Trust your gut, your health depends on it.




The Gastrointestinal tract (GIT), commonly known as the gut, is considered the most complex organ system in the body1. It is responsible for the ingestion, processing, and digestion of food as well as for the transport of micronutrients into our bloodstream and, ultimately, to every cell in our body.

The Gastrointestinal tract is composed of the mouth and associated salivary glands, pharynx, oesophagus, stomach, small and large intestines, and rectum. There are also other organs that are tightly associated with the Gastrointestinal tract, including the liver, gallbladder, and pancreas. Jump here, for a more detailed structure of the Gastrointestinal tract.

Dysfunctions of any part of the Gastrointestinal tract can have important consequences on our health. Hence, it pays to understand the main drivers of gut health.




There are many factors influencing gut health, including genetics, immune function, and the composition of your gut microbiota. Also, environmental factors like your diet, activity levels and other lifestyle options influence the function and wellbeing of your gut.

If you are ill, chances are your gut health is affected in some way, and you need to get tested to understand what factors are at play. Gut health testing can involve different types of advanced tests, depending on what system is targeted, and requires the help of healthcare specialists.

Some of the most important factors you need to consider when addressing gut health are:

  • Genetics

    Your genome is the blueprint that drives all functions in the body, but everyone carries a certain number of genetic mistakes, called mutations, which can affect the function genes, and potentially, proteins in different parts of the body, all of which can affect gut health and health beyond the gut.

      • Certain mutations, for example, can give you a predisposition (an increased chance) to develop gut-related diseases like inflammatory bowel disease (IBD)2, Crohn’s disease3, ulcerative colitis4, or irritable bowel syndrome (IBS)5.
      • Certain genetic mutations can also affect gut health by influencing the way your body responds to some prescription medicines6.
      • Advanced genetic testing can reveal the presence of mutations that can potentially cause gut health problems, which can help us design an optimal treatment plan.


  • Immune function

    The immune system is your body’s defence mechanism against invading pathogens or potentially harmful toxins that enter your body. The immune system also helps clear your body of diseased cells, leading the way for optimal functioning. Malfunction of any portion of the immune system can have serious consequences on your health. Some examples of immune-related conditions include:

      • Autoimmune diseases

        Certain immune diseases result in our own, healthy, cells being targeted and destroyed by the immune system. This is the case of conditions like rheumatoid arthritis, lupus, multiple sclerosis, Type 1 diabetes, psoriasis, hypothyroidism, osteoarthritis, celiac disease, rheumatoid arthritis or Inflammatory bowel disease (IBD), among other conditions.


      • Immune overreactions

        While the role of the immune system is to detect and eliminate potential threats, sometimes this process is faulty. In some diseases, the body overreacts, resulting in an excessive immune reaction. This is the case of conditions like coeliac disease (CD), where the immune system overreacts to the presence of gluten proteins. As a consequence, cells lining the intestinal wall are damaged, causing disease. Another recent example of immune overreaction is being seen in COVID-19 patients. A significant number of deaths associated with this disease is due to an immune overreaction called a cytokine storm, where cytokines, a special type of immune cell, go berserk and harm healthy cells.


      • Chronic inflammation

        This occurs when the body is unable to regulate inflammatory responses, resulting in damage to healthy cells, tissues and organs. Conditions like heart disease, rheumatoid arthritis, type 2 diabetes, obesity and asthma are associated with chronic inflammation.


At our centre, we employ advanced immunological-based testing, the only one currently available in Australia, based on the identification of antibodies against common allergens found in food and other environmental sources. See our article on allergies for more details.


  • The Gut Microbiota

    Our body is home to trillions of microorganisms, known as the human microbiota, inhabiting every part of our body, inside and out. Most of these microorganisms are found in the small intestine, where they are known as the gut microbiota (GM), and they have several important functions related to gut health and health beyond the gut, like:

      • Helping with the digestion of certain types of foods, like resistant starch, which cannot be digested by our body.
      • Producing chemicals that influence the function of different body systems. These chemicals include certain vitamins that our body needs but can’t produce, as well as short-chain fatty acids and other bacterial metabolites, chemicals that interact with different cells in our body.
      • Interacting with surrounding cells, such as certain immune cells. For example, certain gut microbes are known to regulate the maturation and function of specific immune cells associated with the central nervous system, influencing our body’s response to neuroinflammation, brain injury, autoimmunity, and neurogenesis7.


