SIBO and IMO symptoms, causes, testing, diagnosis & treatment: is SIBO or IMO the root cause of your digestive system issues?
Severe bloating that makes you look pregnant by the end of the day. Gas that arrives whether you eat well or not. Exhaustion that sleep doesn’t fix. Brain fog that makes it hard to think clearly.
If you’ve been living with some version of this – and especially if you’ve been through the standard tests without finding answers – you may be dealing with small intestinal bacterial overgrowth, or SIBO.
SIBO is a condition where bacteria that should be further down the digestive tract overgrow in the small intestine – where they don’t belong – causing fermentation, inflammation, and a wide range of symptoms that often have nothing obviously digestive about them.
A closely related condition, intestinal methanogen overgrowth (IMO), involves a similar problem but with archaea rather than bacteria. For the purposes of this article, when we refer to SIBO we’re including IMO too.
If you’ve been diagnosed with IBS but never felt like you’ve found the real answer, SIBO may be a significant part of what’s been missed.
Research suggests it’s present in a substantial proportion of people with an IBS diagnosis – and for many of those people, treating the IBS without ever identifying the SIBO is exactly why nothing has worked.
It isn’t always a quick fix – but when SIBO is properly identified and addressed at the root cause level, the results can be transformative.
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?
Getting a SIBO diagnosis through conventional medicine is possible – but the path is rarely straightforward. In the UK, it typically means a GP referral to a gastroenterologist, followed by a hospital-based breath test. For many people, that process alone involves months of waiting.
But the waiting isn’t the only issue. When clients come to us having already had NHS SIBO testing, we frequently find that the test has only measured hydrogen gas – not methane – and has been run for two hours rather than the three hours recommended by leading SIBO researchers including Dr Pimentel and Dr Siebecker.
That matters, because an incomplete test can return a negative result in someone who genuinely has SIBO, leaving them without answers for even longer.
This isn’t a criticism of individual clinicians – it’s a reflection of how SIBO testing is currently set up within conventional systems.
Understanding what a complete, well-interpreted test looks like is one of the most important things you can do if you’re investigating SIBO seriously.
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?
SIBO rarely appears out of nowhere. When we take a careful health history with clients, there is almost always a moment – or a period – that marks the beginning of things going wrong. Recognising that moment is often the first step toward understanding what’s been driving symptoms ever since.
Common factors that can increase the risk of developing SIBO include:
- Food poisoning - possibly the most significant single trigger, and one we'll explore in detail below (21, 22, 23)
- Frequent or prolonged use of antibiotics (24)
- Low stomach acid or long-term use of acid-suppressing medications such as proton-pump inhibitors (PPIs) (25, 26, 27)
- Chronic conditions affecting the intestinal wall, such as Crohn's disease or coeliac disease (28)
- Prior bowel surgery (29)
- Hypothyroidism and autoimmune thyroiditis - research presented in 2025 found that people with hypothyroidism have more than double the risk of developing SIBO, rising higher still in those with Hashimoto's
That last point is one we’re watching closely. The emerging picture of SIBO as connected to thyroid health, metabolic health, and even neurological function is expanding rapidly – and it’s changing how we think about who might be affected.
One more factor worth flagging specifically: if you are currently taking GLP-1 agonist medications – such as Ozempic or Mounjaro – for diabetes or weight management, research in 2025 found these drugs are associated with developing SIBO within the first year of use.
It’s an important consideration that is rarely discussed alongside these medications, and one we factor into our assessments.
Why your gut's cleaning cycle matters in SIBO
Between meals, your digestive system does something remarkable. Rather than resting, it switches into a cleaning mode – running a series of powerful sweeping contractions along the small intestine that push bacteria, debris, and undigested material down toward the colon.
This process is called the migrating motor complex, or MMC.
Think of it as your gut’s housekeeping shift. And like any housekeeping, it works better when it isn’t interrupted (30).
The MMC operates in four phases – and it’s Phase III, the most active and powerful phase, that does the majority of the sweeping work.
Research has shown that Phase III activity is absent in people with both IBS and SIBO (31) – meaning the gut’s most effective cleaning mechanism simply isn’t firing. Bacteria that should be cleared from the small intestine are instead left to accumulate.
Every time you eat, the MMC pauses. Which is why meal spacing matters so much in SIBO – the more frequently you eat, the less opportunity the MMC has to do its job. For someone with SIBO, that window of cleaning time is already compromised. Grazing throughout the day can make things significantly worse.
When the MMC is damaged or impaired – which happens in many cases of SIBO – the consequences compound over time.
Understanding this is important not just for treatment, but for prevention of relapse.
Restoring MMC function – through prokinetics, meal spacing, and addressing the underlying causes of the damage – is one of the most critical and most overlooked parts of a successful SIBO protocol.
How food poisoning can trigger SIBO months later
This is one of the most important things in this entire article – and one of the findings that, for many of our clients, makes everything finally make sense.
Certain bacteria commonly associated with food poisoning – including E. coli, Campylobacter, Salmonella, and Shigella – produce a toxin called Cytolethal Distending Toxin, or CDT (32).
When you’re exposed to this toxin, your immune system responds exactly as it should – producing antibodies to fight it.
But in some people, something goes wrong at this stage.
The antibodies produced to fight the CDT toxin begin to also attack a protein in the intestinal tract called vinculin (35) – because the two look similar enough to the immune system to cause confusion.
This is called molecular mimicry, and it’s the same mechanism behind many autoimmune conditions.
What makes this particularly striking – and particularly easy to miss – is the timing.
Symptoms from this process can take three to four months to appear (37) after the original food poisoning event.
By that point, most people have long forgotten about it, or simply don’t connect the two.
