SIBO and IMO symptoms, causes, testing, diagnosis & treatment: is SIBO or IMO the root cause of your digestive system issues?
Small intestinal bacterial overgrowth, or SIBO, is a condition in which abnormally high levels of specific bacteria are present in the small intestine.
Intestinal methanogen overgrowth, or IMO, is similar to SIBO, but the problem is technically caused by archaea rather than bacteria. However for the most part, when we refer to SIBO in this article, we are also referring to IMO.
SIBO is also often mistaken for irritable bowel syndrome (IBS), a common digestive disorder.
SIBO can cause a wide range of symptoms, including abdominal pain, bloating, diarrhoea, and weight loss.
In conventional medicine, SIBO can be treated with antibiotics (that work a little differently than most types of antibiotics). However, SIBO is not always considered by doctors, or investigated, and if it is, there are often very long waiting times.
However, as we’ll discover below, in the functional medicine approach to SIBO, there are a number of additional strategies that can help.
Table of Contents
SIBO symptoms
Many clients who attend our Functional Medicine clinics have come to us because conventional medicine (often the NHS here in the UK) hasn’t been able to help, and they’re experiencing:
- Abdominal bloating (1)
- Diarrhoea (2)
- Weakness (3)
- Abdominal pain (4)
- Unintentional weight loss (5)
- Flatulence (6)
- 'Foggy' brain (7, 8)
- Headaches
- Fatigue
- And in some cases, constipation (9)
– all common symptoms of bacterial (or archaea) overgrowth in the small intestine, or SIBO.
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So what’s going wrong?
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 (10), synthesis of nutrients (11), appetite regulation (12), and many, many more functions.
However, when there is an overgrowth of bacteria in the small intestines, they are often associated with a number of adverse symptoms.
The bacteria in the small intestine can be the same bacteria as found in the colon, but at high enough levels to cause symptoms, or can be pathogenic (‘bad’) bacteria, or can be too many archaea (which are technically not bacteria cells).
Some bacteria or archaea in the small intestine can produce gases, either hydrogen gas, hydrogen sulfide gas, or methane gas.
And this is where problems can start.
Common bacteria associated with hydrogen SIBO are Escherichia coli and Klebsiella (there are many more).
Common bacteria responsible for producing hydrogen sulfide gas include Desulfovibrio piger and Bilophilla wadsworthii. Those with hydrogen sulfide SIBO may note gas that smells like sulfur (rotten egg smell).
Archaea such as Methanobrevibacter, produce methane gas (and is called a methanogen).
The hydrogen produced by some bacteria, actually go on to contribute to an increase in methanogens, a couple of such hydrogen producing bacteria, that feed methanogens, are ruminococcaceae and christensenellaceae.
This association has only recently been identified, highlighting that we are continuously learning more about SIBO and how best to help those struggling with this condition.
How does SIBO cause problems and how many people are affected?
Small intestinal bacterial overgrowth (SIBO) is defined as excessive bacteria in the small intestine (14).
SIBO can cause nutritional deficiencies due to nutrient malabsorption (15) and can result in high levels of gas as a result of the bacteria reacting with dietary carbohydrates – causing fermentation (16).
It’s this gas that causes SIBO symptoms such as abdominal bloating, distension and changes in bowel movements, and it can be very uncomfortable.
In the UK, it is estimated that up to 22% of people (17) may be suffering with Irritable Bowel Syndrome (IBS) (although estimates do significantly vary), and the root cause could be SIBO in many cases.
One study reported 84% of IBS patients also had SIBO based on lactulose breath test results, compared to only 20% who didn’t have IBS (18).
However, numerous other studies suggest that a more accurate figure is 60%. Meaning that around 60% of those with IBS, also have SIBO.
What’s the conventional medicine approach to SIBO?
In our experience, we have found that some GPs (including those we’ve worked with in the NHS in the UK but also globally), 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 often 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, and Dr Pimentel, a lead researcher in SIBO and author/co-author of most of the papers published in this area. These experts have successfully helped thousands of patients suffering with SIBO.
Understanding clients symptoms and their health history, performing the right tests, and applying an evidence-based comprehensive approach, is what makes a Functional Medicine approach to SIBO effective.
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.
Whilst a number of research papers dispute the accuracy of breath testing in SIBO, done the right way, with the right preparation (and interpretation), the accuracy increases significantly.
A SIBO breath test measures the levels of the methane and hydrogen gases that are produced by the archaea and bacteria, respectively.
A sugar solution (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 provide fuel for the bacteria are avoided, thereby allowing for greater accuracy of the test.
During this preparatory one-day diet, bacteria and archaea 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 a 3 hour, lactulose breath test at home with our guidance, and samples are returned to the analysing lab for analysis.
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 lactulose 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.
A note on hydrogen sulfide: Currently, there is not a testing option for hydrogen sulfide gas in the UK, however the new ‘trio-smart’ test is available in the United States and Canada, and so hopefully it won’t be long before this is available in the EU and UK. This test measures all three gases; hydrogen, hydrogen sulfide and methane.
The increase in hydrogen gas on a SIBO breath test, compared to baseline (measured in parts per million – ppm) and at what time point the peak level is at, are the key points considered when interpreting the results. For methane, an elevated level even from baseline, is relevant.
When SIBO symptoms are clearly present, however a SIBO breath test shows a flat line at the bottom for methane and hydrogen gas, then hydrogen sulfide SIBO can be considered.
An elevation in hydrogen and/or methane indicates bacteria/archaea in the small intestine which are reacting with the lactulose 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 (19), whereas methane gas, produced by other bacteria, is often associated with constipation (20).