There is currently strong scientific evidence backing important roles for gut microbes in different aspects of our health7-9. Hence, it is important to understand how well your gut is functioning and whether it needs a bit of help. At the Australian Centre for Functional Medicine, we employ a comprehensive microbiome mapping approach, currently the most advanced DNA-based stool test available in Australia.




Malfunction of the gut can result in a wide range of symptoms, depending on which cells, tissues or organs are affected. Alterations to your normal composition of gut microbes, known as dysbiosis, whether on your mouth or small intestine, can have a direct effect on gut health, as well as with the health of the rest of your body. Two important locations along the Gastrointestinal tract where microbial dysbiosis occurs and is known to affect health are your mouth and gut.

  • Oral microbiota

    The mouth is home to more than 600 different species of bacteria, fungi, and viruses, living in the mucosal surfaces of your tongue, cheeks, palate, and tonsils, as well covering your teeth12. In healthy individuals, this diverse menagerie of microorganisms is maintained in a delicate equilibrium. Alterations to this equilibrium cause dysbiosis, where some species overgrow, causing disease10-12. Symptoms and conditions associated with oral dysbiosis include:


      • Periodontal or gum disease

        This is an infection of the tissues surrounding your teeth, caused by poor brushing and flossing habits, which leads to an overgrowth of certain microorganisms. Symptoms: Typical symptoms include bad breath, red, swollen or bleeding gums, painful chewing, loose or sensitive teeth and reduced gums, which make your teeth appear longer.


      • Inflammatory bowel disease (IBD)

        This includes Crohn’s disease and ulcerative colitis, two conditions affecting the gastrointestinal tract and gut health. Certain groups of oral bacteria, including members of the bacteria genera Streptococcus, Prevotella, Neisseria, Haemophilus, Veillonella, and Gemella have been shown to be overrepresented in patients with this condition, causing oral dysbiosis. The causes behind IBD are largely unknown but may include diet, genetics, gut dysbiosis, immune malfunction and environmental factors13-15. Symptoms: Typical symptoms may include diarrhea, fever and fatigue, abdominal pain, bloody stools, poor appetite and weight loss, among others.


      • Rheumatoid arthritis (RA)

        This is an autoimmune disease where our immune system attacks the cell lining of the joints. The causes behind RA are not fully known, but there is a strong genetic component16. More recently, the gut and oral microbiota have also been linked to RA. In one study, patients with RA exhibited altered microbial composition compared to healthy controls. More specifically, the study found that patients with RA had reduced levels of bacteria of the genus Haemophilus and an overrepresentation of the bacterium Lactobacillus salivarius, in their gut, teeth and saliva, compared to healthy people17. Symptoms: Typical symptoms of RA include swollen and stiff joints, fatigue, fever and loss of appetite.


      • Small Intestine Microbiota

        Harbouring billions of bacteria and other microorganisms, the microbiota living in the small intestine represent the largest and most important portion of our gut microbiota. These microorganisms have been extensively studied and their composition has been linked to multiple aspects of our health18-21. Some examples of associations between the composition of the small intestine microbiota and our health include:


      • Obesity

        This is a major problem in Australia, affecting as many as 31% of all adults and almost as many children. Recently, studies have established strong links between the composition of the gut microbiota, diet, and genetic factors22-23. For example, people suffering from obesity-related conditions, such as high adiposity, dysfunctional metabolism of lipids, high blood sugar levels, insulin resistance and dyslipidemia(high levels of lipids in the blood), have been shown to have low bacterial richness. In other words, the gut microbiota of overweight/obese people is composed of a relatively smaller number of species, compared to lean people. This difference holds even when you consider the fact that there is a significant difference in gut microbial composition among healthy people24. Symptoms: overweight and obese persons can suffer from breathlessness, increased sweating, snoring, fatigue, back and joint pains and low self-esteem.


