SIBO (Small Intestinal Bacterial Overgrowth)

Small Intestinal Bacterial Overgrowth (SIBO)

Small Intestinal Bacterial Overgrowth (SIBO) as a diagnosis is very often overlooked and this is particularly the case in patients complaining of reflux symptoms. It is probably far more common than usually perceived and in our view should be considered in all patients thought to have gastro-oesophageal reflux disease. However, it is always important to seek medical advice and to exclude alternative causes for symptoms if necessary.

What is the Gut biome?

It is normal that literally billions of bacteria and other micro-organisms live in our gut. We’re increasingly realising that the right type, diversity and balance of these organisms, mostly bacteria but also viruses, fungi and other microbes including protozoa. These are vital for our gut and general health. We live together in “symbiosis” with these microbes, known as the gut microbiome.  We provide a home and nutrients and they perform multiple vital functions which include;

• Digestion of food and production of nutrients. These include the digestion of complex fibres and production of short-chain fatty acids that nourish the cells of the gut and reduce inflammation.
• Synthesising vitamins. These include B1, B2, B9, B12, K and folate.
• Support the immune system. By helping to distinguish between harmless and harmful agents, the biome trains and regulates the immune system as well as protecting us from infectious and autoimmune diseases.
• Protect against pathogens. Beneficial microbes compete with harmful bacteria for space and resources. They produce substances that inhibit pathogens and help maintain the barrier between the gut and the rest of our bodies.
• Metabolism of bile and other compounds: Gut bacteria help break down and recycle bile acids. This is important for fat digestion and the regulation of cholesterol.
• Metabolism and Weight: The microbiome influences the extraction of  energy from food and therefore weight, blood sugar, and cholesterol levels.
• Mental and Heart Health: There is growing evidence that the gut microbiome communicates with the brain and heart, affecting mood, cognition, and cardiovascular health.

What is SIBO?

The entire gut from “mouth to anus” is home to this biome. There are usually as many as 20 billion microbes living in our mouths but by far the largest number and variety are located in the large bowel, or colon. Here live no less than 38 trillion bacterial cells (3.8x 1013). Estimates suggest that the colon contains between 300 and 1000 different bacterial species. However, the small bowel which lies between the stomach and the colon is relatively sterile particularly. The small bowel is divided anatomical into the jejunum which starts after the stomach and then transitions into the ileum. The ileum is separated from the colon by a valve, the ileo-caecal valve which prevents “reflux” of bacteria from the large bowel into the small bowel. The jejunum in particular contains fewer organsism than the colon and; overall, normally there are about 100,000x as many microorganisms in the colon compared to the small bowel.

SIBO (Small Bowel Bacterial Overgrowth) was first described as long ago as 1939 and occurs when the small bowel becomes colonised by abnormal numbers of micro-organisms.  These tend to ferment carbohydrates which they use for their own nutrition, particularly those high in so-called FODMAPs and during this process produce hydrogen gas which can be detected in the breath. SIBO can cause a variety of symptoms and has been associated with other diseases which in turn can cause symptoms themselves.

We consider SIBO to be a specific type of “dysbiosis”; a condition in which the usual balance of micro-organisms in the gut (the gastro-intestinal micro-biome). There are probably many other forms of dysbiosis which as yet are unrecognised or which we can’t test for. One of these is now recognised as “Intestinal Methagenic Overgrowth” or IMO. In IMO rather than bacteria, organisms called archaea (Methanobrevibacter smithii) produce excess methane rather than hydrogen gas which they may use themselves to generate the methane. Methane slows gut transit and IMO is associated with constipation.

In this short video Mr Nick Boyle, Medical Director at RefluxUK - the UK's largest specialist reflux clinic, talks about SIBO and how it relates to the reflux symptoms patients present with.

What causes SIBO/IMO?

There are thought to be many reasons why SIBO, IMO and other dysbiosis develop but the most likely are:

1. Poor gut motility which prevents the normal "clearing" of bacteria. This can be caused by:
   - Diabetes as this can cause damage to nerves supplying the gut.
   - Connective tissue conditions such as Scleroderma
   - Nervous system disease such as Parkinson's
   - Hypothyroidism
   - Drugs especially opiate pain-killers
   - Viruses. It is also thought that some viruses may influence motility and this can pre-dispose to the development of dysbiosis; among those implicated is COVID.
2. Low stomach acid. The production of acid by the stomach is a normal physiological phenomenon. Hydrochloric acid starts the process of breaking down the food we eat so that it can be digested. But it also helps to create a barrier, protecting the rest of the gut from the micro-organisms that we inevitably ingest when we swallow and eat. Some of these will be on our food but our mouths and throats are also colonised by many different organisms. Normally these are killed in the stomach but in the absence of normal levels of stomach acid these micro-organisms can pass into the small bowel and then the colon. What causes low stomach acid?
   - Proton Pump Inhibitors (PPIs). Studies have shown that the usual balance of organisms in the biome is disturbed in patients taking PPIs. Oral bacteria and potentially pathogenic bacteria are increased in the gut microbiota of PPI users and there are more microbial alterations in the gut associated with PPI use than with antibiotics or other drug use. Read more about PPI, their history, efficacy and side effects.
   - Following surgery
   - h. Pylori infection
   - Pernicious anaemia
3. Antibiotics. By their very nature antibiotics will preferentially kill some gut micro-organisms while others will survive therefore disturbing the normal balance within the gut. Used repeatedly, or over the long-term, drug resistance will develop. Sometimes the alteration in the gut biome will precipitate the sudden onset of symptoms but sometimes these may become problematic even years later.
4. Previous surgery. In patients who have undergone gut surgery with for instance removal of the ileo-caecal valve during colon cancer resection or gastrectomy (removal of the stomach).
5. Diverticular disease. It's thought bacteria can "hide" in blind pouches.
6. Fistulae. These are abnormal connections between areas of the gut.
7. Previous radiotherapy
8. Immunodeficiency
9. Coeliac disease
10. Inflammatory bowel disease
11. Pancreatitis
12. Colon cancer
13. Kidney failure
14. Liver failure

What symptoms does SIBO cause? What does SIBO feel like?

SIBO and other dysbiosis conditions can cause an enormously wide and variable set of symptoms. It is recognised that SIBO can be associated with Irritable Bowel Syndrome (IBS) in which patients can experience alternating loose stools and sometimes constipation and flatulence associated with abdominal bloating and pain. Indeed, studies suggest that when tested, up to 70% of people with "IBS" will be positive for co-existent SIBO. Hydrogen producing organisms tend to be associated with diarrhoea while IMO and methane production with constipation. SIBO can cause vitamin especially B12 deficiency and iron deficiency anaemia and malabsorption syndromes possibly due to inflammation of the lining of the gut and poor fat digestion. Some patients complain of “Brain Fog”. In fact SIBO has been associated with more than 100 other conditions including interstitial cystitis, hypothyroidism, fibromyalgia and skin pathology such as rosacea and eczema to name just a few.

Symptoms can include:

• Bloating
• Abdominal distension
• Diarrhoea
• Abdominal pain
• Gas with belching/flatus
• Nausea
• Constipation
• Unintentional weight loss
• Fatigue
• Nutritional/vitamin deficiencies
• Anaemia

SIBO and Reflux

However, it is less well recognised that SIBO can be the cause of reflux symptoms. Reflux symptoms associated with SIBO are often identical to those caused by true Gastro-Oesophageal Reflux Disease (GERD). This is caused by failure of the lower oesophageal sphincter (LOS). These can include “typical” reflux symptoms but also Laryngo-Pharyngeal (LPR) symptoms. You can read more about LPR/Silent reflux here.

Symptoms can include:

• Heartburn
• Regurgitation
• Belching
• Sore throat
• Throat clearing
• Cough
• Voice problems
• Shortness of breath
• Sinusitis
• Bad taste
• Sore mouth

Commonly SIBO causes bloating after eating especially carbohydrates as these are fermented into gases. Sometimes people mistakenly think they may be gluten intolerant. There can be associated abdominal discomfort, particularly in the upper left side, with belching and flatulence as well as “indigestion” type symptoms. These are frequently attributed to GERD and sometimes “functional dyspepsia”.  Both are usually treated with PPIs which can paradoxically exacerbate symptoms.

How does SIBO cause reflux?

We don’t know for sure. However theories include:

• Belching. Often in patients with reflux symptoms who test positive for SIBO impedance oesophageal physiology studies record the association of belching with reflux events in both the lower and upper oesophagus. It's plausible that this belching causes an aerosol containing substances from the stomach including not only acid but also pepsin and bile that can reach the throat, nose, sinuses and even the lungs. Pepsin is biologically active in relatively non-acidic environments and highly irritant to sensitive tissues. This may explain how Pepsin can be found in these anatomical locations so far from the stomach.
• Constipation. There is also some evidence that constipation can increase the frequency of so-called Transient Lower Oesophageal Relaxations (TLOSRs) which are associated with acid reflux and so use of laxatives can sometimes help reduce reflux symptoms. Since IMO is associated with constipation this may be another mechanism by which intestinal dysbiosis causes reflux symptoms.

