Small Intestinal Bacterial Overgrowth (SIBO): What It Is, How to Test For It

By Dee Brereton-Patel November 17, 2016 March 5th, 2019 Health

Is SIBO the root cause of your digestive system issues?

Many clients who attend our Functional Medicine Nutritional Therapy clinic in Manchester have come to us because they’re experiencing:

  • frequent abdominal bloating
  • diarrhoea
  • ‘foggy’ brain
  • headaches
  • fatigue
  • abdominal pain
  • and in some cases, constipation

– all common symptoms of bacterial overgrowth in the small intestine, or SIBO.

So what’s going on?

We have a complex, living, community of thousands of different strains of bacteria residing in our gastrointestinal system, more specifically in our colon. In healthy individuals, these bacteria can be living in harmony, supporting our immune system, synthesis of nutrients, appetite regulation, and many, many more functions.  However, when these bacteria move higher up in the intestinal system, to the small intestine, they are often associated with a number of adverse signs and symptoms.

The bacteria in the small intestine are usually the same bacteria that are found in the colon, so not necessarily pathogenic (‘bad’) bacteria, but normal colonic bacteria that is in the wrong place – in the small intestine.

And this is where problems can start.

How does SIBO cause problems and how many people are affected?

Small intestinal bacterial overgrowth (SIBO) can cause nutritional deficiencies due to malabsorption (1) and can result in high levels of gas as a result of the bacteria reacting with dietary carbohydrates – causing fermentation. It’s this gas that causes the abdominal bloating and distension in SIBO and it can be very uncomfortable.

In the UK, it is estimated that up to 22% of people (2) may be suffering with Irritable Bowel Syndrome (IBS) (although estimates do significantly vary), and the root cause could be SIBO in many cases.

Where SIBO is not the root cause, it’s one of the factors often associated with the symptoms in IBS.

What’s the NHS approach to SIBO?

In our experience, we have found that some GPs, who may be aware of SIBO, are happy to make a referral to a gastroenterologist.

A gastroenterologist might then approve a SIBO breath test. Due to the length of time the test takes, it’s usually a morning admission to the hospital to have the test performed.

However, we have noted from the results our clients bring to us, that only hydrogen has been measured (see below for why this doesn’t provide everything you need to know about SIBO).

Additionally (unless otherwise requested) the test is usually only performed for 2 hours, rather than 3 hours. 3 hours is the test duration recommended by experts in the field such as Dr Siebecker, who has successfully helped thousands of patients suffering with SIBO.

So how can we test for SIBO?

There are some challenges to testing for SIBO accurately, however arguably the best option available to us at the moment is a breath test. A SIBO breath test measures the levels of the methane and hydrogen gases that are produced by the bacteria.

A sugar solutiScreen Shot 2016-11-17 at 16.14.45on (lactulose or glucose) is taken orally after an overnight fast.

Preceding the fasting period, a very specific diet is followed for one day, where carbohydrates that ferment are avoided, thereby allowing for greater accuracy of the test.

During this preparatory one-day diet, bacteria that may be present in the small intestine are essentially ‘starved’.

Breath samples are collected at baseline and every 20 minutes, for 3 hours, and levels of methane and hydrogen gases are measured.

Our clients perform this test at home, and we are currently using the Biolab SIBO Breath test.

There are a few options around the sugar solution that is used to ‘feed’ the bacteria, but the best option currently is non-absorbable lactulose.  The lab send a sachet of lactulose with the test kit – this is diluted in water and taken at baseline.

We advise our clients to perform this 3 hour test first thing in the morning, as it’s necessary to remain fasted until all samples are collected. Turn around for results is currently around one week.

Interpreting SIBO test results

The results show whether or not there are elevations in hydrogen and methane. How high the gases are compared to baseline (measured in parts per million – ppm) and at what time points, are the key points considered when interpreting the results.

An elevation in these gases indicates bacteria in the small intestine which are reacting with the sugar solution used in the test.

For people suffering with SIBO, the same is happening when they consume carbohydrates in their diet.

Whereas the accuracy of the hydrogen gas detected in the test is questionable to some degree, the result of the methane gas in the breath test is generally accepted to be highly accurate.

Hydrogen gas produced by some bacteria is more often associated with diarrhoea (3), whereas methane gas, produced by other bacteria, is often associated with constipation (4).

