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Gut Microbiome Functional Integrative Nutritional Medicine Adelaide

Gut Microbiome

There has been a dramatic increase in the amount of research being conducted on the gut microbiome over the last 10 years. The microbiome comprises all of the genetic material within a microbiota (the entire collection of microorganisms in the human gut, mouth, or on your skin). More than a trillion, mostly good, microbes live within our gastrointestinal tract. These bacteria are responsible for important metabolic, immune and nutritional functions.

Dysbiosis, meaning an imbalance of the microbiome, is associated with many states of ill health and common diseases, and provides a target for treatment.

Dysbiosis is associated with the following health conditions

  • Digestive issues – bloating, cramps, constipation, diarrhoea, nausea, pain etc.
  • Food intolerances
  • Irritable bowel syndrome
  • Inflammatory bowel disease
  • Obesity
  • Metabolic conditions, such as diabetes.
  • Depression and other neuropsychiatric disorders.
  • Cardiovascular disease
  • Lowered stress resilience
  • Immune dysfunction and autoimmunity
  • Cancer
  • Cognitive decline and Alzheimer’s disease
  • Poor desicion making, memory, and focus
  • Autism spectrum disorders
  • ADD & ADHD
  • Poor hormonal balance
  • Non-alcoholic fatty liver disease
  • Elevated estrogen
  • Toxin accumulation
  • Fibromyalgia
  • Chronic fatigue syndrome
  • Reduced bone density
  • Skin conditions – eczema, rosacea, psoriasis etc.
  • Allergies
  • Oxidative stress
  • Inflammation
  • And many more…

Causes of Gastrointestinal Issues

Poor Diet and Alcohol Use

The most obvious influence on the gut comes from what we eat. Dietary changes have been seen to cause dramatic changes in the gut microbiome in as little as 5 days.

Processed foods are devoid of resistant starches, which are needed to feed our microbiome. Feeding your bacteria with this fibre is the foundation of maintaining a wide diversity and balanced populations of beneficial bacteria. These starches are found in whole grains, legumes, cashews, cold potatoes, green bananas, and many other foods.

Processed foods often have other additives and preservatives, which are also detrimental. Emulsifiers, for example, have been seen to increase inflammation in the gut, which can lead to obesity, high blood sugar and insulin resistance.

Elemental Health Nutrition Gut MIcrobiome
Although small amounts of alcohol can be beneficial for your gut bacteria, higher alcohol exposure can promote the growth of gram-negative bacteria in the intestines, which can cause an increase in endotoxins. It can also result in an accumulation of acetaldehyde, which in turn increases intestinal permeability, reduces energy production, and blocks B12 utilisation.



The vagus nerve is the main communication highway between your brain and your gut microbiome. This communication goes both ways – so not only does the microbiome impact on nervous system function (influencing your mood), but the nervous system also affects gut flora (mood issues cause gut issues).

When under stress, the different types of bacteria in the microbiome become more varied and cease to ‘work together’ in a symbiotic relationship. Their behaviour becomes erratic, and instead of large colonies of beneficial bacteria, there are smaller colonies of many different strains – including less desirable species.

These species can lead to a variety symptoms. These include mood issues, gastrointestinal symptoms, autoimmunity, elevated estrogen, high cholesterol, poor nutrient absorption, food cravings, metabolic changes, and more.

Stress hormones have an impact on gut function. When we’re stressed, the body secretes corticotropin-releasing hormone (CRH). This hormone is a precursor to other stress hormones, such as adrenocorticotropic hormone (ACTH), and cortisol. Excess cortisol reduces gastric acid production, decreases gut motility, causes intestinal permeability, and alters the balance of bacteria in the microbiome.


Poor Sleep

Sleep deprivation causes a significant alteration in the levels of bacteria in the digestive tract. Some microbes can even decrease by up to 50% with just two nights of sleep deprivation. Interestingly, the microbiome changes caused by sleep deprivation can reflect the typical gut flora profile found in people with obesity and metabolic disorders.

Poor-quality sleep can lead to an overgrowth of less desirable strains in the gut. Following poor sleep, bacteria have been found to grow outside of the gut, crossing through the gut lining into other areas of the body. This is called translocation, and can cause issues in other organs, for example, bladder and thyroid concerns. A good sleep cycle is paramount for a well functioning gut. It’s also very important to help regulate cortisol, which takes us back to the relationship between cortisol and changes to the microbiome.


Chronic inflammation occurs in any chronic disease or health condition. But chronic inflammation can also induce further issues within the digestive tract. Dysbiosis can be caused by inflammation, which in turn will cause further inflammation, as many bacteria are able to produce inflammatory compounds (endotoxins). The inflammatory cycle feeds into itself.