Read more about the connection between the gut biome, SIBO and reflux

Testing for SIBO

Firstly, it's important to remember that the symptoms caused by SIBO can also be secondary to many other conditions and occasionally potentially serious disease. Most people we see will be aware that their symptoms are long-standing and many will have been investigated previously. Nonetheless if there are any alarm symptoms it is clearly important to exclude serious disease before assuming SIBO is responsible.

The most accurate method to test for SIBO is to take aspirates from the duodenum (the first part of the small bowel after the stomach) and then culture these to see which bacteria grow. This involves an endoscopy and is both invasive and impractical. So in clinical practice the established gold standard are breath tests which are easy to perform and non-invasive.

How do breath tests work?

You'll be sent a kit so you can do the test at home. You'll swallow a sugar solution (Lactulose) and then breathe into a series of small bottles every 15 minutes over two hours. You'll then send the kit back to us and we'll analyse the contents of the bottles to measure hydrogen and methane gases.

Since the small bowel is normally relatively sterile as the micro-organisms that we naturally swallow are killed in the stomach by hydrochloric acid and enzymes. Therefore lactulose passes through the small bowel unchanged. In most people after 90 minutes it will reach the colon where the micro-organisms that naturally inhabit the large bowel break the lactulose down into glucose. They will then "ferment" the sugar into hydrogen or methane gases, some of which will then be exhaled from the lungs.

In SIBO, the small bowel is “overgrown” by micro-organisms and so the lactulose will be converted to gases earlier than normal. This early rise in exhaled gas is diagnostic of SIBO. When Methane levels are higher than normal IMO is diagnosed.

Is SIBO curable?

Treatment can be difficult and even the most effective treatment regimens can fail when looking for a SIBO cure. The key principles are:

1. Identify and treat the underlying cause
2. Treat SIBO/IMO
3. Treat any complications

The absolute key starts with making the right diagnosis.

We base our advice for diagnosis and treatment on current scientific evidence and best practice.

Identify and treat the underlying cause

Often there is no obvious precipitating factor or cause identified but when identified should be addressed where possible.

However, we see many people with co-existent reflux and Small Intestinal Bacterial Overgrowth symptoms who are taking PPIs. Often, they find these don’t help their symptoms and sometimes can even make them worse. They may have been prescribed these because of "reflux" symptoms. However, the PPIs can then precipitate the development of SIBO which exacerbates their reflux symptoms. Eradicating SIBO while continuing to take PPIs is unlikely to be effective if the PPIs are its cause and stopping these in the context of significant reflux symptoms can be equally difficult. Many people take PPIs for obscure reasons and often their reflux can be better treated with dietary modification, different drugs or even surgery.

We see two main groups of patients with reflux and SIBO. The first have “true” reflux almost always caused by a hiatus hernia and failure of the Lower Oesophageal Valve (LOS), albeit that often the hiatus hernia has not been diagnosed when we see them. Their symptoms are caused primarily by acid reflux in which case appropriate treatment would include PPIs. They often find that initially these drugs helped their symptoms but these have then deteriorated or changed. In this group PPIs have precipitated SIBO and the question is then how best to treat both GERD and SIBO/IMO. Often these patients will benefit from anti-reflux surgery as this will allow them to stop medication although dietary modification and reducing doses of PPIs and substitution with other medications including alginates can sometimes help.

In the second group GERD was wrongly diagnosed in the first place. Their symptoms where never caused by LOS failure but rather SIBO developed independently and has always been their main driver. Commonly they were treated with PPIs which usually don’t help the symptoms and may make them worse by changing the gut biome further and worsening the SIBO/IMO. For this group stopping the PPIs and treating the dysbiosis is the best treatment.

Comprehensive assessment and testing usually reaches the right diagnosis and identifies effective treatment options.

Treat SIBO/IMO

Having eliminated an identifiable and treatable cause of SIBO the main pillars of treatment are:

• Dietary modification
  - LOW FODMAP diet. The evidence that diets can help SIBO symptoms alone is not strong but many patients do benefit from avoiding foods containing "FODMAPS". FODMAP is an acronym for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, And Polyols. These are specific carbohydrates in food that are fermented by microbes, producing gas. Avoiding these can reduce the fermentation which is typically associated with SIBO and is responsible for some of its symptoms, especially bloating and gas. We use low FODMAP diets as part of our eradication regimes as recurrence rates after anti-biotics alone can be high. Read more on FODMAP diets. It can be difficult to know what foods are high in FODMAPS and which aren't and so diets which typically involve exclusion, re-introduction and avoidance phases are ideally undertaken with specialist dietetic advice.
  - Elemental diet. This involves providing nutrition form pre-prepared liquids/powders. These preparations contain all the nutritional components we need but these have been reduced to their basic molecular constituents.  The diet typically lasts two weeks during which no solids or normal food are eaten. The elemental diet formula is absorbed rapidly and its components are therefore not available to the micro-organisms in the small bowel responsible for causing SIBO. This effectively starves them to death. While scientific studies report high success rates in treating SIBO, an Elemental diet is not suitable for many people, can be dangerous without dietetic supervision and is very expensive. Most people can’t tolerate its liquid nature and so is usually used as a last resort.
  - Other Diets. Many other diets are used to treat patients with SIBO; There is poor evidence that these are effective although anecdotally dieticians report that they can help some people. These include:
  -- Low Fermentation/Cedars Sinai Diet. Developed by SIBO expert Dr. Mark Pimentel and emphasises meal spacing.  Can be useful long-term.
  -- Prolon Fasting Mimicking Diet. This is a 5-day diet designed to provide the benefits of fasting while still maintaining nutrients and calories. It is the subject of multiple clinical studies and is thought to encourage a healthy gut biome.
  -- The Specific Carbohydrate Diet (SCD). Highly restrictive and protocol driven.
  -- Paleo/Caveman Diet. This strictly limits sugars, carbohydrates, processed foods and dairy products.
  -- Low Histamine Diet. There are theories that SIBO is a cause of histamine overproduction. There is no scientific evidence that a low histamine diet can help SIBO symptoms.
  - Antibiotics. For people wanting to eradicate SIBO by far the strongest evidence supports the use of specific anti-biotics. Read here for most up to date scientific literature review. This may seem paradoxical and counter-intuitive in that anti-biotics are a cause of biome disruption and associated with SIBO and IMO. However, while common wide spectrum anti-biotics can help SIBO, studies have shown that the Rifaxamin and Neomycin have specific characteristics which help their effectiveness and minimise potential side-effects.
  - Rifaxamin is mostly active only in the small bowel and so does not significantly affect the normal biome of the large bowel/colon. Scientific studies have shown that SIBO symptoms will be improved by a two week course in up to 70% of patients. The evidence is that eradication rates are significantly improved in methane dysbiosis (IMO) when Neomycin is used in combination with Rifaxamin read here. Again. Neomycin is active only in the bowel and is n ot absorbed into the rest of the body.
  
  Typically, we will treat patients with one or both anti-biotics as appropriate for 2 weeks and follow up with a low-FODMAP diet, dependant on the results of breath tests.
• Probiotics. Probiotics have become widely available and believed to help gut health by improving the GI biome. Probiotics are defined as microorganisms that benefit health. Theoretically “helpful” bacteria in probiotic preparations replace the “harmful” bacteria causing SIBO and help to restore diversity and a healthy microbiota. However, the evidence that probiotics can help SIBO is mixed. Some studies have reported that they can improve symptoms and reduce hydrogen gas levels in breath tests while others reported suggest that they may make symptoms worse and even increase methane levels on breath testing. Consequently, more studies are required to identify which if any probiotics may be helpful and you should discuss this with your dietician.
• Pro-kinetics. It is thought that the development of SIBO/IMO is related with poor gastrointestinal motility. In particular there is some evidence that SIBO is associated with disruption of the Migrating Motor Complex (MMC). The MMC are waves of contractions that start in the stomach and run along the entire gut. These are prominent during fasting and are thought to help “clear” the GI tract of food debris and micro-organisms. Some drugs, known as prokinetics improve the function of the MMC. These include:
  - Erythromycin which is a macrolide antibiotic and mimicks the action of motilin, a natural hormone that promotes gut motility. Not used regularly because of its effect on the GI biome.
  - Metoclopramide and Domperidone: Dopamine receptor antagonists. Have cardiovascular effects and not licenced for long term use.
  - Prucalopride: A serotonin receptor agonist. This is an effective drug and indicated for long term use and therefore often used as part of second line treatment regimens especially in patients with constipation.

Ultimately, the key to success is making the right diagnosis and treating each patient as an individual. SIBO is a complicated condition and successful long-term treatment requires a truly holistic approach. Without addressing the underlying causes SIBO often recurs after treatment. Identifying and removing the causes where possible and dietary and lifestyle changes are a pre-requisite for success. While anti-biotic treatment is usually successful repeated courses are not the answer for life long treatment.

At RefluxUK we understand how debilitating "functional" gut symptoms including those caused by acid reflux and SIBO can be. We will work with you to agree a tailored approach to diagnose and treat your symptoms, provide you with specialist medical and dietician advice and hopefully achieve the best likelihood of eliminating them. 

Page reviewed by: Mr Nick Boyle BM MS FRCS 23/04/25