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SIBO and Bloating

Posted 1 year ago by Katie


What is Small Intestinal Bacterial Overgrowth (SIBO)?

Small intestinal bacterial overgrowth (SIBO) refers to a condition in which an abnormally large number of bacteria migrate to the small intestine. The types of bacteria found here with SIBO are what you would normally see in the large intestine, and this migration can therefore interfere with normal digestion and nutrient absorption. The small intestine is approximately 20 feet long and naturally contains far fewer bacteria compared to the colon (large intestine). The issue is with the location of the bacteria rather than the type of bacteria, which is often non pathogenic. 70% of the microbes in our guts reside in our large intestine where they digest and ferment any leftover food that has not been absorbed in the small intestine.  

Up to 78% of Irritable bowel syndrome (IBS) is thought to be SIBO-related, due to the high prevalence of certain bacteria in the small intestine.1  A paradigm shift is underway in to our understanding of IBS and the role that SIBO plays in these symptoms. What we are looking at with SIBO is not necessarily the severity of the bacteria, but the location, although pathogenic strains can also be present with SIBO. These bacteria digest carbohydrates and produce gases that lead to common IBS symptoms such as gas/bloating, diarrhoea and constipation.

Common SIBO gut symptoms:

  • Bloating
  • Constipation
  • Diarrhoea
  • Irritable Bowel Syndrome (IBS)
  • Cramping
  • Gas
  • Nausea
  • Acid Reflux/Heartburn/GERD

An overgrowth of microbes can lead to the production of bacterial toxins in the gut which can provoke an immune response, leading to inflammation. This has a negative effect on your gut lining and can potentially lead to a leaky gut. Therefore, SIBO can be a precursor for leaky gut in some cases. Leaky gut is associated with autoimmune conditions2, rosacea, muscle pain, headaches and fatigue. For more on this topic, you can read the article ‘Healing Leaky Gut’.


 Tipping the microbe balance - dysbiosis


What causes SIBO?

SIBO is generally caused by a lack of muscular activity in and around the small intestine, where by bacteria is not swept away into the colon as it should be, thus leading to dysbiosis.   Gut transit time is an important factor to consider when looking at overall gut health, and SIBO is associated with various digestive and muscular conditions, including diverticulosis3

Ileocecal valve

The majority of our ecosystem of microbes resides in the large intestine and when food reaches the colon about 80-95% of all nutrients have been digested and absorbed. Your small intestine is not meant to be microbe-rich and this is controlled by a valve known as the ileocecal valve which sits in-between the small and large intestine. This valve allows digested food to pass through and prevents bacteria and waste food from travelling back up in to your small intestine. If you have a weak valve, this may cause the translocation of food and bacteria back in to the small intestine. In a small pilot study by Miller et al. 2012 it was found that patients with SIBO had a defective ileocecal valve reflex. To maintain a healthy valve function I advise maintaining hydrated, limiting certain foods such as caffeine, alcohol, spicy foods, and raw foods, and maintaining a mindful eating schedule. By this I mean chewing your food properly, not overeating, not eating too quickly, and not eating too frequently. An osteopath can also diagnose a poor-functioning ileocecal valve. 

PH/stomach acid

The pH of your gut may also play a part with bacterial overgrowth. The first part of the small intestine receives highly acidic food that has been digested from the stomach before being moved along swiftly by peristalsis towards the large intestine. This low pH and fast transit makes it difficult for microbes to survive, and so we only usually see highly acid-resistant strains surviving here.4

However, if you have low stomach acid due to medications, stress, or nutrient depletions the environment is more microbe friendly and so overgrowth could occur. One of the roles of stomach acid is to protect the body from microbial infections. Low stomach acid has therefore been linked to SIBO.5

Similarly, if you have decreased levels of digestive enzymes which will compromise your ability to digest your food efficiently, then undigested food is left sitting around, encouraging the growth of bacteria in the wrong place. 

Migrating motor complex

The rate at which food moves along the gut is controlled by the major migrating complex (MMC). This is the housekeeper of the small intestine and is responsible for moving food along towards the large intestine in between meals. If you have poor gut motility, leading to a build up of fermentable food, bacteria will feed on it and multiply and SIBO can develop.6 

A variety of conditions increase the risk of impaired MMC function, such as:

  • Hypothyroidism
  • Certain medications, such as proton pump inhibitors, which reduce stomach acid
  • Inflammatory bowel diseases such as Crohns and Colitis
  • Diabetes
  • Coeliac disease
  • Gastroenteritis, C. difficile and other infections
  • Lyme disease
  • History of eating disorders

These waves of digestive motility are significantly reduced in IBS patients, which means that food is left sitting around to be digested and fermented by bacteria, leading to gas, retention and bloating.7


There seems to be an association between use of certain medications and SIBO including NSAIDS, reflux medication, and antibiotics. The use of antacids or proton pump inhibitors (PPIs), prescribed for the relief of indigestion and reflux, are known to cause bacterial overgrowth.