      • Autoimmune disorders

        These conditions occur when our immune system attacks our own, healthy cells. They have mostly unknown causes and are likely to have strong genetic and environmental components. However, recent studies have found strong evidence that the composition of our gut microbiota may also be involved with the development of some autoimmune diseases25. For example, human-based genomic studies have analysed stool samples from people with autoimmune diseases. Their results show strong associations between gut microbial dysbiosis and autoimmune diseases like rheumatoid arthritis17, 26, type 1 diabetes27, multiple sclerosis28 and Inflammatory bowel disease (IBD)29. Symptoms: Depending on the disorder, people suffering from an autoimmune disease can experience swollen and painful joints, abdominal pain, diarrhoea, fatigue, increased thirst and hunger, cognitive decline, vision problems, among many other symptoms.


      • Cardiovascular disease

        This group of diseases include ailments of the heart, high blood pressure, arrhythmia and other problems with blood vessels, affecting over 4.8 million Australians. Worldwide, cardiovascular disease is a major cause of disease and death. The composition of the gut microbiota has been associated with atherosclerosis, atherosclerotic cardiovascular disease, high blood pressure, high cholesterol, coronary artery disease, and arterial stiffness30-32. Some common cardiovascular diseases include coronary heart disease, heart failure, cardiomyopathy, stroke, and other conditions. Symptoms: typical symptoms can include shortness of breath, chest pain, numbness or pain in legs or arms.


      • Neurological health

        Studies have shown that the composition of the gut microbiota is correlated with depression, autism, Parkinson and Alzheimer’s disease, schizophrenia, anxiety, stress, pain and migraine, multiple sclerosis, and amyotrophic lateral sclerosis33. This connection between gut microbes and the brain is known as the gut-brain axis. In recent decades, research studies have revealed exciting links, suggesting that the composition of our gut microbes can influence the health of our brain. Symptoms: typical symptoms vary according to each condition, and can include cognitive decline, hallucinations, speech and behaviour disturbances, headache, irritability, tremors in hands, and many others.


Understanding the consequences of gut dysfunction is an important step to discover the best way to deal with a specific medical condition. Another important step is to identify the main drivers of gut dysfunction and gut health.




Optimal gut health depends on multiple factors, involving the different organs participating in the process of digesting food and absorbing nutrients. For example, an optimal enzymatic function is essential throughout the Gastrointestinal Tract (GIT).

  • The Gastrointestinal tract: a primer on function

    The digestive functions of the mouth, stomach, pancreas and intestines depend on the optimal production and function of diverse enzymes. In the mouth, the enzyme amylase is responsible for the initial stages of digestion, breaking down starch into more basic components34. The next stage occurs in the stomach, where, gastric acid and proteases enzymes break down proteins and fats35. The pancreas, an accessory organ of the Gastrointestinal tract, produces enzymes like proteases, lipases and amylases that are used in the small intestine36. The final stage of food digestion occurs in the intestines, where multiple enzymes, including pancreatic amylase, trypsin, nucleases, nucleosidases, lipases, peptidase, maltase and lactase further break down food into basic components, which are then absorbed in the small intestine37.


  • Pathogenesis of the Gastrointestinal tract

    There are multiple factors that influence gut health. For example, alterations in the levels and function of the enzymes and acids that govern the process of digestion are an important cause of disease. Changes in the composition of the gut microbiota can also cause health problems. Multiple diseases have been associated with gut microbial dysbiosis, including various intestinal disorders, allergies, asthma, neurological conditions, metabolic diseases, cardiovascular disease, and obesity38.

Below we highlight some examples of factors affecting gut health, their causes and typical symptoms.


