“All disease begins in the gut.”

    Hippocrates' assertion made over 2000 years ago that “all disease begins in the gut" is increasingly supported by recent medical research.

    Thanks to advances in DNA sequencing techniques in the past decade, we now acknowledge that the gut and its microbes plays a significant role in health and disease. The way we assess and treat physical and mental illness has changed to reflect what we know and continue to learn about the role of the gut.

    The collection of trillions of microbes made up of dozens of co-existing and competing species, each with its own food preferences and habitat requirements is collectively called the microbiome. Estimated to weigh 1-2kg, the microbiome behaves much like an organ. The number of jobs this 'organ' does is astounding and the more we learn the more we realise how OUR health depends on our GUT health.

    Our gut microbiome not only transforms compounds from food into nutrients our body can utilise, but it also produces neurotransmitters, hormones and countless other chemicals which regulate everything from our basic digestive and absorptive processes to our immune system and our metabolism. When certain species are in over-abundance, we are more likely to suffer the effects of systemic inflammation as seen in insulin resistance, eczema and arthritis. Researchers suggest that alongside plenty of other aspects of health, your microbiome has a profound effect on the way your mind works. Low levels of certain species of bacteria in your gut could be associated with depression or anxiety. 


    Gut dysbiosis and disease

    Gut dysbiosis, when the gut microbiome lacks diversity and/or there's been an overgrowth of certain types of bacteria, is:

    • caused by antibiotic use; alcohol abuse; proton pump inhibitors (reflux medication); chemotherapy and radiotherapy; high stress levels; restricted diets (particularly those which are low in plant food diversity, low in fibre, high in fat, high in protein); and perhaps the consumption of foods containing artificial sweeteners and preservatives/emulsifiers or with glycophosphate pesticide residues.
    • associated with irritable bowel syndrome, small intestinal bacterial overgrowth, Crohn's disease, ulcerative colitis, fatty liver disease, liver cirrhosis, antibiotic-associated diarrhoea, chemotherapy- and radiotherapy-associated diarrhoea, coeliac disease and diverticular disease; 
    • implicated in the development and progression of insulin resistance, diabetes, cardiovascular disease, metabolic syndrome, Alzhemier’s, Parkinson's disease, autism, atopic eczema, asthma, allergies, depression, anxiety, chronic fatigue syndrome, acne and rheumatoid arthritis.

    The holistic management of all chronic conditions (both overt gut conditions and any of the chronic conditions above) must include the thorough assessment and treatment of gut dysfunction and dysbiosis.


    "The holistic management of all chronic conditions must include the thorough assessment and treatment of the gut dysfunction and dysbiosis." 


    Recommended tests to assess the health of your gut

    Gut microbial DNA testing to diagnose gut dysbiosis

    A person's medical and diet history reveals a lot about the likely state of their gut microbiome, however specialised DNA stool testing which profiles the gut microbiome in detail is an increasingly valuable tool. It also enables people to track the effectiveness of therapy besides gut symptoms and other clinical parameters. Whilst microbiome testing is not currently covered by Medicare or private health funds, this is likely to change in the next few years. In the meantime, there are a number of labs which offer testing which is both comprehensive and good value-for-money, for instance Ubiome.

    Breath testing for small intestinal bacterial overgrowth (SIBO)

    SIBO is a specific form of gut dysbiosis which occurs when microorganisms are able to migrate from the colon into the small intestine and/or if they are not removed out effectively due to physiological and/or anatomical anomalies in the gastrointestinal tract. Research into SIBO is relatively new but probably plays a role in IBS for many people.

    SIBO can then be treated with either antibiotics or herbal antimicrobial therapy, however it is important to undertake testing prior to treatment given the effects of such treatment on the microbial balance along the length of the gut. Hydrogen and methane breath testing is a helpful tool alongside detailed a clinical and symptom history. There are pros and cons related to both SIBO breath-testing and treatment which will be discussed with you if we suspect SIBO. Furthermore, post-treatment dietary and lifestyle strategies to prevent relapse are critical to long term SIBO management and co-existing dysbiosis in the large intestine must be addressed as part of management. 

    Urinary testing for intestinal permeability

    Damage and inflammation of the lining of the gastrointestinal tract (small and large intestine), associated with gut dysbiosis, causes intestinal permeability also known as 'leaky gut'. It is common in people with food sensitivities and allergies, irritable bowel syndrome, inflammatory bowel disease, coeliac disease and dermatological conditions such as psoriasis, eczema and acne. There are a number of labs offering a simple urine test for intestinal permeability. The testing helps with treatment recommendations and the efficacy of treatment can be assessed with repeat testing after 3-6 months. Long term outcomes include resolution of gut and skin symptoms.


    Restoring the gut to optimal health

    Addressing dysbiosis, SIBO and intestinal permeability are central to therapy and lead to outcomes not achieved in the past. Whilst every individual's microbiome is unique and the ideal are not known, there are certain characteristics which are known to signify a healthy microbiome. For example, better health is associated with higher microbial diversity. To restore your gut to optimal health, you will be advised on the appropriate testing methods and supported with evidence-based strategies, which may include a combination of specific supplements, antimicrobial treatments, targeted prebiotic and probiotic prescriptions alongside dietary changes.


    Food sensitivities 

    Restoring the gut to its healthiest possible state involves specific dietary strategies. A significant portion of people around the world with digestive sensitivities, such as in inflammatory bowel disease, reflux and irritable bowel syndrome (IBS), which means they must avoid a group of foods which cause a slew of uncomfortable symptoms. This group of foods is collectively known as FODMAPs – a mouthful of an acronym that stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. See the excellent work of the Monash University researchers for more information. Though the carbohydrates themselves don’t cause problems, they are easily fermented in the intestines by bacteria that may cause IBS or IBS-like symptoms in sensitive individuals. Healthy foods as varied as apples, pears, asparagus, garlic, beans, or milk, can be the exact trigger for a digestive nightmare.  Dysbiosis is usually a key contributor but there are often other factors and these should be investigated for long term management with the view to enable the consumption of as varied a diet as possible.

    This certainly doesn’t mean that following a low-FODMAP diet means you can’t eat fibre or feed your microbiome well. While you may not be able to tolerate wheat, you can enjoy quinoa; if cauliflower isn’t cutting it, you can substitute with sweet potatoes; if you can’t enjoy store-bought hummus without blowing up like a balloon, it’s pretty easy to make your own, gut-friendly, low-FODMAP version. 

    Trouble is, it’s hard to determine which foods are triggers for your particular system. To solve this,  a low-FODMAP diet, a strict but temporary diet designed to help you figure out your particular sensitivities. Once you identify which foods are giving you trouble, you can feel more confident choosing and enjoying foods that fuel your body and microbiome without causing unnecessary discomfort.

    The low-FODMAP diet is designed in three phases. The first phase is an elimination diet in which you temporarily cut out all high FODMAP foods for 2-6 weeks. The second phase of the low-FODMAP diet is the “testing phase” in which you systematically reintroduce each of the FODMAP categories of foods to determine which food or foods are causing your symptoms. The third phase is the personalisation phase, where we would work together to come up with a diet that accommodates your tolerances and intolerances. When I work with patients to create that diet, my goal is for them to have as varied a diet as possible, and not to exclude healthy, high fibre foods without reason. 

    If your healthy diet is causing you discomfort or pain, that’s a sure sign you should take stock of what is truly healthy for your particular system. With help, you can find the best way to make sure that you – and your microbes – are thriving.


    With what is now known about the gut microbiome, my treatment approach with ALL patients has changed.”