Hydrogen sulfide SIBO is associated with diarrhoea.
Where a person has both methane and hydrogen SIBO, they are more likely to experience constipation, although some people experience inconsistent stools (alternating between hard and loose), or stools may even appear to be normal!
What are the root causes of SIBO?
In our Functional Medicine approach to SIBO, we’re always looking for root cause factors.
Possible factors increasing the risk of developing SIBO symptoms include:
- Food poisoning (possibly the most common causal factor, please see below for further information) (21, 22, 23)
- Frequent or prolonged use of antibiotics (24)
- Low stomach acid or use of medications such as proton-pump inhibitors to reduce stomach acid (25, 26, 27)
- Chronic conditions that affect the wall of the intestinal tract, such as Crohn's disease (28)
- And coeliac disease (28)
- Prior bowel surgery (29)
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 and archaea.
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 and archaea levels in the small intestine increase.
Every time we eat, the MMC is interrupted (30).
Phase III activity of the MMC, the most active phase of its four phases, has been shown to be absent in cases of IBS and SIBO (31).
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, and this is something we actively consider in our Functional Medicine approach to SIBO.
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 several others) are able to produce a toxin known as Cytolethal Distending Toxin (CDT) (32).
Therefore, after a food poisoning event, some people can be exposed to this common toxin, and more specifically to the active component of CDT – Cytolethal Distending Toxin B (CdtB-toxin) (33).
If we are exposed to Cdt-B toxin, then naturally our immune system wants to help us out and we 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 (34).
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 (35). This then changes how our digestive system is functioning.
The time between the food poisoning event and the onset of SIBO symptoms, can be several months, therefore making the link between the two, less obvious.
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) (36).
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, SIBO symptoms / IBS symptoms in some cases only become apparent around 3-4 months after the food poisoning event (37).
Antibodies to vinculin can be measured, thanks to the research performed by Dr Mark Pimentel 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 (38).
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What other factors are associated with SIBO?
Small intestinal fungal overgrowth (SIFO) .
Often what may seem like SIBO (based on SIBO symptoms only, not testing) can actually be SIFO – small intestinal fungal overgrowth.
If so, a different approach is required, and again, this is something we actively consider in our Functional Medicine approach to SIBO.
A candida / fungal overgrowth, combined with SIBO, also makes therapy more challenging, but possible.
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 (39).
HCl levels begin to decline with age and with the long term use of acid blockers, such as Histamine type 2 receptor blockers.
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 also common in those suffering with SIBO.
It is believed that bacteria cause deconjugation (breakdown) of bile acids (40, 41).
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 a Functional Medicine approach to SIBO, 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.
This way we can eventually move to a state of optimal health and well-being, with long lasting benefits.
Let’s look at some SIBO test results
‘Diagnostic’ criteria for SIBO does differ amongst experts.
In the Functional Medicine approach to SIBO at Coho Health 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 the first 120 minutes
- Hydrogen increases by 20ppm or more, after baseline, within 140 minutes with constipation
- Methane rises by 3-11 ppm within 180 min with constipation
- Methane is present at a level of 10ppm or more, at any time point
- 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.
SIBO testing: case study 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 is 11ppm at 120 minutes, higher than 10ppm = SIBO indicated based on methane results.
SIBO testing: case study 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.
SIBO testing: case study 3
In the next example, hydrogen rises by 55ppm at 120 minutes = indicates SIBO.
Methane does not increase to 10ppm or more = negative for SIBO.
Overall, this suggests a positive SIBO presentation, based on hydrogen only.
How can we treat SIBO?
The answer to treating SIBO 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!
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 can take a little 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 in our functional medicine approach to SIBO as Coho Health, our practitioners work very hard, alongside our clients, to ensure we cover all the bases and don’t cut any corners.
Nutrition and diet 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 that are appropriate for SIBO.
Specific nutritional strategies
Specific and highly personalised nutritional strategies are a critical factor in our Functional Medicine approach to SIBO.
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 Coho Functional Medicine 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 SIBO treatments?
Studies have shown the efficacy of prescribed antibiotics; Rifaximin, and Rifaximin combined with Neomycin, in treating SIBO (42, 43, 44).
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 or within the Functional Medicine, 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 (45). In fact, Dr Pimentel notes that he has observed the microbiome establish more (healthy) diversity in some patients after being treated with Rifaximin.
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 (46).
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.
For hydrogen sulfide SIBO, oregano and bismuth are most frequently used.
Berberbine is often used for methane and hydrogen SIBO, often combined with a second anti-microbial.
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.
The use of prokinetics in supplement form, can significantly reduce the risk of relapse, or significantly delay reoccurrence. Prokinetics (such as ginger, or there are many supplemental multi-formulas available) work by promoting the migrating motor complex and are an essential part of the protocol.
Unless it is mild SIBO, it is possible that multiple rounds of therapy and re-testing may be required.
We don’t just want to clear SIBO by 50%, we want 100% eradication, and strategies employed to help prevent reoccurrence (which is common).
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The wrap
We hope this article has been useful and has helped you to gain a better understanding of SIBO, the Functional Medicine approach to SIBO, the options for testing, and the options for eradicating SIBO.
If we can help you, we offer Functional Medicine consultations in the UK, in Mallorca, and to clients around the World through our virtual Functional Medicine clinic.
To make a start addressing your SIBO, or any other chronic health problem you have, our experienced team are ready to help you.
If you’re looking for a Functional Medicine team delivering real health transformation, you’re in the right place.
We’d love to help you.
To your optimised, healthy future,
Dee & the Coho Health team
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