  • Hypochlorhydria

    This condition occurs when our stomach produces low levels of gastric acids, and it is characterised by a higher than normal pH in your stomach. A healthy functioning stomach has a pH below 3, highly acid, but the stomach of a person with hypochlorhydria has a pH between 3-5.
    Symptoms: typical symptoms someone with hypochlorhydria can experience include bloating, diarrhoea, upset stomach when taking vitamins or supplements, heartburn, fatigue, infections of the Gastrointestinal tract, among other symptoms. Chronic hypochlorhydria can result in digestive problems, nutritional deficiencies, increased risk of bone fracture and developing infections. Conditions like stomach cancer, chronic muscle pain and drug sensitivity have also been associated with hypochlorhydria39-44.


  • Low enzyme production

    Abnormal levels of digestive enzymes can result in poor absorption of nutrients, due to incomplete food digestion. Symptoms: typical symptoms of this condition include diarrhoea, fatty or loose stools, caused by fat malabsorption, abdominal pain and flatulence45. Some conditions associated with long-term low enzyme production include like chronic pancreatitis, cystic fibrosis, celiac disease, diabetes, inflammatory bowel diseases, stomach ulcers, cancer and certain autoimmune diseases45-48.


  • Microbial dysbiosis

    The Gastrointestinal tract is laced with vast microbial communities, composed of hundreds of different species of microbes, mostly bacteria, but also fungi, viruses and other microorganisms.

      • Gut Health: What is a healthy gut microbiota?

        There no specific gut microbial composition that can be defined as a “healthy microbiota”. In fact, studies have found that even among healthy people, there is a lot of variation on the types of gut bacteria present49. Instead, what research is showing is that having a rich diversity of gut bugs is what defines a healthy gut. When you are healthy, studies have shown that your gut hosts a large diversity of microbial species, with at least 160 different microbial species found in a single person, according to one study50. However, when you are sick, the gut microbiota (GM) diversity is affected51. Studies have shown that people suffering from conditions like hypertension52, Crohn’s disease53, metabolic diseases54, or bacterial infections55 have reduced diversity of gut bacteria.


      • Microbial infections

        Gut health can be affected by infections from pathogenic microbes, such as bacteria, viruses, and parasites. These pathogens can come from many different places. For example, pathogenic bacteria can enter your body through contaminated food or water. One notable example is Helicobacter pylori, a gut pathogen found in as many as 60% of the world population56. This bacterium is involved with the development of ulcers, chronic gastritis, and stomach cancer, among other conditions. However, many people carrying this bacterium never develop symptoms. Other important pathogenic microorganisms found in the environment are found in Table 1.

          • Two examples of parasite infections causing disease are Blastocystis hominis and Dientamoeba fragilis two microorganisms commonly found in the intestines of humans. These microorganisms can be acquired through contaminated water or from infected people through a faecal-oral route. In humans, B. hominis and D. fragilis may or may not cause symptoms or disease. Symptoms: In some people, it can cause diarrhea, abdominal pain, nausea, vomiting, fever, fatigue, among other conditions. Treatment to eradicate these species is difficult and should only be undertaken if a patient is suffering from detrimental symptoms. Potential treatments involve antibiotics and other drugs, as well as some probiotics and herbal preparations57-58


      • Microbial overgrowth

        Microbial infections can also occur from within your own gut, through the overgrowth of particular microbial species, normally found in the gut at low levels. This is called gut dysbiosis, broadly defined as a status of imbalance in the composition of the gut microbiota. In a gut with gut microbiota (GM) dysbiosis, a gut microbe that is normally innocuous causes harm due to overgrowth. At the same time, your healthy microbial flora is depleted during dysbiosis.