Certain foods are more easily fermented by gut bacteria and carbohydrates (sugars and fibre) are one of them. A diet high in starches and complex sugars will aggravate SIBO, leading to excessive gas, bloating, and abdominal pain. I will discuss the benefits of certain diets, including the low FODMAP diet in resolving bloating, later on in the article.

Other factors to consider in the case of SIBO include food poisoning, constipation, food intolerances, hypothyroidism, endometriosis, and intestinal surgery including appendectomy, which can disrupt the normal ecology and restrict movement. All of these may play a part in disrupting the balance of bacteria in the gut.


Why does bloating occur with SIBO?

Bloating is a common symptom associated with SIBO (especially if it is higher up in the belly) and occurs when undigested food sits around and ferments due to a slow gut transit time. Between meals the motility of the small intestine is controlled by the MMC contractions, which cleanses the gut of food and bacteria. If we are constantly snacking throughout the day and not allowing our digestion to rest and digest between meals, it is thought that this can lead to carbohydrate malabsorption and bacterial overgrowth in the small intestine. 

A large percentage of IBS patients share the common symptom of bloating, and there is a possibility that SIBO may be the explanation. This is supported by many studies reporting an improvement of IBS symptoms after eradication of SIBO, such as that of  Pimentel et al.  In this double-blind, randomized, placebo-controlled study, 111 patients were drawn from the general IBS population, and a reduction in gastrointestinal symptoms was seen when eradication of SIBO was achieved.

IBS has largely been considered a psychosomatic condition in the past, and so research such as this recognises that most people with IBS have distinctly different microbiotas than people without it, and that dysbiosis is the primary cause. For a small subset of IBS sufferers, however, psychological illness drives the IBS, as the indviduals' microbiotas are no different, and yet they report being depressed8.


Is your gut harbouring harmful microbes?

SIBO testing

Hydrogen and methane breath tests are currently the most important diagnostic tests used for testing SIBO gut microbes. The type of gas produced by gut bacteria may be an important factor.  In humans, hydrogen and methane are exclusively produced by intestinal bacteria, predominately in the large bowel in healthy people and also in the small intestine in the case of SIBO. The theory is that if food is not moving down to the bacteria quick enough, then bacteria may be moving to the site of food assimilation for fermentation and gas production to take place. Methane-producing bacteria is associated with constipation and a slow MMC. Hydrogen-producing bacteria is associated more with diarrhoea and a faster MMC.

The primary test for SIBO is a lactulose or glucose breath test, which measures the levels of hydrogen and methane being produced by gut bacteria and exhaled by your lungs. The test is performed after an overnight fast and after the ingestion of a lactulose or glucose solution. The principle behind the test is that after ingestion of food, fermentation produces gas, gas enters the bloodstream, blood carries gas to the lungs, and gas is expired through the mouth which can then be measured.

Breath testing is an excellent tool to assess SIBO, but there are limitations to the test, and the only way to establish whether the symptoms are caused by SIBO is to treat and eradicate the bacteria.


SIBO nutrition & diet 

So how do we shift a dysbiotic gut to a healthier state, and optimise the health of the host and the microbiome?  Bloating is very common among SIBO patients and dietary restrictions of fermentable carbohydrates can lead to symptomatic improvement.

The food we consume feeds bacteria in our body, making nutrition and diet implications for patients with SIBO particularly important. Nutritional interventions are common, and can be used to starve out the bacteria population in the intestine. One effective way to reduce the symptoms of bloating and distension is to reduce the intake of carbohydrates, particularly fermentable fibres such as fructose. Fructose is a type of sugar that is found naturally in fruits and honey, but it is also found in processed foods in the form of modified high fructose corn syrup. When consumed in excess it is poorly absorbed, and is left to the gut bacteria to ferment causing excess gas and bloating.