Inflammation in the digestive tract can also cause issues – for example, consumption of a food that is not tolerated. Both intestinal and systemic inflammation can disrupt the gut lining, increasing permeability. Poor sleep, stress, poor diet, and alcohol use all lead towards inflammatory processes.

Parasites and Foreign Bacteria

Dysbiotic bacteria can produce toxic substances, such as amines, ammonia, hydrogen sulfide, phenols, and secondary bile acids, which may cause damage to the intestinal lining.  If left unchecked, long term damage to the lining can cause leaky gut, allergies, rashes, autoimmune conditions, IBS, fatigue, chronic headaches, joint pain, irregular bowel movements, malabsorption, gastritis, indigestion, and sensitivities to a variety of foods.

Blastocystis hominis and Dientamoeba fragilis are the two most commonly contracted parasites. They are both transmitted via the fecal-oral route, through contaminated food and water, and from drinking unfiltered rainwater and household pets. Common symptoms include nausea, watery loose stools, abdominal pain, flatulence, stomach pain and cramping, itching around the anus, mucus in the stool, loss of appetite, weight loss, and fatigue.

Elemental Health Nutrition Gut MIcrobiome Parasite
Klebsiella is a gram-negative bacterium that is considered a ‘superbug’, and as an opportunistic pathogen, is most common in hospital settings where low immunity is common. It is also commonly contracted from chickens. It can cause a variety of infections, including meningitis, bloodstream infections and pneumonia. When present in the digestive tract, it can present with many digestive issues including loose stools and food sensitivities. It is also commonly associated with joint pain called “Klebsiella-reactive arthritis” and can lead to anklyosing spondylitis.

Yeast Overgrowth

Candida is a yeast that occurs naturally in the body. When an overgrowth occurs, it results in a candidiasis infection that can spread throughout the entire body. An overgrowth can be caused by antibiotic use, low levels of beneficial bacteria (Lactobacillus or Bifidobacteria), oral contraceptives, cortisone, a weak immune system, low levels of sIgA, a high sugar diet, and high stress levels.

The symptoms most commonly associated with candida are thrush in the mouth, genitals and urinary tract. However, candida overgrowth can also cause digestive symptoms. When overgrown, the yeast can penetrate the intestinal walls, increasing permeability, and translocating to other areas of the body. Common symptoms of yeast overgrowth include brain fog, fatigue, recurring bladder or vaginal infections, sensitivity to smells (in particular, perfumes), mood swings, depression, sugar cravings, bloating, constipation, or loose stools.


Any form of toxicity that makes its way into the digestive tract can have disastrous consequences for gut health. Moulds and heavy metals are the most common toxins, but we’re exposed to over 700,000 other environmental toxins daily, which are not researched enough to assess their effects.

Moulds – Although mould exposure is more commonly associated with respiratory symptoms and immune dysfunction, it can also cause digestive issues, nausea, vomiting, cramping and diarrhoea. 24% of individuals are genetically susceptible to poor mould/biotoxin tolerance. In this subgroup, more chronic health concerns may occur, such as fibromyalgia, chronic fatigue syndrome, multiple chemical sensitivity, and severe disruption to the balance of the microbiome.

Heavy metals – One heavy metal known to cause digestive issues is mercury. When ingested, it inhibits production of several essential digestive enzymes in the digestive tract, as well as damaging the microbiome and intestinal lining. Within several minutes, mercury exposure can inhibit sugar and protein absorption by up to 20%. Amalgam fillings allow for constant exposure, so it causes a greater likelihood of gut disturbance.

Elemental Health Nutrition Gut MIcrobiome Parasite
Even when heavy metals are not absorbed into the body, they can disturb gut flora balance, as demonstrated in animal studies. This can have devastating effects on health, as the gut lining weakens and allows heavy metals to accumulate in various body tissues. In one study, an amalgam filling was placed in the tooth of a sheep, and the animal was harvested 30 days later. They discovered mercury in the jaw, stomach, liver and kidneys.

Antibiotic Use

Unfortunately, antibiotics are overprescribed and used inappropriately. Even occasional use can have significant impacts on the gut flora. A single course of antibiotics can significantly reduce the diversity of gut flora for up to a year long, and potentially longer in vulnerable people. This can also impact on intestinal permeability, leaving the body vulnerable to further pathogens.

In the case of regular antibiotic use, the gut flora is permanently altered. This leaves people vulnerable to antibiotic-resistant strains that can cause digestive symptoms, including Salmonella and Staphylococcus aureus.

Assessing Your Microbiome

With so many variables that can affect the delicate balance of gut bacteria, it’s difficult to know what species we really need to be increasing or decreasing.  Comprehensive microbiome testing is available to provide these insights, and avoid guesswork.  This includes extensive testing for dysbiosis, yeasts, parasites, inflammation, digestive markers, and immune function.