Where a person has both methane and hydrogen producing bacteria in the small intestine, stools may be inconsistent, or appear to be normal!

What are the root causes of SIBO?

Common causes of SIBO include:

  • Food poisoning (possibly the most common causal factor, please see below for further information)
  • Frequent or prolonged use of antibiotics
  • Low stomach acid or use of medications such as proton-pump inhibitors to reduce stomach acid
  • Food intolerances
  • Chronic conditions that affect the wall of the intestinal tract, such as coeliac disease or Crohn’s disease
  • Prior bowel surgery

Gut motility is affected in most cases of SIBO

When our digestive system isn’t busy digesting and absorbing nutrients, it’s busy cleaning house.

The migrating motor complex (MMC) is a cyclic motility pattern occurring in the gut – think of the wall of the small intestine causing wave like motions, sweeping contents downwards towards the colon, including bacteria.

The MMC is regulated by gut hormones and by signals from the central nervous system.

If the MMC becomes damaged, this function can be impaired, and bacteria, usually in the colon, can move up into the small intestine.

Every time we eat, the MMC is interrupted (5).  Therefore, for people with SIBO, meal spacing can be especially helpful, so that the MMC is busy at work in between meals.

Besides this ‘sweeping’ motion that occurs in between meals, we also have waves of contraction and release that occurs in the digestive tract, called peristalsis, to help move food along, starting from the oesophagus.

Nerve signals trigger this contraction of the smooth muscle that lines the digestive tract.

Is there an autoimmune link in SIBO?

We believe so. In some, but not all cases of SIBO, the trigger seems to be an episode of food poisoning.

Common bacteria associated with food poisoning include E.coli, campylobacter, salmonella, and shigella.

These bacteria (and some others) produce a toxin, and after a food poisoning event, some people can be exposed to a common toxin called Cytolethal Distending Toxin B (Cdt-B-toxin).

If we are exposed to Cdt-B toxin, then naturally our immune system wants to help us out and we can produce antibodies to fight the toxin.

Symptoms of food poisoning include abdominal cramps and pain, diarrhoea (may contain blood or mucus), vomiting, nausea, low energy, weakness, fever, nausea, and aching muscles (6).

Symptoms from food poisoning usually resolve with a few days, and we may never think anything more of it. It was just a short term, acute event (that we’d rather forget all about).

However, unfortunately in some cases, the immune system becomes confused and instead of our antibodies attacking only the Cdt-B toxin, they also begin to attack a protein that lines our intestinal tract, called vinculin (7).

The role of Vinculin in gut motility & SIBO

In autoimmune conditions, ‘molecular mimicry’ is the reason our antibodies ‘attack’ healthy cells – the antibodies think the healthy cells ‘look’ the same as the toxin (or pathogen) it originally intended to attack.

Vinculin plays a vital role in peristalsis – it helps connect cells including ‘Interstitial cells of Cajal’ (named after the researcher who first identified these cells) (8).

These cells are connected to the smooth muscle of the intestinal tract and are considered the ‘pacemaker’ for peristalsis.

So, we can begin to see how an appropriate immune response to a toxin produced by food poisoning bacteria, is now negatively impacting peristalsis.

It’s also very important to note that if your IBS / SIBO is caused by a food poisoning event, symptoms of IBS / SIBO in some cases only become apparent around 3 months after the food poisoning event.

Antibodies to vinculin can be measured, thanks to the research performed by Dr Mark Pimental and his team.

Dr Pimental’s research led to the discovery that two antibodies, anti-CdtB and anti-vinculin, are elevated in patients with diarrhoea associated IBS, and mixed type (mixed stool consistency) IBS (9).

What other factors are associated with SIBO?

Small intestinal fungal overgrowth.

Often what may seem like SIBO (based on symptoms only, not testing) can actually be SIFO – small intestinal fungal overgrowth. If so, a different approach may be required.

A candida / fungal overgrowth, combined with SIBO, also makes therapy more challenging.

For better long-term outcomes, it is necessary to address the candida overgrowth at a similar time to the SIBO.

In SIBO, we also need to consider if there are optimal levels of hydrochloric acid (HCl, or gastric acid), being produced by the cells lining the stomach.

A lack of HCl can be a predisposing factor for SIBO (10).

HCl levels begin to decline with age, and use of acid blockers, such as Histamine type 2 receptor blockers, or proton pump inhibitors (PPIs), also reduce HCl levels.

