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Could SIBO be the cause of your symptoms?

If you have unexplained or multiple symptoms, like acne, reflux, gut distress, anxiety, fatigue, bad breath, neurological problems or chronic pain, SIBO could be to blame. SIBO is the acronym for Small intestinal bacterial overgrowth, and it refers to pathogenic growth of bacteria in the small intestine. Although SIBO occurs in the gut, it can produce widespread symptoms throughout the body.

The small intestine is where most food is digested, and there shouldn’t be much bacteria there as it interferes with intestinal function. SIBO indicates the presence of excessive bacteria in the small intestine. SIBO causes inflammation of small intestine, blunting of the brush border villi responsible for digestion and absorption, and it can further reduce stomach acid, and slow down gut motility.

Risk factors for developing SIBO include irritable Bowel syndrome, slow gastrointestinal motility, metabolic disorders, medications, structural or anatomical issues in the gut, metabolic conditions, and more.



There are many, and as you can see they often occur outside of the gut. According to Chris Kresser 'Patients may present only with non-GI symptoms such as fatigue, skin issues, or muscle aches/pains. In one study, up to 50percent of SIBO patients didn’t have gut symptoms, but 100 percent of fibromyalgia patients had SIBO.' If you have any of the below conditions, it’s definitely worth checking whether SIBO is an issue for you, and whether you can improve upon your health.

  • Acne / rosacea

  • Anemia

  • Gastritis

  • Celiac disease

  • GERD

  • Cystic fibrosis

  • Diabetes

  • Fibromyalgia

  • IBS / IBD

  • Intestinal permeability

  • Liver cirrhosis

  • Non-alcohol fatty liver

  • Parkinsons

  • Restless leg syndrome

  • Muscular dystrophy

  • Histamine Intolerance / Mast Cell Activation Disorder



There are many associated symptoms which makes treating SIBO challenging. The multi system, multi symptom nature of SIBO makes it challenging to detect, unless you know what to look for. SIBO is especially important to test for if probiotics, fermented foods and fiber rich foods (FODMAPS) tend to make your symptoms worse.

  • Bloating / excessive or foul smelling gas

  • Brain fog

  • Leaky gut

  • Constipation

  • Diarrhea

  • Autoimmunity

  • Fatigue

  • Halitosis

  • Malabsorbtion

  • Nutrient deficiency (especially B vitamins and iron)

  • Neurological symptoms

  • Skin problems

  • aches, pain



In functional medicine, there are 4 main processes that contribute and lead to SIBO:

1. Low stomach acid

Stomach acid or hydroclauric acid (HCL) is important in sterilising the food we eat and assisting the mechanical and chemical breakdown of food for digestion. Low stomach acid is associated with an increased risk for multiple diseases because it is our gastrointestinal tracts major defense barrier against invaders. Low stomach acid can occur naturally from stress, aging, vegetarian diets, food poisoning, nutrient deficiency, poor gut health, parasite or bacterial infections, ulcers etc. It can also occur from taking drugs like proton pump inhibitors or other acid blocking drugs. Long term use of acid blocking drugs is a major risk factor for SIBO.

When stomach acid levels are low, pathogenic bacteria levels are not kept in check as they pass through our gut, and food breakdown is compromised. As food cannot be broken down properly, it sits in the gut for longer periods, fermenting, and is acted upon by our gut bacteria.

Low stomach acid leads to…

Carbohydrate, fat and protein malabsorption which leads to….

Bacterial overgrowth and a fermenting, toxic gut

2. Slow Motility

Another major cause of SIBO is reduced motility, or the digestive transit time. Essentially slow motility means food takes longer to pass through your gut. The longer our food sits in our gut, the greater potential for bacterial digestion of our food, poor absorption, constipation and re-absorption of toxins which were meant for excretion. Slow motility can occur from stress, lack of movement, inadequate enzymes or nutrients, low stomach acid, pharmaceutical drugs or even mechanical or anatomical issues in the gut. A major cause of decreased motility is post infectious food poisoning, which can damage the migrating motor complex (MMC), which creates peristalsis or a wave of movement through the small bowels to sweep the contents through.

A major component of SIBO treatment is prokinetic therapy, to keep the bowels moving regularly, and stress management to help shift the body from a sympathetic state where digestive function is reduced, into a parasympathetic state to rest and digest and encourage peristalsis, the wave-like muscle contractions that move the contents of the gut through the gastrointestinal tract.

3. Disrupted microbiome

Bacteria in our large intestine is abundant, and a a healthy balance and diversity of bacteria is health promoting. We have beneficial, commensal, and pathogenic bacteria, all of which keep each other in check. Problems arise when an imbalance occurs from a lack of beneficial bacteria, or an overgrowth of commensal or pathogenic bacteria. Antibiotics are key players in causing a disrupted bacterial microbiome. When this occurs, inflammation, faulty digestive processes, intestinal permeability (leaky gut), immune system reactions, and more can occur. If motility of the gut is reduced, bacteria from the large intestine can migrate into the small intestine, causing problems.

4. Structural Issues

Hernias, bowel obstructions, adhesion's from surgery, and other structural changes can interfere with the movement of foods through the small intestine, allowing food to stagnate for longer, so that bacteria have more time to ferment the waste.

