What is SIBO (small intestinal bacterial overgrowth)?

Understanding your condition

SIBO (or small intestinal bacterial overgrowth) is an overgrowth of microbial species in the small intestine which would generally be living in the colon. This translocation of bacteria can alter digestive function, cause severe discomfort and lead to nutritional deficiencies. SIBO can lead to intestinal hyperpermeability, which can, in turn, trigger food intolerances and sensitivities.

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functional medicine health coach jessica showing gi map dna stool analysis test kit to patient

SIBO natural treatment 

SIBO is common and yet it is frequently underdiagnosed, and not well understood or treated by conventional medicine. 

Left untreated, SIBO can lead to chronic inflammation and other long term health conditions. Our functional medicine SIBO naturopaths use the functional medicine SIBO approach, which is a comprehensive, personalised natural SIBO treatment that gets to the root of SIBO naturally and effectively to restore digestive health for good.


SIBO symptoms

SIBO is caused by methane-dominant, hydrogen-dominant or sulphur-reducing microbial species, or a combination of those, in the small intestine. Symptoms can differ from person to person, although the most common SIBO symptoms can include:

Methane-dominant SIBO is usually associated with constipation, whereas hydrogen-dominant SIBO can present with symptoms of diarrhoea or loose stools. Less common sulphur reducing bacteria can produce a gas odour that resembles rotten egg. 

SIBO symptoms can both mask and worsen symptoms of other digestive disorders such as coeliac disease, and IBS. SIBO is found in up to 80% of people diagnosed with IBS (irritable bowel syndrome) making diagnosis difficult. Studies show a 9.51 times higher risk of having SIBO in patients diagnosed with inflammatory bowel disease (IBD).

SIBO can cause systemic inflammation and trigger intestinal hyperpermeability (also known as ‘leaky gut’) of the digestive lining by breaking the junctions between cells, allowing large proteins to cross over into the bloodstream. These proteins are detected by the immune system and can trigger new food reactions. A vicious cycle can occur where food reactions cause further inflammation, exacerbating SIBO symptoms. 

Additionally, in all SIBO types, nutritional deficiencies can occur due to poor absorption of Vitamins B12, D, A and E and minerals such as iron and calcium. 

What causes SIBO?

Healthy digestion relies on a sequence of events occurring. Once the food is broken down by chewing and saliva in the mouth, it is further broken down by hydrochloric acid in the stomach and moves to the small intestines where most nutrients are absorbed. The timely movement of food occurs via a wave-like muscular constriction called ‘peristalsis’, and allows proper absorption of nutrients. The migrating motor complex (MMC) is a different and stronger wave-like constriction occurring around every 90 minutes and is a necessary ‘cleaning cycle’ of the digestive system. The disruption of any of these processes can lead to SIBO. 

Common causes can include:

  • Low stomach acid
  • Acid reducing medications such as PPI’s (proton pump inhibitors e.g. Nexium)
  • Coeliac disease
  • IBS
  • IBD (Crohn’s disease, ulcerative colitis)
  • Diverticulitis
  • Slow motility/peristalsis
  • Chronic constipation
  • Hypothyroid (low thyroid hormone)
  • Food poisoning/infection/parasites (Enterococcus, Klebsiella, H. pylori, E.coli )
  • Stress
  • Poor diet (e.g. high sugar, alcohol, processed carbohydrates)
  • Surgery
  • Scarring and adhesions of the small intestines
  • Pancreatitis
  • Gastroparesis
  • Scleroderma, diabetes
  • Ileocecal valve impairment

There are 3 main types of SIBO, with each involving overgrowth of different aerobic and anaerobic microbial species: 

  1. Hydrogen producing bacteria

The abnormal presence of colonic bacteria in the small intestines means that fermentation of foods is occurring much higher up the digestive system than it should be. The small intestines are very sensitive to the excessive production of hydrogen gas, predominantly from Bacteroidetes spp., which causes abdominal bloating and diarrhoea. Other low oxygen (microaerophilic) hydrogen-producing species are Streptococcus and Escherichia coli, along with anaerobic bacteria, such as Lactobacillus and Bacteroides.

  1. Methane producing archaea 

Constipation is a result of methane-producing species of non-bacterial, single-celled species called archaea, such as Methanobrevibacter smithii and Methanospaera stadmagnae. M. smithii and M. stadmagnae feed on hydrogen produced by other species creating a methane gas byproduct which is also responsible for abdominal bloating and slows transit time causing constipation. 

  1. Sulphate reducing bacteria

The third type of SIBO is due to the sulphate-reducing bacteria, commonly Desulfovibrio spp.  This SIBO type is less common and tests negative on traditional breath testing  which only tests for hydrogen and methane gas which this species doesn’t produce.

