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.

Skip to Key Takeaways

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.

Key Takeaways

  • 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.
  • These bacterial 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.
  • Other effects of SIBO can include B12 deficiency, malabsorption of nutrients (e.g. fat soluble vitamins) and development of leaky gut, a trigger for systemic disease and food sensitivities and reactions.
  • The causes of SIBO have been mainly attributed to low stomach acid and/or poor gastrointestinal motility, low digestive enzymes and poor immune function.
  • Dietary interventions include avoiding FODMAP foods. A FODMAP diet is intended to be short term and is best instigated under the guidance of a Nutritional Therapist.
  • Interventions to support gut motility may be important – ensuring adequate water/fluids intake, exercise (walking is ideal), fibre intake (although some fibres may be restricted on a FODMAP diet) and vagal nerve exercises (vigorous gargling and singing loudly – every day!)
  • Supplements to support gut motility include 5-HTP*, magnesium, live bacteria and fibre supplements
  • Other supplements to consider include the use of anti-microbials, digestive enzymes, apple cider vinegar (or betaine HCl), lecithin and nutrients to support the gut barrier lining (vitamins A, D, zinc, curcumin, Aloe vera, L-glutamine)

NB: *5-HTP is not suitable for people taking anti-depressant medication (eg SSSRIs, MAO inhibitors)

If you have questions regarding the topics that have been raised, or any other health matters, please do contact me (Jackie) by phone or email at any time., 01684 310099

Jackie Tarling and the Cytoplan Editorial Team

Relevant Cytoplan Supplements

Caprylic Acid Plus – Provides a mix of powerful anti-microbial and anti-fungal agents. This formulation is designed to help as part of a programme to address systemic candida and to promote digestive health.

Cyto-Zyme – A high potency, multiple digestive enzyme complex providing a broad spectrum of plant-sourced enzymes which digest protein, fat, fibre, dairy sugars and carbohydrates.

Betaine & Pepsin – Each capsule provides betaine HCl 345mg and pepsin NF 10mg. Hydrochloric acid has a number of important functions within the stomach – it assists with the digestion of food; creates an acidic environment in the stomach necessary for the enzyme pepsin to work; assists with the absorption of some minerals e.g. iron, calcium and zinc and kills undesirable bacteria in the food.

Biofood Magnesium – Magnesium is an essential mineral that is a cofactor for over 300 enzymes. Food sources of magnesium are far better absorbed than inorganic sources.

Organic Turmeric Plus – A herbal complex containing turmeric (curcumin), cat’s claw and gotu kola. Certified organic by the Soil Association.

CytoProtect GI Tract – A synergistic multi-nutrient, botanical and live native bacteria formula designed to support integrity and stability of the surface membranes (i.e. lining) of the entire GI tract.

L-Glutamine – Comprises pure crystalline free-form L-Glutamine. Glutamine is stored in ther muscles of the body and is involved in the repair and building of new muscle. It is often used as possible support for muscle recovery.

Aloe Vera Inner Leaf – A single concentrate containing only pure, unprocessed inner leaf gel. Traditionally Aloe products have been used as digestive aids, as well as for immune and anti-inflammatory support.

Psyllium Husk – Cleaned to 99.9% purity, dry-processed and importantly, contains no solvents. Psyllium is used both to speed up and slow down stool transit time.

Slippery Elm – Containing only Slippery Elm Bark to maintain the potency of the plant. The bark is pure and no additives have been used.

5-HTP Plus – Containing 5-HTP (the safe precursor to serotonin) and the nutrients necessary for the conversion of 5-HTP to serotonin. Made from the shrub Griffonia, with added magnesium and vitamin B6.


  1. Dukowicz, et al (2007) ‘Small intestinal bacterial overgrowth: a comprehensive review’. Gastroenterol Hepatol (N Y);3(2):112-122.
  2. Reynolds KH (2015) ‘Small Intestinal Bacterial Overgrowth: A Case-Based Review’. J Patient-Centered Res Rev;2:165-173.
  3. Takahashi T (2012) ‘Mechanism of Interdigestive Migrating Motor Complex’. J Neurogastroenterol Motil;18(3):246-257.
  4. Stotzer P-O et al (1996) ‘Interdigestive and Postprandial Motility in Small-Intestinal Bacterial Overgrowth’. Scand J Gastroenterol;31(9):875-880.
  5. Deloose E et al (2016) ‘Redefining the functional roles of the gastrointestinal migrating motor complex and motilin in small bacterial overgrowth and hunger signaling’. Am J Physiol Liver Physiol;310(4):G228-G233.
  6. Vantrappen G et al (1977) ‘The Interdigestive Motor Complex of Normal Subjects and Patients with Bacterial Overgrowth of the Small Intestine’. J Clin Invest;59(6):1158-1166.
  7. Husebye E et al (1995) ‘Abnormal intestinal motor patterns explain enteric colonization with gram-negative bacilli in late radiation enteropathy’. Gastroenterology;109(4):1078-1089.
  8. Pimentel Met al (2002) ‘Lower frequency of MMC is found in IBS subjects with abnormal lactulose breath test, suggesting bacterial overgrowth’. Dig Dis Sci. 2002;47(12):2639-2643.

