SIBO: rebalancing gut bacteria by addressing root causes
SIBO can lead to bloating, pain, and nutrient deficiencies. Functional medicine identifies the underlying imbalances, supporting gut healing and microbial balance for lasting digestive health.
Natural SIBO treatment in Melbourne and Australia-wide
Are you looking for SIBO natural treatment in Melbourne or Australia, or want to find out how to test for and treat SIBO? This page covers:
Our SIBO treatment offers natural SIBO care through our revolutionary approach to healthcare.
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. Many health conditions are associated with the presence of SIBO.
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. Many health conditions are associated with the presence of SIBO.
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 microbial bacteria producing methane, hydrogen or a combination of both or sulphur-reducing microbial species residing in the small intestine. Symptoms can differ from person to person, although the most common SIBO symptoms can include:
- Bloating and abdominal distention
- Loose bowel motions or diarrhoea
- Food allergies, intolerances and sensitivities
- Abdominal pain and/or cramping
- Excessive, smelly flatulence
- Constipation
- Alternating constipation and diarrhoea
- Belching/burping
- Nausea
- Brain fog & memory loss
- Histamine intolerance
- Joint pain
- Reflux/heartburn
- Skin complaints such as hives, eczema, psoriasis, acne or rashes
- Joint pain
- Intestinal hyper-permeability
- Sleep disruption
- Anxiety, depression and neuropsychological symptoms
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 60% of people diagnosed with IBS (irritable bowel syndrome) making diagnosis difficult (see our article on IBS and SIBO to find out more). And for patients diagnosed with inflammatory bowel disease (IBD), studies reveal they are 9.5 times more likely to develop SIBO.
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.
Want to treat your SIBO, naturally?
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 )
- Chronic stress
- Poor diet (e.g. high sugar, alcohol, processed carbohydrates)
- Abdominal surgery
- Traumatic brain injury, concussions
- Side effects of medications e.g. opiates, antispasmodics, PPIs
- Scarring and adhesions of the small intestines
- Pancreatitis
- Endometriosis
- Gastroparesis
- Scleroderma
- Diabetes
- Mould toxicity
- Ehlers-Danlos Syndrome (EDS)
- Ileocecal valve dysfunction
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.
2. 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. These microbes feed on the hydrogen produced by species of bacteria, creating a methane gas byproduct which is also responsible for abdominal bloating and slows transit time or migrating motor complex of the GIT, leading to constipation or irregular bowel motions.
3. Hydrogen sulphide producing bacteria
The third type of SIBO is due to the hydrogen sulphide producing bacteria, commonly Desulfovibrio spp or Fusobacterium spp. This SIBO type is less common and tests negative on traditional breath testing which only tests for hydrogen and methane gas which these species don’t produce.
The by-product of these 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. Hydrogen sulphide metabolisation is normal in the cecum and in the colon, but not when it occurs in the small intestine. These species reduce sulphate to hydrogen sulphide gas and are also referred to as sulphur reducing bacteria (SRB). High concentrations of hydrogen sulphide are involved in gut inflammation.
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
Diagnosing SIBO accurately is essential for effective treatment. The most common diagnostic tool for SIBO is a breath test that measures hydrogen and methane gas levels. These gases are produced by certain bacteria and archaea in the small intestine.
Unlike a Helicobacter pylori test, which detects the presence of H. pylori in the stomach, the SIBO breath test is specifically designed to identify bacterial overgrowth in the small intestine. It involves collecting breath samples after consuming a specific sugar solution (e.g., lactulose or glucose) and analysing them for gas production over time.
Our functional medicine approach goes beyond breath testing to develop a comprehensive understanding of your condition. In addition to the SIBO breath test, we may also recommend:
- Food allergy, intolerance, or sensitivity testing
- Gut microbiome analysis
- Digestive function and nutrient absorption assessments
- Stool testing for bacteria, including Enterococcus, Klebsiella, H. pylori, and E. coli
- Other functional tests tailored to your specific symptoms
These tests help uncover underlying factors contributing to SIBO and guide a personalised treatment plan. Our practitioners combine test results with a detailed health history to identify triggers such as antibiotic use, genetic predispositions, and lifestyle factors.
Through this holistic approach, we ensure that every aspect of your health is considered, leading to more effective and lasting relief from SIBO symptoms.
Case study
See how our approach helps our patients achieve better health and richer lives.
