Site Logotype

Could it be Small Intestinal Bacterial Overgrowth?

If you’ve read anything in the digestive world of late, chances are you’ve come across the term SIBO. This stands for Small Intestinal Bacterial Overgrowth. Bloating, flatulence and abdominal pain are just some of the symptoms to look out for.

What exactly is SIBO?

SIBO is an overgrowth of bacteria in the small intestine. It can be an increase in the number of bacteria, or abnormal types of bacteria. These bacteria produce methane, hydrogen & other gases that contribute to the uncomfortable symptoms of SIBO.

In the medical literature, SIBO is specifically defined as more than 100,000 colony-forming units of bacteria per mL of proximal jejunal fluid, which means a high concentration of bacteria in one specific section of the small intestines. The small intestine isn’t designed to be sterile, but bacteria counts rarely exceeds 1000 per mL. To put bacteria numbers into perspective, the large intestine is thought to home 100 billion bacteria per mL of fluid!

The 2 types of SIBO that can occur, with corresponding bacterias are:

  • Gram positive bacteria from the upper respiratory tract and oral cavity
  • Aerobic bacteria: streptococcus, staphylococcus, enterococcus, micrococcus, lactobacillus, corynebacterium
  • Anaerobic bacteria: Fusobacterium, peptostreptococcus
  • Colonic bacteria translocating from the large intestine
  • Aerobic bacteria: Escherichia coli, Klebsiella, Proteus, Acinetobacter, Enterobacter, Neisseria, Citrobacter
  • Anaerobic bacteria: Bacteroidetes, Clostridium

* Aerobic bacteria need oxygen to survive, whereas anaerobic bacteria do not.

Why is it a problem?

SIBO negatively affects both the structure and function of the small bowel. It interferes with the digestion of food and absorption of nutrients via a number of mechanisms. Absorption is reduced due to damage that can occur to the cells lining the small intestine – which has its own flow-on problems and immune reactions. Additionally, bacteria can sequester the nutrients before our own cells have had a chance to absorb them, leading to deficiencies in vitamin B12 and Iron. Absorption of fat soluble vitamins, such as vitamin D, can also be affected due to the bacteria’s ability to deconjugate bile acids.

Signs & symptoms

As with any digestive condition, the signs & symptoms can vary. The main gastrointestinal symptoms to look out for are:

  • Bloating
  • Flatulence
  • Abdominal discomfort
  • Increased burping
  • Nausea
  • Diarrhoea is more common, although constipation can occur if there is methane dominant bacteria.

Symptoms beyond the gut to consider are:

  • Unexplained weight-loss
  • Signs of malnutrition
  • Signs of nutrient malabsorption, such as iron deficiency anemia & low vitamin B12.

What causes it?

The human body has many natural defense mechanisms against bacterial overgrowth, which include:

  • Gastric acid: this has an important role of killing undesirable bugs.
  • Intestinal motility: which refers to the functions & muscles of the intestinal tract which propel food from the mouth, through the gastrointestinal tract, to excretion. A function of motility is the migrating motor complex (MMC), which is a process of cleansing waves that clear remenance from the small intestine into the large intestine, to ensure bacteria numbers in the small intestine stay relatively small.
  • A well functioning ileocaecal valve: this is the ‘door’ that separates our less populated small intestine from our intensely populated large intestine.
  • Intestinal immunoglobulin (IgA) secretion: these are digestive secretions that break down bacterias – our immune defense.
  • The bacteria inhibiting properties of pancreas and bile secretions: these are secretions involved in the digestive process, which help to keep bacteria numbers in check.

When these protective barriers fail, SIBO can occur. The causes are complex, but fit into three main categories. In some people, more than one factor can be involved.

Disorders of the protective antibacterial mechanisms

  • Low stomach acid is the most common contributor to SIBO, caused by:
  • Antacid and PPI use. These medications decreases stomach acid and create an alkaline environment, which bacteria love to grow in!
  • High stress directly decreases the production of hydrochloric acid.
  • Low fibre Western Diet. Fibre helps to ‘acidify’ the gastrointestinal environment, which is what we want!
  • Pancreas insufficiency or pancreatitis.
  • Immune deficiency syndromes: including coeliac & crohn’s disease.