Diet tips for active SIBO:

  • Avoid raw food, salad, and beans, as these are harder to digest
  • Be careful with whole grains, nuts/seeds, and winter squash
  • Choose low-FODMAP fruit and vegetables (see below)
  • Starch may be tolerated: white rice, white potato, white flour (if able to eat gluten); often one starch is tolerated but not another
  • Lactose-free dairy, sugar, clover honey, and cocoa are often tolerated
  • Quantity matters - small amounts of individual foods may be tolerated, when larger amounts aren’t
  • Experimentation and customization is necessary for best success

Avoid high FODMAP foods

FODMAP stands for Fermentable Oligo-, Di-, Monosaccharides And Polyols, and these specific carbohydrates are found in a variety of foods and can be a problem for some people because they feed gut bacteria and encourage them to proliferate.  

A diet with low fermentable foods can decrease the chance of bacterial overgrowth by creating a less favourable environment for bacteria. In a small study by ONG et al looking at the effects of a low-FODMAP diet on hydrogen gas production in IBS patients, they found that those on a high-FODMAP diet produced a significantly greater amount of hydrogen gas compared to IBS patients on a low-FODMAP diet. 

Monash University has developed an excellent app to help you stick to a low-FODMAP diet but I would always recommend working with a practitioner as it can be very restrictive and is not advised long-term.

Elemental Diet

Elemental diets may be an extremely safe and effective alternative to antibiotics but must be medically supervised. These formulations are believed to be absorbed within the first few feet of the small bowel and potentially limit the delivery of nutrients to the bacteria residing towards the end of the small bowel. The diet consists of macronutrients (high protein, low carb) broken down into liquid form allowing for fast absorption to prevent food sitting around, and also allowing time for the gut to rest.

In one small-scale study, 80% of participants with SIBO had a normal breath test result after following an elemental diet for 15 days. 


How do I reverse SIBO?

Treatments for SIBO work towards inhibiting the overgrowth of bacteria in the small intestine. The synergy of nutrients is key here as we want to accelerate the gastric emptying. Adding foods in to the diet that support bile production and pancreatic enzyme production will support the movement of food along the digestive tract. This is important because if food gets left behind in the small intestine this will promote the growth and migration of bacteria from the large intestine in to the small. Foods to include are bitter foods such as dandelion, rocket and watercress and artichoke. You can also take a herbal bitters formula that is taken prior to eating meals.


Prokinetics are substances that stimulate gut motility and support your migrating motor complex. If your migrating motor complex is unable to move food along and remove waste there is a higher chance of a small intestinal bacterial overgrowth developing. Taking prokinetics in-between meals and before bed is a great way of supporting the movement of food along the digestive system.

Some of my favourite prokinetics to use are:

Ginger tea




5HTP (an amino acid involved in the synthesis of serotonin, which supports gut motility)

Stress reduction

In order to prevent a reoccurrence of SIBO, it is important to manage your stress levels due to the link between the HPA axis and microbiota. The gut is connected to the brain via the gut-brain axis, and for more on this fascinating topic you can read ‘Stress and bloating-can one cause the other?' Stress impacts the HPA axis and can impact the balance of gut microbes, gut motility, and stomach acid secretions. If you know stress is an issue for you, you could look into yoga, meditation, breath work, or massage to try and help reduce the fight-or-flight stress response.


Fast intermittently and avoid snacking

Constant snacking and not fasting between meals will result in a dysfunctional migrating motor complex - we are officially a nation of snacking and people aren’t allowing that fasting window to occur. Allowing your digestionperiods of rest between meals will enable your gut to clear out and your migrating motor complex to work more efficiently. Between meals the gut should be allowed to sweep away any digestive leftovers which helps to control the growth of bacteria in the small intestine. If you are eating every 1-2 hours you are not allowing that sweep to occur. Do your best to space your eating opportunities four hours apart and try not to eat right before bedtime. 


According to different studies, the antibiotic rifaximin improves symptoms in 33%-92% of people, and eradicates small intestinal bacterial overgrowth in up to 80% of patients9. Research also demonstrates that prebiotics and probiotics can be used to crowd out pathogenic bacteria in the gut, produce natural antibacterial substances, inhibit bacterial translocation, strengthen the immune system, reduce inflammation, and increase gut motility10. Probiotics can be useful alongside SIBO treatment as they support gut motility, and certain strains such as Bifidobacterium lactis HN019 have shown benefit alongside antibiotic therapy because of this.11

In a randomised placebo-controlled study by Waller et al, looking at the effects of B. lactis HN019 on whole gut transit time and gastrointestinal symptoms, they found that the probiotic group showed significant improvements in gut transit time and symptoms compared with the placebo group.12 If we can speed up the transit of food through the intestine then there is less likelihood of it fermenting and causing symptoms.


