Small Intestine Bacterial Overgrowth (SIBO) – causes, symptoms & nutritional interventions

Small Intestine Bacterial Overgrowth (SIBO) – causes, symptoms & nutritional interventions

Millions of people suffer from gastrointestinal (GI) symptoms and distress each year. Diagnoses of leaky gut syndrome, Crohn’s, coeliac disease, and irritable bowel syndrome (IBS) continue to grow. Recently, researchers have acknowledged another digestive disorder: small intestinal bacterial overgrowth, or SIBO. It is more prevalent than previously believed, and occurs in many people suffering from IBS and certain other conditions.1

This article will review what SIBO is, its causes, how it is identified and dietary and supplemental interventions to address the underlying cause.

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What is SIBO?

SIBO is an overgrowth of bacteria in the small intestine. These bacteria normally live in the large intestine but have abnormally overgrown in a location not meant for so many bacteria. In a healthy individual, the small intestine, whilst not necessarily completely sterile, should have a very low count of bacteria. SIBO occurs when bacteria colonise the small intestine and then overgrow (this overgrowth is referred to as a dysbiosis).

These bacteria can:

  • Ferment dietary sugars and carbohydrates which leads to a build-up of gas. The gas causes abdominal bloating, abdominal pain, constipation, diarrhoea or both (also symptoms of IBS).  Excess gas can also cause belching and flatulence
  • Remove B12 from intrinsic factor, which is required for B12 absorption, and therefore SIBO is associated with B12 deficiency
  • Cause damage to the small intestine leading to malabsorption and potentially the onset of ‘leaky gut’, a trigger for systemic disease. Undigested food particles, can enter the body and trigger immune activation.  This can cause food intolerances/sensitivities
  • Consume food which has not been absorbed due to epithelial lining damage; this continues the overgrowth (a vicious cycle)
  • Reduce dietary fat absorption. They are also able to de-conjugate bile acids from fat (bile is essential for emulsifying fat to allow it to be absorbed); this can lead to poor fat absorption and therefore deficiency of essential fatty acids and fat soluble vitamins (i.e. vitamins A, D, E and K) as well as diarrhoea caused by excess fat in the stool

What causes SIBO?

The causes of SIBO seem to be multi-faceted but have been mainly attributed to:

Low stomach acid – hydrochloric acid in the stomach plays many roles, one of which is to sterilise food that has been consumed. If stomach acid is low then excess bacteria can colonise the small intestine.

Poor motility – normal gastrointestinal motility involves a complex, tightly coordinated series of events designed to move material through. It decreases the potential for SIBO by ensuring that food particles and bacteria are moved through the digestive tract, rather than accumulating in the small intestine.

Three patterns of motility are seen – known as peristalsis, segmentation contraction and the migrating motor complex (MMC)

  • Peristalsis begins in the oesophagus when a bolus of food is swallowed. It is a series of wave-like muscle contractions that propels foodstuffs through the oesophagus and intestines
  • Segmentation contraction is a type of intestinal motility which occurs in the small and large intestine, predominantly in the former
  • During periods of fasting, a migrating motor complex (MMC) occurs approximately every 90-120 minutes to sweep residual debris through the GI tract.1 The migrating motor complex (MMC) is a pattern of gut contraction that creates movement through the gut when it is empty. Regulation of the MMC is complex, requiring the release of many hormones and neurotransmitters, as well as the activity of the enteric and autonomic nervous systems.2 This contraction moves through the stomach and small intestine, towards the ileocaecal valve. These waves occur in cycles, playing a housekeeping role, clearing the small intestine of remnants of food and bacteria left behind during peristalsis and segmentation contraction. A small amount of bile and enzymes are released with each MMC and these secretions may also help clean out the small intestine of bacteria build-up. It is this ’sweeping’ of the small intestine that is responsible for the rumbling felt or heard between meals

