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Fed up with digestive discomfort? Four steps to gut health

You don’t just have to put up with digestive discomfort, acid reflux or GERD, bloating, diarrhea, constipation, or food sensitivities. Using a Functional Medicine approach, which looks at the root causes of any health issue, it is possible to find the root causes of a gut complaint. Once you know the root causes driver your condition, you can follow a step by step approach to heal your gut. In this article, I’ll explore what that process might look like.

Basically, there are four logical steps to regaining gut health: Remove, Repair, Reseed, and Rebalance. It is possible to do this on your own, and Dr. Ruscio offers a good protocol in his book. However, I would suggest working with a Functional Medicine practitioner such as myself, to provide personalised guidance and support which can be invaluable during this process.

1) Remove

In the Remove phase, we identify and then remove triggers of intestinal inflammation and digestive discomfort.

Candida, a bacterial or protozoa overgrowth, SIBO, Helicopter Pylori, and viruses can all drive gut conditions. These are often associated with an overly reactive intestinal immune system which can, in turn, drive inflammation throughout the body through a permeable intestinal barrier (leaky gut).

A stool test that can be done from the comfort of your home can test for these pathogens. I recommend the GI Map test or the GI 360 test in Australia. These tests analyse the DNA of the microbes in your stool and are therefore very precise. They also include markers for leaky gut, digestive enzymes, secretory IGA, gut inflammation, and short-chain fatty acids, making them very complete tests. Small intestinal bacterial overgrowth (SIBO) testing may also be appropriate depending on your symptoms (bloating with 90 mins of eating is a tale-tale sign).

When working with a practitioner, lab testing isn’t always necessary or within budget. In which case, the approach is based can be based on clinical symptoms, history, and treatment response.

If parasites are found or are likely, then there are a number of options including herbal anti-microbials, specific probiotics, and antibiotics. I work with the first two options but you always have the option of talking to your GP about the antibiotic option.

Particular foods can also be a stressor for some people. This can include trigger foods such as gluten, dairy, added sugar, oxalates, or histamine containing foods. When I work with someone, I always start by looking at their diet, identifying potential trigger foods and looking at the impact of high FODMAP foods. Ensuring enough digestive enzymes and stomach acid production is also vital to digesting our food properly. Food sensitivity testing is an option.

I find the Low FODMAP diet helps many people with IBS. The first phase of the diet removes all high FODMAP foods which may be causing your gut symptoms. After three to six weeks, we systematically re-introduce these foods. This allows us to identify your personal trigger foods that can then be avoided whilst maintain as diverse a diet as possible.

2) Repair

When there’s inflammation in the gut, you can also expect there to be increased intestinal permeability, commonly known as Leaky Gut. A leaky gut allows toxins, larger food molecules, unwanted bacteria, and viruses to enter the bloodstream. Lining the gut, we have the mucosal system which protects us from these threats. 

When foreign substances pass through the gut barrier, the immune system launches an inflammatory response to defend us from these invaders. The associated intestinal inflammation has been linked to a diverse range of symptoms such as food sensitivities, fatigue, brain fog, nutrient malabsorption, and has been linked to diseases in remote organs in the body e.g. kidney, lungs, liver. 

Calming the intestinal immune system, and repair the gut lining is therefore an essential step in regaining gut health.

To heal a leaky gut, you also need to consider your lifestyle such as stress levels, making time for yourself, and getting enough sleep. Getting the nutrients you need to support the immune system lining our gut, as well as repairing the gut wall are important. Foods, which contain these nutrients include bone broth, stewed apples, as well as polyphenol-rich foods such as blueberries, blackberries, purple sweet potatoes, purple carrots. The choice of supplements varies from person to person but could include such as Colostrum, L_Glutamine, and Zinc, probiotics such as Sacchromyces Boulardi or Lactobacillus GG. 

3) Reseed

This phase is all about encouraging a diverse range of ‘good’ gut bacteria. This is vital as, without it, your gut issues are likely to return. Time needs to be spent fixing your gut microbiome. It’s a necessity for ongoing gut health!

We can reseed our guts through probiotics, fermented foods, and also soluble fibres known as prebiotics. Our gut bugs love fiber-rich veggies and whole grains such as flaxseed, chia seed, buckwheat, and other non-gluten containing grains.

By this stage, you should be able to handle more prebiotics than you could in stage 1. Healthy high FODMAP foods and resistant starches can be introduced to feed your ‘good’ gut bacteria. Remember high FODMAP foods are often healthy foods and we are working towards being able to tolerate them.

For probiotics, there a number of options including a Lactobacillus / Bifidobacterium blend, Saccharomyces Boulardii, and soil-based probiotics. Different people can find different types of probiotics effective, and I urge you to experiment with a different type if you are not responding to a particular one. For instance, if you are not responding to a Lactobacillus / Bifidobacterium blend after a 4-6 week trial, then try a soil-based probiotic. When trialing a probiotic like this, you are looking for a reduction in your personal symptoms and noticing how it makes you feel. People often find a combination of these probiotic types can be effective.

Saccharomyces Boulardii and Lactobacillus GG have also been found to combat Candida, Blastocystis Hominis and pathogenic bacterial overgrowth.

4) Rebalance

This final stage is focussed on preserving the gains from the previous stages into the future so that your gut stays resilient and tolerates a wide range of foods. Here, we pay particular attention to lifestyle choices such as sleep, exercise, and stress.