If you had a significant bout of food poisoning at some point in your history, and digestive symptoms followed – even months later – this mechanism may be exactly what happened to you.
The role of Vinculin in gut motility & SIBO
So what does vinculin actually do – and why does it matter so much when it’s damaged?
Vinculin plays a critical role in peristalsis – the wave-like contractions that move food and bacteria through the digestive tract.
It does this by helping connect the specialised cells that act as the pacemaker for peristaltic movement – known as the Interstitial Cells of Cajal.
When vinculin is attacked by misdirected antibodies, that pacemaker function is disrupted. Peristalsis is impaired. And when peristalsis is impaired, bacteria accumulate in the small intestine – creating exactly the conditions in which SIBO develops and persists.
This is why, for clients where a food poisoning trigger is identified, addressing the autoimmune component isn’t optional – it’s central to the treatment approach. Without it, clearing the bacterial overgrowth alone is unlikely to produce lasting results.
Antibodies to both CDT and vinculin can now be measured through specific testing, thanks to the research of Dr Mark Pimentel and his team at Cedars-Sinai.
His research also identified that these two antibodies – anti-CdtB and anti-vinculin – are specifically elevated in people with diarrhoea-predominant IBS and mixed-type IBS (38).
For anyone who has been living with either of those presentations and never found a satisfying explanation, that’s a potentially significant finding. It gives us a clearer picture of whether this autoimmune pathway is at play – and shapes the protocol accordingly.
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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?
Treating SIBO effectively almost always requires more than one strategy – and rarely follows a single, linear path.
Depending on the type of SIBO, the severity, the root causes identified, and how your body responds, the approach may combine several interventions simultaneously or work through them in a carefully considered sequence.
We want to be honest with you here: for some people, SIBO resolves relatively quickly and they go on to feel significantly better within a few months.
For others – particularly where SIBO has been present for a long time, where multiple factors are at play, or where previous treatment attempts have been incomplete – the road to recovery takes longer and requires patience from both the client and the practitioner.
What we can tell you is that cutting corners doesn’t work. One of the most common reasons SIBO comes back is that the underlying causes weren’t fully addressed the first time around – or that treatment stopped as soon as symptoms improved, rather than continuing until eradication was confirmed. We work hard to make sure that doesn’t happen.
Nutrition and diet in SIBO
Diet is a foundational part of SIBO treatment – but we want to be clear about what that means in practice, because there’s a lot of confusing and sometimes contradictory information out there.
Dietary changes in SIBO are necessary.
But the goal is never long term restriction for its own sake. A diet low in fermentable carbohydrates can significantly reduce symptoms by starving the bacteria of the fuel they need to thrive – but it’s a short term strategy designed to reduce the bacterial load while other interventions do the deeper work. It’s rarely a solution, on its own.
What we see regularly in clinic is people who have been following a low FODMAP or similar SIBO diet for months or even years because it keeps their symptoms manageable.
We understand why – when something reduces pain and bloating, it’s natural to stick with it. But longer term, these diets can deplete the beneficial bacteria in the colon, because the fermentable carbohydrates being avoided are the same ones that feed the good bacteria.
Symptom management and genuine resolution are two very different things – and diet alone rarely delivers the latter.
The most effective approach combines appropriate dietary changes with targeted interventions to address the overgrowth directly – and then, as the bacterial load reduces, gradually reintroduces a broader, more diverse diet to support long term gut health.
Specific nutritional strategies
One of the most common misconceptions about SIBO is that there’s a standard diet that resolves it. In reality, the right dietary approach depends entirely on the individual – their SIBO type, their sensitivities, their symptoms, and what else is going on in their gut environment.
The two dietary approaches we most frequently refer to are the low FODMAP diet and the SIBO Specific Food Guide, developed by Dr Siebecker.
Both reduce fermentable carbohydrates that fuel bacterial overgrowth, but they work slightly differently.
The SIBO Specific Food Guide is often preferable because rather than eliminating a food entirely, it specifies the quantity that is usually well tolerated – a more nuanced and sustainable approach that tends to work better for people who are already highly reactive to a wide range of foods.
But even these are starting points, not prescriptions. In practice, we adapt both frameworks significantly based on each individual’s symptoms, food sensitivities, and test results.
Someone with a concurrent histamine intolerance, for example, needs a very different dietary approach to someone without it.
Someone with methane-dominant SIBO may tolerate foods differently to someone with hydrogen-dominant SIBO. The diet has to fit the person – not the other way around.
For a small number of clients – typically those experiencing significant food reactions across the board, unintentional weight loss, or severe malabsorption – a more intensive short term intervention called an elemental diet may be recommended.
This involves consuming nutrients in a pre-digested form that requires no digestion at all, allowing the gut to rest completely while the body continues to receive the nutrition it needs.
It isn’t easy, but for the right person at the right stage it can be genuinely transformative.
As with everything in our approach, the dietary strategy evolves as you do. If something isn’t working – if a food is causing unexpected reactions, or a protocol feels unsustainable – we adjust.
That responsiveness is built into everything we do and is why working closely with a Coho Functional Medicine practitioner can be extremely helpful.
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).
What about conventional and naturopathic SIBO treatments?
- Allicin – consistently our first consideration where methane-producing archaea (methanogens) are indicated, due to its well-established efficacy against this population. It’s worth noting that allicin in supplement form, while derived from garlic, is not the same as consuming whole garlic – which many people with SIBO find poorly tolerated
- Oregano and bismuth – most frequently used in hydrogen sulfide SIBO
- Berberine – commonly used for methane and hydrogen SIBO, typically combined with a second antimicrobial agent.
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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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