In a normal MMC cycle, there are four phases. Phase I is a quiescent period with virtually no contractions. Phase II consists of intermittent, irregular low-amplitude contractions. Phase III consists of short bursts of regular high-amplitude contractions. Phase IV represents a short transition period back to the quiescence of phase I.3

If there is dysfunction within any of these movement patterns, gut motility may be decreased, leading to constipation, changes in the gut microbiome, pain, and other digestive symptoms. Particularly, a decrease in phase III activity of the MMC, the most active phase of its four phases, has been shown to be absent in cases of SIBO as well as IBS.4 One of the main contributors to the development of SIBO is small intestine dysmotility.5 Several studies have demonstrated that abnormalities in the MMC may predispose to the development of SIBO.6,7,8

In this case, a prokinetic agent may be useful. The term prokinetic means to promote movement and, in the context of the gastrointestinal tract, was introduced to refer to a class of drugs that promote gastrointestinal motility and, thereby, transit. This stimulatory effect is considered clinically relevant to the management of disorders characterised by impaired motility.  In addition to drugs, there are some natural nutraceuticals with prokinetic effects such as 5-HTP, ginger and triphala.

If motility is poor, which is consistent with constipation, the bacteria present has an opportunity to migrate from the colon to the small intestine.

Other causal factors associated with SIBO are:

  • Low pancreatic (digestive) enzymes
  • Poor immune function
  • Previous bacterial infections e.g. Campylobacter

It is important to address these underlying causes but doing this alone will not eradicate SIBO, this is discussed in more detail later.

How is SIBO identified?

Symptoms that are associated with SIBO include:

  • Gas, bloating and flatulence
  • Diarrhoea
  • Abdominal cramping
  • Fat in the stool (stools may have a pale and oily appearance and often float)
  • Intolerance to lactose (sugar found in milk)
  • B12 deficiency (megaloblastic anaemia)

If these signs and symptoms are seen (particularly in combination) SIBO can be suspected. However there are simple breath tests available to identify the production of hydrogen or methane, which are produced through bacterial fermentation in the small intestine.

Dietary and Supplementary interventions for SIBO

There are dietary and supplement interventions that can specifically support individuals with SIBO, which are outlined below. It can also be beneficial to follow a 5R programme in order to fully rebalance and repair the digestive system, this programme is discussed in our Cytoplan blog: Nutritional support for Irritable Bowel Syndrome.


FODMAPs are dietary sugars and carbohydrates which are easily fermented by the bacteria and can exacerbate symptoms of gas, bloating and pain. Therefore it is often very useful to remove them from the diet for a limited period of time.

FODMAPs stand for:


Oligosaccharides (e.g. fructans found in wheat, garlic, onion and chicory etc. and galactans found in legumes including beans, peas and lentils)

Disaccharides (e.g. lactose found in milk products)

Monosaccharides (e.g. fructose found in fruits, honey, high fructose corn syrup etc.)


Polyols (found in sweeteners containing isomalt, mannitol, sorbitol, xylitol plus stone fruits such as avocado, apricots, cherries, nectarines, peaches and plums)

After excluding high FODMAP foods for a month, foods from each FODMAP group should be reintroduced, one at a time (e.g. foods containing fructose, then foods containing lactose etc.).

During the reintroduction, symptoms should be monitored and if a FODMAP group of foods causes problems then continue to eliminate this group. It should be noted that avoiding FODMAPs will not remove SIBO but help modulate the symptoms.

Please note that a low FODMAP diet involves initially restricting a considerable number of foods which some may find very difficult; however it is not intended to be a long-term diet and because of the restrictive nature and complexity it is best followed with the guidance of a practitioner.

Remove dysbiotic bacteria from the small intestine

Primarily, the main intervention for SIBO needs to be the removal of bacteria, as addressing underlying causes and avoiding foods which are exacerbating symptoms will not be enough.

Natural antimicrobials can be useful for removing bacteria from the small intestine. These include:

Caprylic acid – a natural dietary fatty acid which assists in the maintenance of normal intestinal micro-flora and can help inhibit the growth of opportunistic fungi such as Candida albicans. Coconut oil is a good source.

