March 19, 2025

One of the key issues is that the hallmark symptoms of SIBO can also be associated with other gastrointestinal (GI) disorders including fungal overgrowth, irritable bowel syndrome (IBS) and food intolerances, but there are a few key differences as to how these will present with SIBO so let’s run through them.

Bloating. Super common, it might be after eating or relatively continuous depending on the level of overgrowth and is due to fermentation of undigested food in the small intestine.

Gas. There can be a lot! Because the issue is in the small intestine this can often get trapped causing pain, or pass as excessive flatulence or belching – burping. Depending on the type of SIBO it could be odorless or have a strong sulfur smell.

Diarrhoea or constipation. Diarrhoea is common in hydrogen-dominant SIBO, while methane dominant SIBO will cause constipation.

Abdominal pain or discomfort. Cramping, dull aches, or pressure-like sensations due to gas build up in the small intestine. This often sets it apart from other GI conditions as the pain can be quite severe and intense due to that pressure build up. But that can then be confusing, as people think it's to do with their stomach, but that's just getting shoved up by the inflated small intestine.

Fatigue, body aches and brain fog are really common and due to malabsorption of essential nutrients as well as toxin release from bacterial overgrowth. Significant tiredness, muscle aches and difficulty concentrating are often what actually get people to seek help in the end. Headaches and migraines are also quite normal.

Weight Changes. Some people lose weight due to nutrient malabsorption in the more diarrhoea-linked forms, whereas others gain weight with the slower motility form of methane-dominant SIBO.

Progressive food intolerances, especially increased sensitivity to dairy, fruit, high fibre foods, histamine and/or sulfur-containing foods can happen and will depend on the type of SIBO, and they can occur frequently.

And inflammatory skin issues including acne, eczema, psoriasis and rosacea, may worsen due to gut dysbiosis, which is the technical term for imbalances in gut bacteria, or present for the first time in people who haven’t had them before if SIBO goes untreated for a while.

So, now lets cover how SIBO can be mistaken for other GI conditions, and how you can start to tell the difference between them.

IBS vs. SIBO. Recent research suggests that 60-80% of IBS cases may actually be caused by SIBO. And the generalised approach that IBS is something you cope with rather than recover from is part of the reason so may SIBO cases get missed. Because focus is placed on symptom management as opposed to looking for root cause of the IBS. The slightly viscous cycle here is that IBS where there weren’t initial bacterial changes is a nervous system induced condition where stress impacts the gut, and if that stress is left unchecked over time then that makes someone more vulnerable to SIBO because they naturally get microorganism changes happening as a result of the stress.

Coming back to the IBS cases that are caused by SIBO though:
IBS-D (diarrhoea-dominant IBS) → up to 80% of cases are suggested to be linked to hydrogen-dominant SIBO.
IBS-C (constipation-dominant IBS) → a lower incidence but between 30-60% are associated with methane-dominant SIBO.
IBS-M (mixed IBS) → this varies but around 50-70% of people with this type have a form of SIBO or what we call combination SIBO.

So in summary, if you have been suffering with IBS, I would always scan back and look at your symptoms. If there is an obvious stress-induced trigger then that needs to be addressed first. If you think SIBO could also be involved then keep listening for how to address this too!

SIBO vs. fungal or yeast overgrowth - which can commonly be referred to as candida overgrowth, but it’s not always candida that is the problem species so we’ll go with the broader terms.

Both of these - fungal and yeast overgrowth - can cause bloating, body pain, headaches and brain fog, but there are some key differences to differentiate between these if you know what to look for. Fungal and yeast overgrowths will present with bloating that is related to consumption of more sugar rich foods and would tend to concentrate in the lower abdomen, passing of lots of gas after eating can happen but not always. This person will also have strong and continuous sugar cravings, and fatigue is often pretty bad. Brain fog and headaches are common and sufferers are hugely prone to fungal infections like athletes foot and thrush. Dandruff and skin rashes are common too. Oral/Genital thrush are actually hallmarks of fungal overgrowth and antibiotic treatment will make this much worse as they kill all bacteria allowing yeast to overgrow further.

Food sensitivities are uncommon as a side effect.

SIBO comparatively will cause a different sensation of bloating, it is more internal and feels severe but won’t necessarily cause as much visible distention of the abdomen as its this pressure of lots of gas being trapped. If that gas passes it can be foul smelling, and that sense of fullness and internal bloating can be pretty continuous and present strongly after eating fermentable fibre from things like carbs and vegetables. Sugar cravings are uncommon though unless someone is very malnourished due to malabsorption. Brain fog, headaches and fatigue are common due to high toxin levels but any skin issues are more likely to be inflammatory due to increased histamine levels. It would be more things like eczema, psoriasis and rosacea rather than the more flakey dandruffy stuff.

