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SIBO: What causes small intestinal bacterial overgrowth & Functional Medicine approach to SIBO

SIBO: What causes small intestinal bacterial overgrowth & Functional Medicine approach to SIBO

SIBO: What causes small intestinal bacterial overgrowth & Functional Medicine approach to SIBO

Small Intestinal Bacterial Overgrowth (SIBO) is a form of gut dysbiosis affecting the small intestine, requiring specialised SIBO treatment to return the gut to optimal health and improving overall wellbeing. We specialise in the treatment SIBO at our Perth clinic of Advanced Functional Medicine, treating patients both in Perth and Australia wide.

Initially thought to occur in only a small number of patients, it is now apparent that this disorder is more prevalent than previously thought. 1 SIBO affects millions of people around the world but is still a relatively unknown condition and often goes undiagnosed for years, if not decades. 

What is SIBO?

sibo treatment perth
Image source: Dr Hagmeyer

SIBO occurs when there is an increase in the number of bacteria, and/or changes in the types of bacteria present in the small intestine.

In most patients, SIBO is not caused by a single type of bacteria but is an overgrowth of the various types of bacteria that should normally be found in the colon.  Less commonly, SIBO results from an increase in the otherwise normal bacteria of the small bowel. 2

The excess bacteria feed off of the undigested food in the small intestine, particularly sugar, simple and complex carbohydrates, starches and alcohol. As the bacteria feeds, it causes the carbohydrates to ferment, which produces hydrogen. Hydrogen can feed single-celled organisms in your small intestine called archaea, which then produce methane. 

So, when you have SIBO, you have excess levels of hydrogen, methane, or both in your digestive system. 3

SIBO has been shown to negatively affect both the structure and function of the small bowel. It interferes with digestion of food and absorption of nutrients, primarily by damaging the cells lining the small bowel (the mucosa). Additionally, this damage to the small bowel mucosa can lead to leaky gut (when the intestinal barrier becomes permeable, allowing large protein molecules to escape into the bloodstream), which is known to have a number of potential complications including immune reactions that cause food allergies or sensitivities, generalized inflammation, and autoimmune diseases. 4

SIBO causes

After enzymes break down our food, our gut relies on nerves, muscles, and neurotransmitters to move the food through our digestive tract from the stomach to the small intestine and to the colon. In a healthy gut, bacteria get passed through the digestive tract along with the food to its final destination in the colon. Problems arise when something interferes with this process.

SIBO can be caused by a number of factors, including:

  • Damaged nerves or muscles in the gut can result in leftover bacteria in the small intestine, increasing your risk of SIBO. For example, diabetes mellitus, hypothyroidism, and scleroderma can affect the muscles in the gut.
  • Physical obstructions in the gut, such as scarring from surgeries or Crohn’s disease, can also cause an abnormal build-up of bacteria in the small intestine. Diverticuli, which are tiny pouches that can form in the wall of the small intestine, can also collect bacteria instead of passing it on to the colon, where it belongs.
  • Decreased motility in the small intestine caused by a diet high in sugar, refined carbohydrates and alcohol, and inadequate dietary fibre.
  • Hypochlorhydria – as people get older, the amount of stomach acid they secrete declines. If there is less stomach acid, bacteria are more likely to proliferate. Overuse of antacids such as Gaviscon, Rennie, and Tums is also thought to lead to bacterial overgrowth.
  • Immune deficiency, chronic stress, and pancreatic enzyme deficiency.
  • Medications that influence or disrupt the normal gut flora, including antibiotics, acid-blocking drugs, birth control pills, and steroids. 

SIBO is associated with various conditions, such as:

  • Viral gastroenteritis, or a stomach bug
  • Celiac disease
  • Crohn’s disease
  • Hypochlorhydria, or low stomach acid levels
  • Gastroparesis
  • Nerve damage
  • Cirrhosis
  • Portal hypertension
  • Irritable bowel syndrome
  • Certain gastric bypass procedures 
  • Surgeries that cause strictures or adhesions

SIBO symptoms

Bacterial overgrowth symptoms vary in individuals, ranging in severity and presentation. SIBO symptoms can include:

  • Bloating
  • Abdominal pain and/or cramping
  • Constipation
  • Diarrhoea
  • Alternating constipation and diarrhoea
  • Food intolerances and sensitivities
  • Belching and/or flatulence
  • Nausea
  • Heartburn / acid reflux
  • Fatigue
  • Brain fog
  • Memory loss
  • Chronic digestive complaints
  • Joint pain
  • Depression and/or anxiety
  • Respiratory symptoms, such as asthma
  • Skin issues such as itchy skin, hives, rashes, eczema, psoriasis, acne 
  • Vitamin and mineral deficiencies, especially Vitamin B12 and iron 5
sibo symptoms
Image source: News Medical

Types of SIBO

Depending on which gas is predominantly produced, you can develop different symptoms and respond to different treatments. 

Hydrogen-dominant SIBO typically leads to diarrhea or loose stools, whereas methane-dominant SIBO is usually associated with constipation. 