Last updated on 3rd November 2022 by cytoffice


14 thoughts on “Small Intestine Bacterial Overgrowth (SIBO) – causes, symptoms & nutritional interventions

  1. As a huge proportion of SIBO cases re-occur within 9 months we should be looking wider than this. I have found sluggish gallbladder is a key to appropriate motility and upper gut immune function. The full CCK feedback loop needs attention and this can come from dopamine pathway support with DLPA. This also supports CCK production. `Nigh (2019) also says SIBO may be an adaptive mechanism for humans being unable to sulfate. I believe Nigh has the science bang on but his recipe needs some attention. Working on that.

  2. An interesting article but as a long term sufferer a précised edition may help the non medical readers, coupled with a short list of possible outcomes with what to do or take.

  3. Hi I am taking Rivaroxaban Blood thinners. And pantoprazole for a Haetius hernia. I have quite a few stomach probs. Gas. Sometimes constipation. I am just about to start taking B 12 to help fatigue. I am female 72 years of age. Swim 3 times a week. But generally not very fit
    Recovering from a hip operation which is my third hip operation
    I know certain thing do not mix with my
    Medicines Could I take licorice root for arthritis. Jan B

    1. Hi Jan,

      Thank you for your comment.

      There is a potential interaction of licorice root with blood thinners, as licorice root can affect certain liver enzymes and so in theory could increase breakdown of the rivaroxaban, making it less effective. So you would need to be cautious and get advice in regards to the specific product you want to use.

      As an alternative to the licorice for joint support you could consider
      CytoProtect Joints – this is a powdered hydrolysed collagen and glycosaminoglycans product. It is taken mixed with a little water
      Celadrin capsules (start on 2 per day and then reduce to 1 per day maintenance after a few weeks).

      In terms of other support, in addition to the B12, an all-round multivitamin and mineral would be a good idea. You could take our Wholefood Multi – 1 or 2 capsules per day.

      In addition as you mention constipation, you might consider a live bacteria supplement e.g. CytoBiotic Active. This is again a powder and is best taken on an empty stomach, e.g. bedtime.

      Also you may be interested in the free health questionnaire service we offer. If you complete and return a health questionnaire we will send you some written diet and lifestyle recommendations. You can download a questionnaire here.

      Best wishes, Clare

  4. Thank you for all this information. Would it be possible to have a short list of supplements. Also can you advise me on how to get tested for Sino I live in ireland

    1. Hi Bernadette,

      Thank you for your comment.

      There are some suggested relevant products linked at the end of the blog. If you would like us to make specific recommendations, we would be very happy to do so via our free health questionnaire which you can download here. If you complete and return a health questionnaire we will send you some written diet and supplement recommendations. Alternatively if you would like to email me ( with more information about your symptoms, your age and any other health conditions and medications you are taking then I can make some recommendations.

      Some G.P.s are able to arrange a test for SIBO. You could also consider a consultation with a Nutritional Therapist local to you.

      Best wishes, Clare

    2. Hi,
      Gastrolife test for hydrogen and methane SIBO in Ireland. They are based in Dublin, Kildare, and Galway

  5. An extremely useful and informative article which, I found, had direct relevance for my family. Cytoplan at its’ best

  6. Hi, are stools suppose to sink or float generally?

    If they are not suppose sink, why not?

    If they are not suppose float, why not?

    Thanking you

    1. Hi Mary,

      Thanks for your question. Stools would usually be more dense than water, so sink. Floating stools can be an indication of poor fat digestion/absorption or a lot of intestinal gas being produced. If it happens occasionally then it would not necessarily be a cause for concern – as foods can also cause this, so may be a response to something eaten.

      If stools always float then this should be investigated as if fats are being poorly digested and absorbed this could eventually lead to deficiencies in essential fatty acids and fat soluble vitamins – A, D, E, K.

      One reason for poor fat digestion and absorption is lack of gallbladder. If the gallbladder has been removed, bile is not stored and released in response to a meal (in this case it is continuously released in small quantities) so there will be lower levels available to emulsify fats. Fat emulsification provides a greater surface area for digestive enzymes to work and break fat down. Another reason for poor fat digestion is reduced production of pancreatic enzymes. In addition to poor digestion, there may be absorption issues.

      In terms of supplements, lecithin (eg our product Cell Active Phospholec) may be considered with main meal (it helps emulsify fats) and a broad spectrum digestive enzyme (eg our Cytozyme – take one with main meal). A live bacteria supplement would also be worth considering.

      We do offer a free health questionnaire service that may be of interest – if you complete a health questionnaire we will send some written diet and supplement recommendation – available here.

      In addition I would advise that any concern about bowel habits or changes in bowel habits is discussed with the GP.

      I hope this helps.


  7. Hello, I have enjoyed reading your article about bacteria overgrowth in the intensines. I sure have the symptoms of poor appetite am, undigested food in stool, bloating and heartburn. My gi is treating me for ibs. My gi is running a breath test in 3 weeks for a clear diagnose. I am in so much pain, would you please recommend something so I can move around a little.
    Thank you for listening. Cindy zuniga

    1. Hi Cindy – thank you for your comment. I can see you have recently completed our health questionnaire service and one of our Nutritional Therapists will have come back to you with a tailored protocol. If you have any further queries, please respond to the member of our Nutrition team who will be able to answer any queries you may have.

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