Jenny came into the program with significant health concerns, which included bloating, constipation, brain fog, and migraines. These, plus other ongoing issues had severely impacted her ability to work, as she struggled with unpredictable health fluctuations. After finding little help from allopathic medicine specialists, Jenny turned to us as a last resort, hoping for answers and a path to recovery.
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 practitioners 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 will 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, and magnesium for reducing inflammation, improving gut lining 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. aloe vera, turmeric, gentian, 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 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 healthcare 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.
Jenny’s story
Jenny came into the program with significant health concerns, which included bloating, constipation, brain fog, and migraines. These, plus other ongoing issues had severely impacted her ability to work, as she struggled with unpredictable health fluctuations. After finding little help from allopathic medicine specialists, Jenny turned to us as a last resort, hoping for answers and a path to recovery.
An in-depth analysis of the problem
To understand the root causes of Jenny’s symptoms, several targeted tests were conducted:
- SIBO breath test: This checked for bacterial overgrowth in the small intestine, which can cause bloating, constipation, and nutrient malabsorption, contributing to brain fog and fatigue
- Nutristat panel: This assessed nutrient levels, hormones, and toxicity, helping to identify deficiencies (e.g., B-vitamins, magnesium) and imbalances linked to her neurological symptoms and digestive issues
- GI360: This evaluated gut inflammation, pathogens, and parasites that could worsen her digestive symptoms and migraines
- MyDNA test: This identifies genetic susceptibilities, offering insights into why Jenny was prone to certain symptoms and guiding her treatment plan
These tests provided a comprehensive view of her condition, allowing for a more precise treatment approach.
Through this testing, we discovered that Jenny tested positive for SIBO. Small intestine bacterial overgrowth is a condition where bacteria normally found lower in the large intestine have overgrown in the small intestine.
The investigation phase was crucial in revealing the underlying issues contributing to Jenny’s symptoms. Based on the results, her practitioner developed an individualised plan, focused on Jenny’s specific conditions and health goals. The main components of her treatment included:
- SIBO bi-phasic diet: This diet is designed to eliminate fermentable fibres – the primary food source for bacteria in the gut. The diet is divided into two phases: Reduce and Repair, and Remove and Restore. This diet can be challenging due to its restrictiveness, particularly for patients like Jenny, who was already dealing with brain fog and chronic exhaustion
- Herbal treatments and antibiotics: Jenny was prescribed rifaximin by her doctor, an antibiotic specifically designed to kill off unwanted bacteria in the small intestine. This phase came with its own challenges, as the “kill-off” process often leads to a detox reaction, temporarily worsening symptoms
Implementing the solution
Jenny faced several barriers during her treatment, including:
- Constantly feeling the need to be productive
- Limited mental clarity to understand and implement dietary changes
- An extensive and complex treatment plan
- A limited support network
Breaking down these barriers was a central focus of the discussions between Jenny and her health coach. Through motivational interviewing and active listening, Jenny realised the importance of slowing down and prioritising her own health. She learned to release the pressure of needing to do everything for everyone else, and give herself the space to heal.
Jenny’s health coach provided ongoing support by helping her create a manageable plan for the restrictive phase of the diet. This included identifying a rotation of meals she could consistently eat, which made the diet feel more “doable” to her.
Jenny had felt isolated in her health journey, with few people truly understanding what she was going through. The support from her practitioner and health coach was pivotal in helping her implement the treatment strategies and begin regaining her health.
The weekly coaching calls provided Jenny with a safe space to be herself, feel heard, and be valued. This support was something she had not experienced before, and it played a crucial role in her healing process. As Jenny expressed, “I feel like I’m not falling through the cracks. Like I have a voice and am being heard.”
Through the exercise of setting a health vision, Jenny connected deeply with her health goals. This vision motivated her to make the necessary lifestyle changes, even when faced with setbacks. Regular check-ins with her health coach allowed Jenny to tune into her body’s needs, whether it was rest, better food choices, or creative endeavours.
Achieving an incredible result
After the initial 3-month treatment of SIBO, a retest showed significant improvement and an overall downward trend in her symptoms. Jenny’s digestive system felt much better, with regular bowel motions and reduced bloating. She shared her excitement:
“I feel like I’m on the way now – really excited. I know that I will achieve the goal of getting well – I feel it coming . I’m ready to thrive in my life.”
Her brain fog had also subsided with reports of “getting my brain back!”
After treatment, Jenny’s energy levels improved to the point where she could participate in a much-loved activity – hiking with friends – without the fear of being unable to complete it. She continued to make steady progress toward her goals.
