbiota is involved in functions that support the health of the gut lining, but has also got a wider systemic role in health. Beyond aiding digestion, gut microorganisms are responsible for producing vitamins (including B1, B12, folate and K2),  supporting peristalsis (movement of food along the intestines) and are involved in the synthesis of neurotransmitters such as mood-altering serotonin. The gut microbiota also aids the production of a protective mucous layer that coats the gastrointestinal lining, stimulates the growth of intestinal epithelial cells to maintain gut barrier integrity and protects against infection by competing with pathogens. With up to 70% of the immune system located in the gut, the gut microbiota also plays a key role in the induction, training and function of the immune system. 


Gut health and what disrupts it

Hippocrates was right when he said “all disease begins in the gut” over 2000 years ago.  We now know that gut health is critical to our overall health. A disruption to the balance of the gut microbiota, with alteration in number and diversity of gut microflora is known as dysbiosis. Common gastrointestinal symptoms associated with dysbiosis include bloating, abdominal pain, belching, flatulence, acid reflux, diarrhoea and constipation. Other manifestations of dysbiosis include cravings for sugar and carbohydrates, skin rashes and hives. If left untreated, dysbiosis can result in gut inflammation and increased intestinal permeability (‘leaky gut’), which collectively contribute to the onset of a number of chronic diseases, including autoimmune diseases (like type 1 diabetes, inflammatory bowel disease and MS), allergies, eczema, IBS, diabetes, obesity, anxiety and depression.

Common causes of dysbiosis include:

Western style diet – consuming too much processed foods, refined sugar, refined grains, and industrialised seed oils (e.g. canola, sunflower) feeds non-beneficial microorganisms and promotes inflammation which affects gut microbiota. The typical Western style diet is also deficient in dietary fibre, which are prebiotics that feed gut bacteria. This diet starves and kills off beneficial gut bacteria. 

Inorganic produce – eating pesticide sprayed produce, especially the “dirty dozen” crops that have the highest pesticide residue, impacts the health of the gut microbiome. Exposure to glyphosate (a herbicide also known as Roundup), has been linked to a reduction in beneficial Lactobacillus species and overgrowth of opportunistic gut bacteria. 

Antibiotics and other pharmaceutical drugs – Antibiotic use can kill off beneficial gut microorganisms, reducing microbial diversity and causing the overgrowth of non-beneficial opportunistic microorganisms, such as Candida albicans. Recent studies have shown that a single course of antibiotics is enough to destroy the balance of the gut microbiome for up to a year. 

Other pharmaceutical drugs that disrupt the gut microbiome include the oral contraceptive pill, non-steroidal anti-inflammatory drugs (NSAIDs) like nurofen and proton pump inhibitors including Omeprazole, commonly prescribed for acid reflux.  

Chronic stress – Stress affects gut motility and stomach acid levels, which contributes to dysbiosis. Catecholamines, including norepinephrine released during the stress response, alter gene expression of certain gut bacteria, which can lead to dysbiosis. 

Gut Infections – the gut microbiota is affected by pathogenic gastrointestinal infections, including both acute and chronic infections with bacterial, viral, parasitic and fungal pathogens. 


How to improve the balance of the gut microbiome

Healing dysbiosis and rebalancing the gut microbiome to improve gut barrier function requires a holistic approach of dietary adjustments, lifestyle changes and in some cases herbal medicine and supplementation. Below are some easy changes to improve the balance of gut flora. However, more targeted treatment under the guidance of a naturopath may be required. 

  • Eliminate refined grains and refined sugar to regulate the gut microbial balance by eliminating unhealthy sugar-eating microorganisms. 
  • Avoid non-organic produce, particularly grains and the dirty dozen list of fruit and vegetables. 
  • Eat more fibre-rich foods and resistant starches that fuel beneficial gut bacteria. Include whole food plant sources such as green leafy vegetables, carrots,  kumara and other root vegetables, garlic, onions, unripe bananas, flaxseed and oats. 
  • Include fermented foods in the diet such as sauerkraut, kimchi and kefir to provide probiotic cultures that repopulate the gut with beneficial bacteria.
  • Include polyphenol rich foods that inhibit growth of pathogenic bacteria while increasing beneficial gut bacteria. This includes berries, plums, ground flaxseed, dark chocolate, globe artichoke, green tea, apples, almonds and hazelnuts. 
  • Add bone broth to your diet, for gut healing amino acids 
  • Adopt techniques to manage stress such as meditation, deep diaphragmatic breathing, time in nature and exercise.


Written by Shaz Andrew, Naturopath & Holistic Nutritionist