Lactose intolerance, fructose intolerance and food sensitivities are common because of altered function in the digestive tract.

Going a bit higher up the chain now to the stomach, chronic reflux and H. pylori infection are another common mix up.
H. pylori is a bacteria found naturally in the stomach that can overgrow if given the opportunity, which can lead to low stomach acid causing chronic reflux and heartburn, bloating and excessive fullness after meals, burping and also sometimes nausea as well as slower gut motility and intermittent bowel movements.

A key difference is timing. Issues with the stomach will present pretty immediately on eating whereas there can be a slight delay with SIBO. This does depend on the level of fermentation in the small intestine however as this could be made unclear. And the other thing is things like mucus, sinusitis and chronic coughs which are all going to link to stomach acid issues with H. pylori but not SIBO so much.

If someone has very active SIBO the force of upward pressure from excess gas in the small intestine can create some of those symptoms as soon as someone eats so testing to determine would always be indicated. But often cases of chronic reflux that don’t improve with stomach acid stimulation are due to SIBO and so treating the stomach won’t improve things.

Food intolerances are the last one, and they are tricky as SIBO can lead to reactions to FODMAPs, dairy and histamine-containing foods making it easy to misdiagnose. Food intolerances as an immune response occur due to changes in the lining of the intestines and are more inflammatory or stress related in origin. Comparatively SIBO is causing issues with the function of the gut and excess fermentation where certain foods are more triggering for symptoms but both will cause things like inflammatory skin issues and increased allergy symptoms.

If someone is becoming increasingly narrowed in their diet because of food reactions then first port of call is always to look at inflammation and the gut lining as opposed to continuously eliminating foods from their routine. I would also start to look at the clustering of their symptoms and see if the SIBO picture fits.

So what actually Is SIBO?
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SIBO occurs when bacteria that typically reside in the large intestine migrate to the small intestine, where they are not meant to be in high numbers. This overgrowth disrupts digestion, damages the gut lining, and interferes with nutrient absorption.
As I said there are three types of SIBO, categorised based on the dominant gas produced by the bacteria:

Methane-Dominant SIBO, also called IMO which stands for Intestinal Methanogen Overgrowth, causes constipation, bloating, slow digestion, and weight gain.

Hydrogen-Dominant SIBO causes diarrhoea, bloating, and nutrient malabsorption, leading to fatigue and weight loss.

Hydrogen Sulfide-Dominant SIBO is associated with foul-smelling gas, diarrhoea, brain fog, and increased food sensitivities.

So now you know what it is, how do we treat it? And can you make a full recovery?

Yes, but relapse rates are high if treatment is not addressed as a multi-faceted approach.
It's not just about eliminating the overgrowth bacteria but also reconditioning the environment of the small intestine to prevent recurrence in future, and looking at why that person ended up with it in the first place. If they do not address that they would likely find it comes back.

I also find it is incredibly important to address the trauma around the symptoms someone has been experiencing because they are really uncomfortable and can lead to all kinds of fear/anxiety related behaviours around eating certain foods which is something we want to free them from.

In terms of treatment options, if someone were to visit a gastroenterologist as opposed to a functional medic like myself they would likely be prescribed triple threat antibiotic therapy which sadly has an incredibly low efficacy rate and is why a lot of the stories and statistics say SIBO is a real tough nut to crack. This treatment is also often untenable for people to continue with as it makes them feel so incredibly unwell during the process. This is due to the fact there is no support for gut motility or toxin removal so as the overgrowth dies off with the antibiotics those toxins circulate around the body causing flu-like symptoms, body aches, migraines, nausea and intense fatigue.

In terms of efficacy and side effects I’ll quickly run through the main approaches.

Antibiotics (Rifaximin, Neomycin, Metronidazole).
Pros: Fast-acting, can be effective for hydrogen and methane SIBO if someone tolerates the treatment.
Cons: Will cause nausea, bloating and are associated with a high recurrence rate.
Methane SIBO: Requires all three of those due to the resilience of methanogens. Very poor treatment outcomes and high die off symptoms because you’ve got all of those going into a gut which is chronically constipated so there is nowhere for toxins being liberated o go

Herbal antimicrobials examples being Berberine, Oregano, Allicin (garlic extract), Neem, Pau D’Arco and Black Walnut.
Pros: Comparable efficacy to antibiotics, fewer side effects, lower relapse rates.
Cons: Slower action, some people experience die-off symptoms (temporary worsening of symptoms) if not paired with appropriate motility support. But the hope would be that if you are seeing someone who would use these then they would be paired with dietary and lifestyle adaptations to support evacuation.