Herbal antibiotics

Herbal antibiotics work in a similar way to pharmaceutical antibiotics, in that they remove bacterial and fungal overgrowths and are an option for people who want to try a more natural approach. Herbs to consider are oregano, goldenseal, echinacea, berberine, garlic, cloves, and pomegranate.


As a framework for understanding IBS and other gut disorders, SIBO provides a target for exciting research. If you are having trouble getting to the bottom of your digestive symptoms, SIBO may just be the piece you were missing in your digestive puzzle. If you have already investigated common culprits like lactose intolerance, coeliac disease and irritable bowel syndrome, talk to your doctor or a registered nutritionist about testing for SIBO.

Do you have more questions about SIBO, gut health or probiotics? Let us know in comments below! For more information on digestive health please see the following articles.

Healing leaky gut

Stress and bloating - can one cause the other?


1 Ghoshal et al (2017), Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy, ‘Gut and Liver’, Vol 11.2, pp.196-208, [online], Available at: [Accessed 3/3/19]

2 Fassano A (2012), Leaky Gut and Autoimmune diseases, ’Allergy and immunology’, Vol 42:1 pp.71-78 [online] Available at:[Accessed 3/3/10]

3 Tursi A et al (2005), Assessment of small intestinal bacterial overgrowth in uncomplicated acute diverticulitis of the colon, ‘World Journal of Gastroenterology’, Vol 11:18, pp. 2773-6 [online] Available at: [Accessed 3/3/10]

4 Hao W L, Lee Y K (2004), Microflora of the gastrointestinal tract: a review. ‘Methods in Molecular Biology’, Vol 268, pp.491-502 [online] Available at: [Accessed 3/3/19]

5 Dukowicz A C et al (2007) Small Intestinal Bacterial Overgrowth, 'Gastroenterology and Hepatology', Vol 3:2, pp.112-122 [online] Available at: [Accessed 3/3/19]

6.Roland B C et al (2015) Small Intestinal Transit Time Is Delayed in Small Intestinal Bacterial Overgrowth, ‘Journal of Clinical Gastroenterology’, Vol 49:7, pp.571-6 [online] Available at: [Accessed 3/3/19]

7 Henry C (2004) Small Intestinal Bacterial Overgrowth:A Framework for Understanding Irritable Bowel Syndrome, ‘JAMA’, Vol 292-7, pp.852-858 [online] Available at: [Accessed 3/3/19]

8 Collen A 2015 10% Human: how your Body microbes hold the key to Health and Happiness, 2nd Ed, London, William Collins, p 65,

9 Bures J et al (2010) Small Intestinal Bacterial Overgrowth Syndrome, ‘World Journal of Gastroenterology’ Vol 16:24 pp.2978-2990 [online] Available at: [Accessed 3/3/19]

10 Chung Chen W, Quigley E M (2014) Probiotics, prebiotics & synbiotics in small intestinal bacterial overgrowth: Opening up a new therapeutic horizon! ‘Indian Journal of Medical Research’, Vol 140:5 pp.582-584 [online] Available at: [Accessed 3/3/19]

11 Rosania R et al (2013) Effect of Probiotic or Prebiotic Supplementation on Antibiotic Therapy in the Small Intestinal Bacterial Overgrowth: A Comparative Evaluation, ‘Current Clinical Pharmacology’, Vol 8:2 pp.169-172 [online]Available at: [Accessed 3/3/19]

12 Waller, P. A. et al., (2011) Dose-response effect of Bifidobacterium lactis HN019 on whole gut transit time and functional gastrointestinal symptoms in adults. ‘Scandinavian Journal of Gastroenterology’. Vol 46:9 pp. 1057–1064  [online] Available at: [Accessed 3/3/19]

About Katie Wheaton

Katie holds a Bachelor of Arts (BA) degree, a diploma in Naturopathic Nutrition (DIP) mBANT, CNHC, and is a certified DNA life practitioner. As well as writing for, Katie is a practicing Nutritional Therapist and Natural Chef in London. She specializes in digestive health and skin, and the driving force behind her Nutritional Therapy consultations is a deep desire to help individuals achieve their long-term diet and nutrition goals. Katie's knowledge of nutrition and healing foods extends to her plant-powered nutritional catering for individual clients and wellness events/retreats.

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