The by-product of this species is hydrogen sulphide gas, which is highly toxic to the cells of the intestinal walls and is distinguished by the foul odour of rotten eggs. These species also consume hydrogen, competing with the methane producing species. In some cases, they can keep each other in check, however treatment of one species can allow the other to proliferate and overgrow.

What causes eczema?


Research has found people with the ‘atopic triad’ have a defective barrier of the skin and upper and lower respiratory tracts.

These genetic alterations cause a loss of function of filaggrin (filament aggregating protein), which is a protein in the skin that normally breaks down to create natural moisturisation and protect the skin from penetration by pathogens and allergens.

Filaggrin mutations are found in approximately 30 percent of people with atopic dermatitis, and also predispose people to asthma, allergic rhinitis (hayfever), keratosis pilaris (dry rough patches and bumps on the skin), and ichthyosis vulgaris (a chronic condition which causes thick, dry, scaly skin.)If one parent carries this genetic alteration, there is a 50 percent chance their child will develop atopic symptoms. And that risk increases to 80 percent if both parents are affected. 

Food allergy and sensitivity

Food hypersensitivity has been found to cause or exacerbate atopic dermatitis in 10-30% of cases, and 90% of these are caused by eggs, milk, peanuts, soy and wheat.

Compromised gut health

The connection between the gut microbiome and skin health is complex, however, research has found the microbiota contributes to the development, persistence, and severity of atopic dermatitis through immunologic, metabolic and neuroendocrine pathways.

Nutritional deficiencies

Deficiency of Omega-6 essential fatty acids (EFA) has been linked with the increased incidence of atopic dermatitis, along with the inability for the body to efficiently metabolise EFA’s to gamma linoleic acids (GLA) and arachidonic acids (AA).

Weather and environment

Changing weather conditions can certainly aggravate eczema symptoms, but the triggers are subject to change among individuals.


Hormones also play a role in the course of atopic dermatitis, including the stress hormone cortisol which triggers an inflammatory immune response affecting all organs of the body, including the skin.

Mould exposure

Mould exposure and susceptibility to mould can cause Chronic Inflammatory Response Syndrome (CIRS), of which dermatitis is a manifestation.

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SIBO treatment - the conventional approach

Diagnosis via conventional testing alone is imperfect and is made via either hydrogen and methane breath testing, or the gold standard is jejunal aspirate testing. This test extracts a small sample of fluid from the middle part of the digestive system called the jejunum via an endoscope. The limitations of jejunal aspirate tests are cost, the invasive nature of the testing, and potential for false negatives due to difficulties in growing cultures.

Conventional methods of SIBO treatment usually includes antibiotics such as rifaximin, and whilst it may kill undesirable species, it is indiscriminate and also kills beneficial species. This can allow opportunistic species to overgrow in much the same way as weeds that grow back in the garden when the ground is cleared. In addition, studies show that rifaximin is not effective at treating SIBO symptoms.

Usually, SIBO takes a long time to heal, and requires a holistic approach to uncover the factors involved in causing or aggravating SIBO, along with a staged approach that patients are supported through. 

SIBO test Melbourne and Australia-wide

The SIBO test available in Australia is a breath test that helps identify if hydrogen or methane producing species are causing SIBO. SIBO tests in functional medicine are used in conjunction with detailed case taking involving your personal health history which includes antibiotic use, family history and genetic predispositions, current and historical medications, your symptom picture and any other conditions.

Additional to the breath test for SIBO, we may also test for:

SIBO natural treatment - the functional medicine approach

Our SIBO functional medicine naturopaths will identify the root cause of SIBO and treat these underlying causes. Our team of SIBO specialists have a holistic understanding of SIBO, with access to the most up-to-date scientific insights. 

After interpreting SIBO breath test results and other functional testing, the functional medicine SIBO approach involves your practitioner identifying underlying issues causing your symptoms, and tailor a treatment plan to suit you. 

Your personalised natural SIBO treatment may include:

  • Probiotics to alter the gut environment and support beneficial species
  • Prebiotics to feed beneficial species and increase production of beneficial short chain fatty acids
  • Nutritional supplementation such as zinc, vitamin A, magnesium for reducing inflammation, improving gut linings and improving digestion
  • Tailored dietary modifications/SIBO diet
  • Herbal medicines e.g. specific microbial modulators; pomegranate husk, codonopsis pilosa, garlic and Korean ginseng, and for symptomatic relief e.g. slippery elm, chamomile and ginger
  • Identifying and addressing food intolerances/sensitivities to prevent relapse or recurrence of symptoms
  • Supporting digestion via digestive enzymes, improving transit time or supplementing with targeted probiotics to prevent dysbiosis or parasite recurrence
  • Lifestyle modifications to enhance stress resilience

The benefits of herbal medicine as treatment for SIBO is their ability to target specific microbes, ensuring that the beneficial species are supported while the pathobiont species (those that are not beneficial when in the wrong location, or number) are suppressed. Optimising digestive function is an important part of a holistic treatment, as well as addressing any other conditions that you may have, in addition to SIBO.