This vicious cycle is why SIBO is so hard to treat, and why antibiotic therapy often doesn’t quite address the root causes of SIBO, or prevent it from reoccurring, unless the above main causes are rectified.


SIBO Testing

Unexplained chronic symptoms often stem from the gut. If you seek a conventional medicine approach to testing your gut, your doctor will likely screen for major health threatening parasites, a colonoscopy, and possibly some inflammation markers, or examine your nutrient status. Functional medicine testing is better for detecting chronic gut problems like SIBO or gut Dysbiosis, which is an imbalance of beneficial, commensal and pathogenic bacteria.

When it comes to SIBO testing, it cannot be tested for in a stool test, which is better for measuring large intestinal function. SIBO is tested with a breath test which screens for the gases produced by bacteria in the small intestine. SIBO can also be diagnosed with an endoscopy, an invasive and costly procedure.

As the test substrate reaches the small intestine, bacteria will act upon it and release gas which will travel to the lungs, and be expelled into the test tube. Higher levels of gas indicate overgrowth. The two gases that are measured are hydrogen and methane, which will catch the most amount of cases.

SIBO testing has limitations, and it’s important to note that a negative SIBO test, in a client with many symptoms, may indicate the overgrowth of a different type of bacteria, which produces different gas (eg hydrogen sulfide) that cannot yet be tested for. Another limitation of SIBO testing, is that it cannot test for Small Intestine Fungal Overgrowth (SIFO), or Hydrogen Sulphide gas, the third major gas present in SIBO. There is no current test that can diagnose this condition.

SIBO breath testing requires a preparation diet, drinking a test substrate and then taking breath samples every 20 min at home, for 3 hours. Because multiple types of bacteria exist, it’s best to run two substrate tests for both lactulose and glucose. Each substrate has it’s own limitations. Glucose testing is more specific, but less sensitive, whereas lactulose testing is more sensitive, but less specific.

Don’t use the 2 hour SIBO test!

Opt for the more comprehensive 3 hour SIBO test. Given that the SIBO test interpretation is subject to your transit time, (the speed at which the test substrate reaches both your large, and small intestine) that extra hour of information is imperative in thorough and accurate SIBO testing. Lets say for example you are constipated, then it’s likely the testing substrate might take longer to reach your small intestines. The opposite is true for faster motility in cases of diarrhea. The best source for testing in Australia is, who use a 3 hour testing method.



Treatment depends on the type of gas produced by the bacteria, and must be customised to the patients other health indications, and root causes of the SIBO.It's important to remember SIBO is a symptom, and so treating the underlying causes (slow motility, low stomach acid, structural defects etc) is crucial for successful treatment, to avoid relapse. Given the extreme complexity of the mechanism of SIBO, there is definitely no 1 size fits all SIBO protocol.

There are 3 main approaches:

  • Pharmaceutical drugs – Rifaxamin and Niastatin are safe antibiotics that acts locally to the gut. Research has even shown that Rifaxamin promotes beneficial bacteria! As with all antibiotic therapy there are associate symptoms and risk, and as a whole antibiotics are not effective at treating biofilms. Biofilms are collonies of bacteria, fungus or parasites that for a carbohydrate based sludge that serves as a force field to prevent detection by the immune system. Biofilm bacteria can resist up to 5,000 x the antibiotic concentration that would normally be needed to resolve infections (which is why antibiotics and herbs may fail to kill the pathogens if those pathogens are surrounded by biofilms, and biofilms aren’t also addressed.)

  • Antimicrobial herbs and biofilm busting herbs with probiotics - botanical protocols efficacy has been shown to be equivalent, or better than rifaximin treatment, with less side effects. Herbal protocols are also more gentle, offer less side effects, and can target biofilms. Treatment is highly customised dependent on what type of bacteria and gas are produced.

  • Elemental diet - When all else fails, a liquid diet consisting of powdered nutrients in pre-digested, easily absorbed form high in the GI tract. It has an 80 to 84% success rate in eradicating SIBO, so it’s the most effective treatment but hard to implement, and best used as a last resort.


Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAPS)

Although clients with SIBO often experience a worsening of symptoms when they eat FODMAP rich foods, a low FODMAP diet isn't advised in treating SIBO or other gut infections. In order to target the bacteria, it's essential to feed the bugs so they do not go into remission, and you can kill them! Also long term low FODMAP diets compromise large intestine gut ecology, because FODMAPS are prebiotic fiber we need to feed beneficial bacteria.


People with SIBO can have many food intolerances, histamine, sulfur or salicilate sensitivities, and there is no blanket food recommendations that suit all SIBO sufferers. With sensitive people it may be necessary to reduce exposure to certain foods depending on sensitivities and the type of bacteria and gases present, however a long term restrictive diet should be avoided as it can create nutrient deficiencies, and further disrupt the gastrointestinal terrain and microbiome. Speak to a qualified health practitioner who can talk you through nutrition and your unique case.

This is a very brief overview of one of the most challenging conditions to diagnose, and treat, in functional medicine. If you need assistance in SIBO testing, treatment or gaining more insight into this condition, reach out and email us here. You can also go ahead and order SIBO testing direct here, by using Priscilla Flynn as your practitioner. There is a great quiz you can take to help determine whether SIBO is likely the cause of your issues.


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