HCl not only plays a critical role in digestion but it also helps to keep bacteria in check.

It suppresses the growth of ingested bacteria and limits the amount of bacteria in the upper small intestine. Chronically low stomach acid can contribute to an environment where it is easier for bacteria, and therefore the bacteria that contribute to SIBO, to thrive.

Fat malabsorption is common in those suffering with SIBO.

It is believed that bacteria cause deconjugation (breakdown) of bile acids (11, 12).

This leads to insufficient concentrations of bile to support fat absorption. Consequently fat soluble vitamins may also be reduced, such as vitamins A, D, E and K.

Additionally, as a result of the deconjugation, the free bile acids can damage the intestinal mucosa (cells lining the intestinal tract) causing inflammation and malabsorption. This can lead to further micronutrient deficiencies such as iron and vitamin B12.

The Functional Medicine Approach to SIBO

When applying the functional medicine approach, we can begin to see that it is rarely the case that SIBO exists in isolation.

In our own clients, we have seen that SIBO is often the end result of other imbalances, and it is also the trigger for developing further imbalances.

Our approach is therefore to consider the whole picture – what events preceded the onset of current signs and symptoms, and what needs to be done to unravel and address the various layers of imbalances to eventually move to a state of optimal health and well-being, with long lasting benefits.

Lets look at some results

‘Diagnostic’ criteria for SIBO does differ amongst experts.  At Optimised we are using the criteria set by leading expert, Dr Siebecker.

What are we looking for in the test results?

  • Are the baseline readings (breath samples prior to drinking the lactulose solution), at zero (0)? If not, it is possible the preparatory diet was not performed correctly, and/or there was an insufficient fasting time
  • Hydrogen gas (in parts per million (ppm) increases by 20 or more, after baseline, within 120 minutes
  • Hydrogen increases by 20ppm or more, after baseline, within 140 minutes with constipation
  • Methane increases by 12ppm or more, within 180 minutes (including baseline)
  • Methane is 3-11ppm within 180 minutes with constipation
  • Combined hydrogen and methane of 15ppm or more after baseline (at any timepoint)

If any of the above are true, this is indicative of SIBO.

Example 1

In the below example we can see that hydrogen at 120 minutes is 95ppm, this is 94ppm greater than at baseline = SIBO indicated based on hydrogen results.

Methane at 180 minutes is 14ppm, a rise of 14 ppm from baseline = SIBO indicated based on methane results.

Example 2

In the below example we can see the classical ‘double peak’ presentation, where the first peak is suggesting bacteria in the small intestine, whilst the second peak (from 160 minutes) is the normal (expected) colonic bacteria.

Hydrogen increases by 19 at 120 minutes, however this client suffers with constipation, meaning that we need to look at the increase at 140 minutes. Increase at 140 minutes is 53ppm = indicates SIBO.

Methane (with constipation) increases by 5ppm at 180 minutes = indicates SIBO.

Example 3

In the next example, hydrogen rises by 55ppm at 120 minutes = indicates SIBO.

Methane does not increase to 12ppm or more = negative for SIBO.

Overall, this suggests a positive SIBO presentation, based on hydrogen only.

How can we address SIBO?

The answer is often with multiple clinically relevant strategies, embraced either simultaneously or in a phased manner. Plus a huge level of commitment and patience from our practitioners and clients! Dealing with SIBO isn’t always easy.

Our experience is that in some people, SIBO is resolved relatively quickly and clients go on to reach optimal health and wellness. But, typically, the road to recovery is longer and patience is required.

While ‘diet only’ interventions can be sufficient to overcome SIBO for some people, in our experience it’s often not enough.

Often, we need to combine nutritional changes, which are vitally important, with other clinically relevant strategies to resolve SIBO (and resolve it for good).

As practitioners, one of the most disappointing outcomes, is when our clients work extremely hard to resolve SIBO symptoms, only for the symptoms to come back again shortly afterwards.

And we know this is hugely disappointing for clients too!  So our Functional Nutritional Therapists at Optimised work very hard, alongside our clients, to ensure we cover all the bases and don’t cut any corners.

Nutrition in SIBO

The bottom line is that we don’t want our clients to restrict their nutritional choices more than necessary, and for any longer than necessary.

However, in SIBO, changes are absolutely necessary – a diet low in carbohydrates is usually recommended, ideally short term only to avoid any deficiencies, and there are various carefully designed diets appropriate for SIBO.