SIBO-D: Diarrhoea and hydrogen-producing bacteria

Diarrhoea-dominant SIBO is the more common form of diagnosed SIBO and is the result of carbohydrate-fermenting bacteria that produce hydrogen gas in the small intestine. And unlike the large intestine, the small intestine is very sensitive to the production of hydrogen. This excessive production of hydrogen in the small intestine is what causes the abdominal bloating and the diarrhoea / loose stools.

SIBO-C: Constipation and methane-producing archaea

It’s not technically bacteria, but single-celled organisms called archaea.  Archaea are mostly responsible for the constipation-dominant form of SIBO. 

Archaea, such as Methanobrevibacter smithii, feed off the hydrogen produced by bacteria during the fermentation of carbohydrates and produce a by-product of their own – methane. As with hydrogen in the small intestine, methane gas will also cause abdominal bloating, plus a much bigger problem – slowing down transit time which leads to constipation. 

Constipation allows more bacteria to grow, which causes more methane and more constipation. And to make matters worse, archaea are more stubborn and difficult to treat with antibiotics and antimicrobial herbs. They can also survive for a while without hydrogen, so killing their food source can also have minimal short-term benefits. 

Hydrogen sulphide-producing bacteria and ‘rotten egg’ gas

While less common, the third type of SIBO is gaining attention because of its prevalence amongst those with SIBO symptoms, who test negative on traditional breath testing.

Sulphate-reducing bacteria (SRB) in the small intestine produce hydrogen sulphide, a highly toxic gas to the cells of the intestinal wall, best known for its distinctively foul odour of rotten eggs. Because they also consume hydrogen, these bacteria compete with methanogenic archaea (SIBO-C type) and may keep levels of each other in-check. But for those with both types, this means that killing only one species may allow the other to overgrow further. 6

SIBO treatment Perth and Australia wide

SIBO is a tough condition that often comes back and requires multiple rounds of treatment.

For the best outcomes, the infection should be eradicated, any associated nutrient deficiencies should be corrected, and the root cause(s) should be identified and managed.

There are three ways in which SIBO is commonly eradicated:

  • Prescription antibiotics
  • Herbal antimicrobials
  • Elemental diet

While antibiotic treatment for SIBO is generally considered safe and effective, there are high rates of SIBO recurrence after treatment.

SIBO diet

Functional Medicine health practitioners often recommend a diet that limits the intake of sweet and starchy foods. One such diet is the specific carbohydrate diet, which restricts grains, starchy vegetables, and some legumes, and was created to address digestive disorders such as bacterial overgrowth, Crohn’s disease, and ulcerative colitis.

Other recommendations include:

  • Medium-chain triglycerides. Unlike regular oils, which a person with bacterial overgrowth may not be able to assimilate, medium-chain triglycerides are absorbed directly without the need for digestive enzymes. Medium-chain triglycerides, such as coconut oil, are often recommended for people with bacterial overgrowth or any type of malabsorption. 
  • Digestive enzyme supplements can support the body’s digestive enzymes until the function is restored. They should be taken before meals. 
  • Vitamins and minerals that may be deficient in people with bacterial overgrowth include vitamin B12, folate, magnesium, calcium, iron, zinc, copper, vitamin A, D, E, K.
  • The final step is to restore the good bacteria in your gut. This will help support a strong immune system, optimal digestion, and nutrient absorption. 7 Probiotics are needed to replace healthy bacteria in the intestines. Lactobacillus Plantarum and Lactobacillus GG are some probiotic strains that are used for SIBO. 

Herbs to treat SIBO 

Enteric-coated peppermint oil is one of the more common supplements for small intestine bacterial overgrowth. A typical dose of enteric-coated peppermint oil is one to two capsules three times a day, taken in between meals with a glass of water. Side effects can include heartburn, rectal burning, and minty burping.

Other herbal antimicrobials used to treat bacterial overgrowth include:

  • Grapefruit seed extract
  • Oregano oil capsules
  • Garlic
  • Berberine – goldenseal, Oregon grape
  • Olive leaf extract
  • Pau D’arco – a herbal supplement made from the inner bark of several species of Tabebuia trees that grow in the rainforests of Central and South America 8
sibo natural treatment

SIBO Test Perth and Australia-wide

At Advanced Functional Medicine in Perth and throughout Australia, we perform a number of tests to ascertain if you have SIBO and what type of SIBO you have.

The “gold standard” test is to take bacterial cultures of small intestine fluid, but the most common test is the lactulose hydrogen breath test because it is less invasive.

Lactulose is a non-absorbable sugar that’s fermented if there are intestinal bacteria, resulting in hydrogen production. If there is bacterial overgrowth, fasting hydrogen levels will be high. In addition, after ingesting glucose, there will be a significant rise in hydrogen.

We run hundreds of SIBO tests each year from our clinic and have experience treating all types of SIBO including methane dominant SIBO and hydrogen dominant SIBO.

SIBO treatment Perth

If you would like to find out more about SIBO testing and SIBO treatment, please get in touch with our Perth clinic of Advanced Functional Medicine on 1800 11 22 36 or complete the form below.  We see patients in Perth and Australia wide.


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The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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