Dysmotility & motility disruptors

  • Dysmotility is a key contributor. Anything that impairs flow through the small intestinal will lead to stagnation and bacterial overgrowth. Generally bacteria are moved out of the small bowel into the large bowel via peristalsis and the MMC function, and the ileocecal valve prevents movement of bacteria from the colon back into the small intestine. But if we have disruptions in intestinal motility, bacteria begin to accumulate in the small intestine.
  • Constipation &/or diarrhoea: are both altered motility functions.
  • Certain medications: such as opiate painkillers which significantly delay bowel transit time
  • Constant snacking: which interrupts the body’s natural sweeping (MMC) process
  • Being over 75yo: as gastrointestinal motility naturally decreases with age

Anatomical abnormalities

  • Small intestinal obstruction
  • Diverticula
  • Ileocaecal valve resections or functional problems
  • Gastrectomy
  • Surgical blind loop
  • Short bowel syndrome

How do we find out if we actually have SIBO?

At the moment SIBO has an imperfect gold-standard diagnosis, being the Jejunal Aspirate and Culture, which is obtained by means of patient intubation and aspiration at multiple intestinal sites. This is imperfect because intubation is very invasive & costly.

This leaves us with the next best option which is breath testing. Breath testing involves consuming a sugar, and if there is sufficient bacteria in the small intestine they will ferment the sugar and produce hydrogen and/or methane and carbon dioxide, which is captured in the breath. A sufficient rise in either hydrogen and/or methane within a given timeframe, would indicate SIBO.

Two commonly used sugars in the breath test are:

  • Glucose: This is the preferred choice, at it has a higher diagnostic accuracy of 71.7%. With the glucose breath testing a hydrogen rise of >20ppm within 90 minutes, or a methane rise of >10ppm within 90 minutes, would confirm positive for SIBO.
  • Lactulose: While this is commonly used, it only has a diagnostic accuracy of 55.1%. There are a number of concerns with lactulose testing giving false positives. Lactulose is a laxative and can increase transit time. A faster transit time could mean the rise in gas production that we see in the test is because the lactulose has reached the colon – which would mean a false positive diagnosis of SIBO.

Conventional Treatment of SIBO:

Antibiotics are the conventional treatment for SIBO with Rifaximin being the best tolerated and least damaging to the large intestines bacterial population. Antibiotics have varying success rates, although without correcting the underlying cause of SIBO, relapse is likely.

Prokinetic medications may be prescribed to encourage healthy movement through the small intestine post antibiotic treatment.

What can we do about it?

The work in SIBO, like most gut work, is done in stages and includes the following elements:

Remove the contributing factors

  • Work with the GP to remove any medication that may be contributing, such as PPIs and opiate pain killers.


  • Consume a wholefood diet with a variety of fresh vegetables, wholegrains, good quality protein, and healthy fats.
  • Leave 3-5 hours in between meals.
  • Remove refined sugars and refined carbohydrates.
  • If reflux is a problem, avoid coffee, alcohol, chocolate, citrus, tomato, and spicy foods.
  • Work to acidify pH levels in the gastrointestinal tract by consuming a variety of fibre.


  • If stress levels are elevated, management of this is key!
  • Yin yoga, meditation and breathing exercises may all be effective.


  • Pomegranate, garlic, clove, thyme, oregano & berberine have all shown to be effective.
  • Antimicrobials are powerful modulators of gut flora! Therefore they should only be prescribed under the guidance of a practitioner.


  • Ginger & globe artichoke can both work to promote bowel motility. Dosages vary depending on the form used.


  • PHGG: take 7 to 15g per day, starting slow and titrating up.
  • GOS: take 3 to 15g per day, starting slow and titrating up.
  • Lactulose: works as a prebiotic and can also enhance small bowel motility. This may cause gas related symptoms in some people, therefore should be prescribed via a practitioner.


  • Lactobacillus rhamnosus GG: 20 billion CFU daily.
  • Lactobacillus Plantarum 299v: 20 billion CFU daily.

Gut Healing

  • Glutamine: 10g twice daily.
  • Saccharomyces cerevisiae (boulardii): 500mg twice daily.

Correct Nutritional Deficiencies

  • Assess for and correct any nutritional deficiencies, such as iron, vitamin B12 and vitamin D.

Preventing Relapse

Relapse in SIBO is very common with research from 2019 stating that approximately 44% of patients with SIBO may experience a relapse of symptoms within 9 months of initial treatment after antibiotics.

Relapse will also occur after naturopathic treatment if the initial contributing issue is not addressed and resolved! Ways to prevent recurrence are maintaining a high fibre diet to keep the bowel environment acidic, using prokinetic herbs to encourage gastrointestinal motility, and reducing snacking to enable the MMC to sweep the stomach and small intestine clear as it needs to.

If you are experiencing digestives symptoms and would like individualised support, please get in touch by booking in a Base Chat or Simplify Session here.


Brooke Schiller, BHSc Nat & Nut, BCom

Brooke is a qualified naturopath with a focus on digestive health, hormones, and adrenal conditions.

Learn more about Brooke here

Book a session with Brooke here


J Hawrelak SIBO Master Class