Garlic – long standing use as an anti-microbial.

Oregano extract – broad spectrum anti-microbial activity.

Grapefruit seed extract – research shows evidence for anti-bacterial activity against gram-positive and gram-negative bacteria.

Green tea extract – anti-bacterial and anti-fungal activity.

It is sometimes advisable to take a live bacteria supplement along with the anti-microbial (although take at least two hours apart from each other) to help ensure a healthy balance of gut flora in the large intestine.

Address the underlying cause

Low stomach acid

If stomach acid is low this needs to be addressed as there will be a risk of SIBO returning following anti-microbial use if stomach acid insufficiency persists. Symptoms associated with low stomach acid are:

  • Poor appetite in morning
  • Undigested food in stool
  • Bloating and /or pain shortly after eating (30 minutes)
  • Heartburn and reflux
  • Suspected malabsorption or nutrient deficiencies

It is also possible to test hydrochloric acid levels by consuming a ½  teaspoon of bicarbonate of soda dissolved in a small glass of water on an empty stomach (on rising in the morning is a good time), then timing how long it takes to belch. If it takes longer than 5 minutes (it should happen within 2-3 minutes) this indicates that levels of hydrochloric acid maybe low.

You can support stomach acid levels by:

  • Supplementing with betaine hydrochloride just prior to meals or 1 teaspoon of apple cider vinegar in a small amount of water
  • Ensuring adequate zinc levels (zinc is important for production of stomach acid)
  • Avoiding drinking large quantities of water 30 minutes before and during a meal, as this can dilute stomach acid

Poor motility

If motility is poor, then there will be likely be constipation as there is limited movement of the bowel.  Methane-dominant SIBO is almost always associated with constipation.

Gut motility can be supported by:

  • Drinking 1.5 to 2 litres of water and herbal teas per day
  • Consuming soluble and insoluble fibre from vegetables, fruits and moderate amounts of wholegrains. Ground flaxseed (linseeds) can be useful
  • Moderate exercise and physical activity – walking is ideal
  • Vagal nerve exercises – stimulate the vagus nerve by singing loudly and gargling every day (vigorous gargling several times a day if possible)
  • Supplementing with
      –    a live bacteria supplement (although some people prefer to wait until symptoms have improved before adding in probiotics)
      –   a magnesium supplement (magnesium is involved in muscle relaxation)
      –   a 5-HTP supplement – which has prokinetic action in the small intestine
      –   Psyllium fibre, slippery elm and

Low pancreatic (digestive) enzymes

If levels of digestive enzymes are low, larger undigested food molecules will be more available for fermentation by bacteria in the small intestine. There are tests available to determine digestive enzyme levels, but in cases of SIBO it is likely that digestive enzyme function is already somewhat impaired and therefore supporting pancreatic enzymes as well as bile production, in the short term, may help with symptom relief.

Pancreatic and digestive function can be supported by:

  • Taking a digestive enzyme supplement with meals
  • Consuming bitter foods (lemon, rocket, chicory, watercress) which stimulate bile secretion
  • Obtaining phospholipids from the diet or as a supplement to aid fat emulsification (e.g. lecithin)

Support for the gut barrier lining

An important part of any intervention to address SIBO is to consider support for the digestive barrier lining – to reduce intestinal permeability or leaky gut. Overall nutritional status should be considered along with specific nutrients such as vitamins A and D and zinc; curcumin, Aloe vera, lactoferrin and L-glutamine are other examples of nutrients used in gut healing programmes. If barrier integrity is not restored then you may not see a full resolution of symptoms.


There is an increased recognition of SIBO as a contributing factor in IBS, functional abdominal pain and a host of other chronic conditions.  Although SIBO can be challenging to work with and tends to be recurrent, there are many options that can provide significant relief as detailed above.

This article is from Cytoplan Blog –