Of particular interest is that when we eat, as well as what we eat. Nowadays, we tend to eat all day (16 hours) and fast for just 8 hours overnight. It’s during this fasting period that the gut lining repairs itself and the body clears out unprocessed foods and bacteria from the small intestine. This helps prevent small bacteria overgrowth or SIBO through a process known as the ‘migrating motor complex’.

Spending longer periods without food, say 12 or even 16 hours overnight, and reducing snacking, may help your gut health, improve your overall health and prevent chronic diseases.

Everyone is different

These four steps provide a framework for regaining gut health. But that doesn’t mean that the steps look exactly the same for everyone. A  practitioner can help you identify the root causes of your health issues, identify appropriate lab testing, diet, and supplements, and provides the expertise to filter the scientific research to help you improve your gut health.

If you have any questions, I’m always happy to help so please get in touch. To know more about how you can work with me, you can find out more here.

Stephen Ward Headshot Image


Stephen Ward (MSc) is trained in assessing the root cause of chronic health issues through Functional Medicine.

He uses nutrition, lifestyle changes, and nutraceuticals (targeted supplements) to help you achieve your goals and improve your health.



Understanding the underlying causes of digestive discomfort and IBS

Understand the common root causes of digestive discomfort and IBS and what you can do..

What is Functional Medicine anyway?

In the olden days, it was thought that disease was caused by some entity, such bad air (a miasma), that we needed to get rid of in some way. We now know that this idea of something that we need to get rid of only makes sense in specific cases. Traditional Western medicine works wonders in these areas of infectious disease, surgery, and acute trauma. But what about preventing or treating chronic health conditions such as auto-immunity, depression, heart disease, diabetes, cancer or Alzheimers? Or complex cases where the patient has an endless list of symptoms (and is often given an endless list of drugs)? Are we merely putting bandages on an inevitable disease process? Can anything else be done? We have a pill for everything but those pills rarely, address the root cause of the disease.

Do diseases actually exist?

You might answer ‘of course they do!’. And you are right, the symptoms obviously exist. But at the level of our biochemistry, disease is just a result of poor function at the cellular level, which results in poorly functioning organs and systems in the body. For example, Dr. Dale Brdesen argues that Alzheimer’s is not a single disease, but identifies three major metabolic imbalances that contribute to Alzheimer’s:
  1. Inflammation from things like poor diet and lifestyle choices, infection, and other issues
  2. An insufficient amount of supportive elements like hormones, nutrients, and brain-supporting compounds that result in poor functioning and repair of neurons in our brain.
  3. Toxic exposure to heavy metals like mercury, arsenic, or lead, and biotoxins like mold and other microbes
Based on this understanding, a disease becomes only a convenient label for a collection of imbalances and diseases don’t actually exist in and of themselves. Although a ‘disease’ may present in a seemingly consistent way, in this case ‘Azheimer’s’, the actual causes associated with that disease and the imbalances in the body may be different. And that’s why Dr. Rangan Chatterjee has boldly declared that he can make diseases disappear. His approach to making ‘diseases’ disappear is largely based in Nutritional Therapy and Functional Medicine, and addressing the root cause of the disease rather than the symptoms.

So, What is Functional Medicine?

Functional Medicine is the identification of the root causes of the imbalances that give rise to disease.
Once the root causes are identified, they can be addressed through personalised and targeted lifestyle interventions such as nutrition, sleep, rest, and movement. Pharmaceuticals may be required in some cases, but lifestyle interventions will always benefit the patient. In our Alzheimer’s example, inflammation and poor functioning of neurons can be addressed in part by nutrition and lifestyle changes. Similarly, we can reduce our exposure to toxins by changing our environment and take steps to eliminate toxins that are stored in the body (sauna anyone?).

“The doctor of the future will give no medicine, but will instruct his patient in the care of the human frame, in diet and in the cause and prevention of disease.” – Thomas Edison

Functional Medicine sees a return to this care for the body and answers questions such as:

Why do you have this problem in the first place?

Why has function been lost?

What can we do to restore function?

Functional Medicine in Action

Functional medicine is based in systems theory.
system is a cohesive grouping of interrelated and interdependent parts
Because of this interconnectedness and interdependence, our digestive health may have an impact on our immune system and hormonal system and vice versa. And inflammation and oxidative stress may affect all systems in our body, and are in-turn affected by our diet and stress levels. Functional Medicine looks at the functioning of the systems within the body, and looks to improve their functioning to regain or maximise health. We use nutrition and lifestyle interventions (e.g. rest, sleep, movement), rather than a single pharmaceutical. This allows us to target multiple systems in the body at the same time and address root causes, rather than symptoms. We may look at environmental toxins, genetics, nutrient status, poorly functioning detoxification, cellular energy pathways. Advanced laboratory testing may be used to help get to the root cause where necessary… This process may take some time and money, but it is generally a very effective investment. Although it may appear expensive, resolving issues at their root, may reduce the amount spent on healthcare in the future. Of course, the most important outcome is that you get back your health and vitality and that you feel the difference. If you have any questions, I’m always happy to help so please get in touch. To know more about how you can work with me, you can find out more here.
Stephen Ward Headshot Image


Stephen Ward (MSc) is trained in assessing the root cause of chronic health issues through Functional Medicine. He uses nutrition, lifestyle changes, and nutraceuticals (targeted supplements) to help you achieve your goals and improve your health.