In our six month signature program, your practitioner along with a health coach will provide you with all the support you need to overcome SIBO, empowering and educating you to implement the changes needed so you can feel happy and healthy in your body again.

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What are the symptoms of SIBO versus IBS?

SIBO can occur alone or alongside IBS, and both conditions have similar symptoms, making clear diagnosis difficult.

The most common symptoms of SIBO include loose stool/diarrhoea, constipation, bloating, abdominal pain, excessive and/or smelly flatulence, belching/burping, nausea, reflux and heartburn.

Vitamin & mineral deficiencies due to poor absorption of nutrients can cause symptoms that may not appear to be connected such as skin, mood disorders, joint pain, and brain fog/memory problems can also occur.

Functional testing and detailed case taking can help to ascertain whether symptoms are due to SIBO or IBS, or both. This is the essence of the functional medicine SIBO approach.

How long does it take to heal SIBO?

Depending on the root cause, any other conditions and how long the symptoms have been experienced, it may take some time to heal SIBO.

Malabsorption and maldigestion as a result of SIBO may cause other conditions such as intestinal hyperpermeability which can then trigger new food intolerances and sensitivities.

Nutritional deficiencies need to be addressed to ensure your body has the cofactors it needs to restore healthy digestive function.

Our Melbourne SIBO specialists take the functional medicine SIBO approach, and treat each of the underlying issues in turn, with latest science-backed treatments to ensure your optimal recovery. 

What is SIBO, and what causes SIBO?

SIBO is a form of gut dysbiosis, where the presence of particular microbial species that normally live in the large intestines are located in the small intestines, causing fermentation of carbohydrates much higher up in the digestive process than it should.

This results in pain, bloating, diarrhoea, constipation, and a range of other symptoms.

If left untreated, other conditions can develop due to poor nutrient absorption, and depletion of vitamins and minerals and intestinal hyperpermeability (also known as ‘leaky gut’).

SIBO has a number of causes, from stress and anxiety, to medications, poor diet, surgery, and other health conditions.

SIBO testing by a specialist SIBO functional practitioner can help isolate the root cause of SIBO.

Does SIBO cause bad breath, or GERD?

Maldigestion due to SIBO can cause bad breath, and GERD, as well as a variety of other symptoms. 

Can SIBO cause acne?

Poor digestion can be associated with skin symptoms such as acne, rosacea, psoriasis and eczema.

This can be due to inflammation of the gut, and malabsorption of nutrients essential for healthy skin maintenance and turnover.

SIBO can cause intestinal hyperpermeability which can also affect the cells of the skin surface, via food allergies or sensitivities.

Poor production of short chain fatty acids (SFCA) by disturbed gut microbiome species in the colon can also affect the ability of the body to repair damage to skin and cells that line the body (epithelial cells), whether they are on the outside or on the inside of the body. 

Is there a natural SIBO specialist in Melbourne, able to interpret SIBO breath test results?

Our SIBO naturopath specialists located in Melbourne specialise in SIBO breath test interpretation, and natural SIBO treatment plans using a functional medicine SIBO approach.

SIBO test interpretation is most effective when combined with detailed, holistic case taking to ensure that the root cause is identified and addressed.

To find out how to test for SIBO, read our SIBO test Melbourne and Australia-wide section above.

Can SIBO be detected in a helicobacter test?

The helicobacter pylori test cannot detect SIBO.

This test investigates the presence of H. pylori in the stomach.

A specific SIBO breath test is the first step to identifying if you have SIBO, which tests for methane and hydrogen gases which are a byproduct of hydrogen or methane producing microbial species that may be present in the small intestines.

If you’re looking for a SIBO test Melbourne and Australia-wide, our SIBO specialists can interpret the test and provide a natural SIBO treatment.

Is there a SIBO specialist near me?

Yes if you’re looking for a SIBO treatment Melbourne and Australia-wide, we are based in South Melbourne and are also available via telehealth to guide people across Australia back to better health.

Our functional medicine trained SIBO naturopaths are SIBO specialists, and can help you optimise your recovery to feel well again.

Can’t find what you’re looking for? Reach out to the team directly – we’ll be happy to assist.

Can’t find what you’re looking for? Reach out to the team directly – we’ll be happy to assist.