As she moved into Phase 2 of the SIBO bi-phasic diet, Jenny faced new challenges, such as the apprehension about reintroducing certain foods and maintaining her newly found vitality. However, she managed these challenges by focusing on enjoying the process of making her own food, and finding joy in the “sweetness of life” beyond just sugary treats.
Throughout her journey, Jenny began reconnecting with her true, authentic self. With the guidance of her health coach, she learned to regularly check in with herself, asking, “What do I need right now?” . This practice allowed her to listen to her body’s needs and respond accordingly, whether that meant taking a walk, choosing a better food option, resting, or engaging in creative activities.
Along with the expert guidance from Jenny’s practitioner, and uncovering the root cause of her symptoms, the coaching space provided Jenny with the opportunity to be seen, heard, and validated, which was a powerful catalyst for healing and the continued restoration of her health.
Ready for a personalised, natural functional medicine treatment?
Our unique model of care was designed with you in mind. Find out how, then book a call today
Frequently
Asked
Questions
What are the symptoms of SIBO versus IBS?
SIBO and IBS share many overlapping symptoms, which is why they are often confused and can occur together.
Typical SIBO symptoms include:
- Bloating and abdominal distension
- Abdominal pain or discomfort
- Diarrhoea, constipation, or alternating between both
- Excessive or smelly flatulence
- Belching or burping
- Nausea, reflux, or heartburn
SIBO may also lead to nutrient deficiencies from poor absorption, causing less obvious symptoms like skin issues, brain fog, memory problems, joint pain, or mood changes.
Functional testing and thorough case-taking are the most reliable ways to identify whether your symptoms stem from SIBO, IBS, or a combination of both. This comprehensive approach is central to functional medicine treatment for SIBO.
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 practitioners 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?
Small Intestinal Bacterial Overgrowth (SIBO) is a form of gut dysbiosis where bacteria that should normally remain in the large intestine migrate into the small intestine. This leads to premature fermentation of carbohydrates, causing bloating, abdominal pain, diarrhoea, constipation, and other digestive symptoms.
If left untreated, SIBO can also contribute to nutrient malabsorption, vitamin and mineral deficiencies, and intestinal hyperpermeability (often called “leaky gut“).
Can SIBO cause acne or other skin conditions?
Yes. SIBO can affect the skin through several pathways:
- Inflammation and malabsorption: Poor digestion can lead to nutrient deficiencies (e.g. zinc, vitamin A, essential fatty acids) that are critical for healthy skin repair and turnover
- Intestinal hyperpermeability (“leaky gut”): This can trigger immune reactions to foods, contributing to acne, rosacea, psoriasis, or eczema
- Reduced short-chain fatty acids (SCFAs): Disrupted gut microbes produce fewer SCFAs, which are vital for repairing epithelial cells, including those on the skin surface
This gut–skin connection explains why SIBO may be linked with chronic skin concerns that don’t respond to topical treatments alone.
Can SIBO be diagnosed from a stool test?
No. Diagnosis of SIBO cannot be confirmed via stool testing.
Stool testing provides an assessment of the large intestinal environment only and does not provide any information regarding the small intestine.
Can SIBO cause weight gain?
Yes, but it can also cause weight loss. The impact of SIBO on weight depends on how it disrupts digestion and metabolism:
- Insulin resistance: Impaired digestion and microbial imbalance can affect blood sugar regulation, promoting fat storage and weight gain
- Gut barrier damage: Increased intestinal permeability (“leaky gut”) and higher endotoxin levels drive inflammation, which is linked with obesity
- Nutrient malabsorption: In some cases, SIBO reduces nutrient absorption so severely that it leads to weight loss instead
This activity in the gastrointestinal tract influences the body’s ability to manage both inflammation and obesity. Because SIBO can push metabolism in either direction, a personalised assessment is needed to understand how it affects your weight.
What causes SIBO?
SIBO can develop for many reasons, often involving a disruption of the normal digestive environment. Contributing factors may include:
- Stress and anxiety that alter gut motility
- Medications that disrupt the gut microbiome
- A poor diet lacking in diversity and fibre
- Previous abdominal surgery
- Other digestive or systemic health conditions
Because the underlying cause varies, functional SIBO testing and a thorough case assessment are essential for identifying why SIBO has developed and guiding treatment.
Can’t find what you’re looking for? Reach out to the team directly – we’ll be happy to assist.