  •  Gut microbiota (GM) and other body systems

    The Gastrointestinal tract also interacts with multiple other systems in the human body. From the brain to the immune system, our body’s interaction with the gut has been implicated with multiple diseases, including cardiovascular disease, obesity, diabetes, immune disorders, anxiety, depression, and neurological disorders. Some of the most studied systems that interact with the gut microbiota include:


      • The Brain and Central Nervous System

        The connection between the gut microbiota and the brain is one of the most studied topics in the past decades. The so-called brain-gut axis refers to the bi-directional communication pathway that connects the gut microbiota with the brain. This pathway involves the vagus nerve, the enteric nervous system, the endocrine and immune systems as well a myriad of chemicals such as short-chain fatty acids, certain amino acids, and peptidoglycans, produced by gut microbes64-66. Neurological conditions like pain, depression, anxiety, autism, Alzheimer’s diseases (AD), Parkinson’s disease (PD), and stroke have been linked to gut dysbiosis, imbalances that occur in the composition of gut microbiota. For example, people suffering from PD commonly suffer from gut problems, like SIBO, malnutrition, H. pylori infection, and constipation67. Other studies have also identified alteration in gut microbiota (GM) composition in people with this disease. Butyrate-producing bacteria and bacteria producing anti-inflammatory compounds, such as Blautia, Coprococcus, and Roseburia, are depleted in the gut of people with PD. In contrast, other bacterial groups, such as H. pylori, E. coli, Ralstonia, Oscillospira and Bacteroides are found in high abundance, compared to healthy people68. These findings suggest that gut microbiota (GM) composition may be involved with some aspect of PD development. Comparable findings have been reported for many other neurological conditions, summarised in this table from reference 68.


      • The Immune system

        Endowed with the task of protecting our body from pathogens and other potentially harmful invaders, the immune system is a complex organ system that keeps us healthy. Dysfunctions of the immune system can lead to pathogens entering the body and causing disease. Another form of immune dysfunction is autoimmunity when our own, healthy cells are targeted and destroyed by the immune system.

        In recent years, the gut microbiota has been recognised as an important factor in immune function. For example,

          • Many autoimmune disorders, including Type 1 diabetes, multiple sclerosis, rheumatoid arthritis, celiac disease, and asthma are associated with alteration in the gut microbiota (GM) composition69-73.
          • The gut microbiota (GM) can also influence the function of specific immune cells, through the many metabolites it produces, succinctly presented in this figure, from reference 7.


      • The HPA axis

        The hypothalamic-pituitary-adrenal (HPA) axis, along with the sympathetic nervous system, are responsible for the regulation of stress responses. In recent years, a lot of studies have explored how the gut microbiome is connected to the HPA axis. A key finding concerns the role stress has on the composition of the gut microbiota and on the development of the HPA axis. For example, stress is known to affect babies, even before they are born and in their first years of life, influencing the way their HPA axis develops and function, including the production of important hormones, like cortisol.  Studies are now suggesting that gut microbiota (GM) dysbiosis may be a mechanism through which stress affects the HPA axis64-67.

        The interplay between stress, the HPA axis and the gut microbiota (GM) is an active field of research. Multiple studies show that alterations to HPA function are influenced by gut bacterial dysbiosis, dysfunctions of the intestinal barrier, and inflammation.


      • Other systems

        Recent studies have revealed links between gut health, the gut microbiota (GM) and other organs in the body. For example, researchers are now talking about Gut-Kidney axis. Animal and human-based studies have established links between gut dysbiosis in patients and animal models of hypertension and chronic kidney disease (Table 2)


gut health experiment table

Table 2. Evidence for the gut-kidney axis. (Adapted from Table 2, Reference 70).



At the Australian Centre for Functional Medicine, we seek to understand the biology behind the conditions and symptoms you experience. Most importantly, we take a comprehensive approach to improve gut health and your health beyond the gut.

Our main goals are to understand and to cure, not just calming symptoms. Before we can prescribe treatment to cure an ailment, we need to understand the underlying causes behind the ailment. To address this question, we employ advanced diagnostic testing technologies, which allows us to inquire about your health status at multiple levels. Our tests include intestinal permeability screening (blood and urine), breath testing, stool analysis, urine analysis, comprehensive blood testing, metabolic analysis profile, testing for nutrient deficiencies, methylation profile and DNA testing and profiling.

Using this approach, We have successfully treated autoimmune disorders (Addison’s disease, Grave’s disease, celiac disease, rheumatoid arthritis, multiple sclerosis, and others), gut and gut microbiota disorders, nutritional deficiencies, parasite infections, fungal infections, among several other conditions, including:




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