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Gastrointestinal (GI) complaints are among the leading reasons people see their doctors and are one of the most common reasons for hospitalisation. Functional Medicine doctors are taught that if they start treating from the gut out, many gut and body-wide symptoms can be resolved, and conventional medications and treatments avoided.

We all know the phrase ‘You are what you eat’ - Functional Medicine expands on this phrase: ‘You are what you eat, absorb and then do or don’t detoxify.’ A properly functioning digestive system is critical to good overall health.

Below, is a simple protocol for healing your gut and beyond. It's called 'The 5 R's for Gut Health': Remove, Replace, Repopulate, Repair, Rebalance. You can do one step at a time or you can do them all together. It all depends on your unique symptoms, the severity of your symptoms and your time frames. We've added advanced gut tests as a 6'th step if you would like to investigate further, and measure and track your progress. 

Take a read and please email us if you have any questions. As with any health intervention, we suggest you contact your healthcare practitioner before starting anything new.

- Dr Heidi


The best place to start is to remove all gut stressors. A gut stressor is anything that causes stress, inflammation, and imbalance in your gut and, very possibly, intestinal permeability or 'leaky gut'. Stressors include foods to which you are sensitive, intolerant, or allergic; 
imbalances between beneficial and harmful gut bacteria; the presence of harmful gut bacteria, yeasts, and fungi; gut infections and ongoing infections (even if they are elsewhere in your body); raised general inflammation in your body; medications; recreational drugs including alcohol and smoking; environmental toxins; toxic heavy metals; stress; and a lack of sleep.

For around 3 months, or until your gut heals, you may need to remove all the main food allergens from your diet; stop alcohol, smoking and other recreational drugs; stop taking or swap certain medications (only under the guidance of your doctor); treat harmful gut bacteria, parasites and yeasts; treat any ongoing infections elsewhere in your body; remove exposure to environmental toxins; remove dental fillings that contain mercury; remove any other sources of heavy metal exposure; manage your stress; improve your sleep habits; and exercise to encourage sluggish bowels to move.


'Replace' refers to encouraging your gut to start producing normal digestive secretions that might be lacking or limited in your gastrointestinal (GI) environment. You may have reduced GI secretions due to diet, medication, diseases, ageing or other factors.

Depending on your symptoms, you might need to supplement hydrochloric (stomach) acid, digestive enzymes, bile acids, nutrients such as intrinsic factor, vitamin C and zinc-carnosine, mucosal secretion protectants such as phosphatidylcholine and plantain polysaccharides, magnesium and fibre to support bowel movements and general GI health.


'Repopulate' refers to the reintroduction of beneficial gut bacteria to obtain a more desirable balance of microflora and support for these probiotics with prebiotic fibres.

Beneficial gut bacteria are also called 'friendly bacteria' or 'probiotics'. The two main sources of probiotics are probiotic supplements and fermented foods. Once you've added more beneficial bacteria into your gut, you need to feed them to keep them alive. Enter: prebiotics. Probiotics LOVE eating a diverse variety plant food. Think of probiotics like little sea monkeys!

Repopulating your gut is important if you were born via cesarean, have taken more than one antibiotic in your life, are not eating a diet that contains a diverse range of foods, not eating enough prebiotics (lentils, chickpeas, beans, oats, bananas, Jerusalem artichokes, asparagus, garlic, leeks, onions, nuts), drinking too much alcohol, not doing regular exercise, smoking, are exposed to too much stress, are not getting enough sleep...

The latest research is showing how crucially important probiotics are for so many of our body functions, as well as for the treatment of weak digestion, gas, bloating, diarrhoea, constipation, irritable bowel syndrome (IBS), estrogen detoxification, chelation of heavy metals, various skin conditions, weight loss, strengthening of the immune system, and GI tissue (mucosal) health, intestinal barrier function and digestion.

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Oaklands Whey is a very special, handcrafted range of fermented foods made using an ancient process on a permaculture farm in the Free State. 

The main benefit of fermented foods is the production of various strains of probiotics, including the lactobacillus bacteria genus, that boost and replace our body’s populations of healthy bacteria. These bacteria unleash minerals from the food, produce vitamins and enzymes that aid digestion, and provide B-vitamins, omega-3 fatty acids. Many of today’s grocery store varieties of pickles, olives, yoghurt, cheese, sauerkraut, are acidified and pasteurised for extended shelf life. As a result, they no longer contain the beneficial bacteria of traditionally fermented foods.

The Kraut and the Beet Kvass have been lacto-fermented - a process in which natural bacteria feed on the sugar and starch in the food, creating lactic acid which acts as a natural preservative. Caroline uses milk from her 2 grass-fed, naturally-raised cows for the whey. The whole process is very old-school, slow and full of love. 

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'Repair' refers to providing nutritional support for the regeneration, healing and growth of the cells in your gastrointestinal (GI) lining. Factors that support this include adequate overall nutrition and an oligoantigenic diet; glutamine; micronutrients shown to support GI healing (vitamin B5/pantothenic acid, vitamin C, the carotenoid astaxanthin); mucosal lining support (phosphatidylcholine, plantain fruit, licorice); support for GALT function (lactoferrin, lactoperoxidase, whey immunoglobulins); antioxidants known to function in the GI (catechins), and nutritional anti-inflammatories (curcumin, GLA, EPA, DHA). Shoo! That's a lot to get in every a day! Focus on eating a wide variety of fibre-rich, rainbow-coloured plant foods, combination supplements like GI Sustain, good omega 3 oils, reducing stress and avoiding your food allergens. 


Retain the health and function of your GI tract with foundation nutritional support, healthy eating, adequate sleep, regular exercise and stress management.

At this stage of the 5 R program, it's very important to maintain the work you have done above. You might need to continue taking stomach acid support, digestive enzymes, probiotics, glutamine and other key nutrients but you may be able to reduce the frequency. Metagenics GI Sustain is a great maintenance supplement. Stress can wreak havoc on your gut health so I've included a few supplements you can use to manage stress and support your adrenal glands. Explore our 'Foundation 5 Shop' to ensure you are starting on a solid foundation.

- Dr Heidi


You may be able to just start the 6 R program and see which symptoms are left at the end to treat or you may decide to start with a gut test upfront to better personalise your 5 R program. It all depends on your unique symptoms. I'm here to help if you have any questions.

- Dr Heidi

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