Specific nutritional strategies

Two of the common diets we advise clients to use are the low FODMAP diet, or the diet developed by Dr Siebecker – the SIBO Specific Food Guide.

What we love about the SIBO Specific Food Guide, is that rather than a food being completely eliminated (as some foods are in a Low FODMAP diet), the SIBO Specific Food Guide may propose that the food can still be included. But only a specific quantity of it should be consumed.

We have to remember, that these diets are just templates – we need to make the diet bespoke and individualised for each person, taking into consideration food sensitivities and sometimes complex symptoms.

For instance, other factors may be at play also such as a histamine intolerance. That’s why working closely with a practitioner can be extremely helpful.

On occasion, it’s also necessary to follow a nutrition protocol that is much more restrictive, such as an Elemental Diet.

This is particularly the case when clients report a high degree of sensitivity to many different foods and drinks, and perhaps are also experiencing unintentional weight loss due to malabsorption or reduced caloric intake.

An Elemental Diet involves making shakes using nutrients that require no digestion, so the nutrients can be absorbed quickly (although there are some pre-mixed elemental shakes or formulas that can be purchased).

In our practice, we’ve come across many people who have been following a low FODMAP or other SIBO diet for months or even years. Since these diets can really help to reduce symptoms in some people, we can see why.

But longer term, these diets have the potential to negatively impact our beneficial bacteria levels. The reason for this is that the fermentable carbohydrates that are avoided, actually help to ‘feed’ the beneficial bacteria in our gut (acting as prebiotics).

In summary, strategies such as low FODMAP diets aren’t a sustainable, long term solution for dealing with SIBO.

Rather than managing symptoms, we need to eliminate them completely by addressing the underlying cause(s).

An approach that has worked well for our clients is limiting these fermentable carbohydrates in their diet while also working to eradicate the abnormal overgrowth of bacteria in the small intestine.

What about conventional and naturopathic treatments?

Studies have shown the efficacy of prescribed antibiotics such as Rifaximin, and Rifaximin combined with Neomycin in treating SIBO.

Rifaximin is not like most antibiotics, it is a non-absorbable antibiotic, meaning that it stays within the gastrointestinal tract and is used to treat non-systemic gastrointestinal infections such as travellers diarrhoea.

The worry for most of us working naturopathically, is that antibiotics can impair the microbiome.

However Rifaximin has minimal impact on this area, has a good safety profile and doesn’t seem to induce significant bacterial resistance (SS).

Rifaximin is a popular choice for treating SIBO in the US, but it is not licensed for SIBO in the UK. Despite this, we have worked with some clients who have managed to get an NHS prescription for this indication.

Our first choice where possible would be to reduce the bacterial overgrowth through dietary interventions and herbal antimicrobial products that have been shown to be just as, if not more, effective than medications (10).

The type of herbal antimicrobial use, the duration of therapy, and adhering to an appropriate diet for each individual, is key to success!

For mild cases of SIBO, an antimicrobial formula containing several herbs, could be considered.

But for moderate to severe cases, where multiple rounds of antimicrobials may be required, it is advisable to use two herbs at a time (thus minimising bacteria resistance to herbs).

We would always consider allicin, if methane producing bacteria (methanogens) are indicated, due to its efficacy.

Please note that using allicin in supplement form, although it is a garlic extract, is not the same as taking whole garlic which may not be well tolerated by some people with SIBO.

Repeat testing is recommended, to inform if further rounds of therapy are required.

Assessing symptoms alone (without repeat testing) could be misleading. Symptomatic improvement may suggest SIBO has been eradicated, yet low levels of bacteria may remain, that over time begin to increase again, bringing us back to square one.

Unless it is mild SIBO, please expect multiple rounds of therapy and re-testing. We don’t just want to clear SIBO by 50%, we want 100% eradication, and strategies employed to help prevent reoccurrence (which is common).

We hope this article has been useful and has helped you to gain a better understanding of SIBO, the options for testing, and the options for eradicating SIBO.

If our Functional Medicine Nutritional Therapy team can help you, we offer consultations at our Manchester clinic, or online for those who can’t travel to Manchester.

To make a start addressing your SIBO, or any other chronic health problem you have, our experienced team are ready to help you.

Contact us now

To your optimised health,

Dee & the Optimised clinic team

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