You then have the sole dietary & lifestyle approaches (Elemental diet, fasting, prokinetics) which are effective but require a lot of discipline. The elemental diet starves bacteria in 2-3 weeks but is difficult to maintain. These are only really indicated for those with chronic and treatment resistant SIBO, or if they have a structural issue such as a loss of the swallowing reflex which means other options aren’t available. You’ll often get issues with things like oral thrush and weight loss during the process with these so they need to be carefully monitored.

In terms of how I address those who come to see me with SIBO, it would depend on their individual presentation but as a general flow of the process...

We start with a full assessment. As I have specialised in chronic and complex digestive health for close to 13 years now in some instances I will forgo breath testing if I can clearly see that someone has SIBO. The reason being that the use of the sugar rich solutions (lactulose and glucose) for the breath tests increases the activity of the bacteria which can then cause symptoms to worsen.
But for conclusive diagnostic proof of SIBO you would need to conduct both a glucose and lactulose breath test to determine the type of SIBO. The process involves a prep diet for a couple of days, then you drink the solution and take breath samples at timed intervals. Those are then tested for methane, hydrogen and hydrogen sulfide levels.

I will always then begin with diet, both to manage someone’s symptoms and start to rework things internally. I personally do not use strict low FODMAP diets with my clients as these add another layer of fear to foods being the cause of their issues. Instead I favour a low fermentable fibre diet, remove dairy and fruit for the short term if needed, and get them to focus on simple meals centred around whole food ingredients.
I also add in herbs and spices with antimicrobial properties, which makes things taste delicious as well, as well as adjusting their eating habits to decrease the activity of the bacteria for comfort. In some cases where an individual is really suffering due to excessive fermentation I may consider a short term ketogenic diet where they focus on energy from fats as opposed to carbohydrates as this can make them immediately more comfortable but this requires quite a mindset shift and discipline to do so I consider it on a case by case basis.

At the same time, and partly with the dietary tweaks, we stabilise their gut motility. As before adding in any kind of antimicrobial interventions we have to establish a route out for the bacteria we are aiming to get rid of.
For diarrhoea dominant SIBO those stools need to be slowed and formed, and for constipation that has to get moving to allow for proper toxin excretion. This could be through the use of prokinetics, soluble fibre, magnesium citrate and/or upper GI support like digestive enzymes and betaine hydrochloride.

Then come the antimicrobials to target the overgrowth. The ones used would depend on the type of SIBO, dosage should be at the lowest effective level to prevent irritation to the gut, and this is always done with a progressive opening of someone's diet to concurrently restore normal function and prevent recurrence whilst eliminating that totally normal fear and trauma around eating and being uncomfortable.

And what has been happening all the way through? Addressing root causes of course!
For me the story of how someone got there is the key to the puzzle. Usually there was a period of chronic stress that then led to low stomach acid and changes in the digestive system as a whole. Colonic irrigation is also often a cause as the backward force of the water being used to ‘wash’ the colon forces bacteria through the ileocecal valve into the small intestine. Chronic constipation due to poor dietary habits can do the same. Food poisoning is another trigger and often more than one of those will have happened. Unwinding these and the habits around foods that occur as a result (often a narrowing of someone’s diet, anxiety over eating in general or at specific times) is what actually frees someone from the cycle in the end.

I would then embed the following practices as habits to prevent recurrence and support long-term gut health. They are generally things we all want to be doing for good digestion, blood sugar balance and optimal health anyway.

Maintain meal spacing. Allow at least 3-4 hours between meals to enable the Migrating Motor Complex (MMC) to clear bacteria from the small intestine. Grazing is the enemy of good gut health!

Chew food thoroughly. This enhances digestion and reduces fermentation. Make your meals textural, add crunch! Be aware when you are eating and try to incorporate bitter foods at the start of your meals like nuts, seeds and bitter leaves like rocket.

Manage stress and improve sleep. If our body is under rested or stressed then our digestive system becomes less effective and more vulnerable. We also see lower levels of good gut bacteria which will make us more susceptible to opportunistic overgrowth and issues with bowel motility

Address underlying digestive issues. Ensure proper stomach acid production which is often decreased by stress and lack of rest so reinforcing what I've just said! And ensure you are naturally passing daily bowel movements by being properly hydrated and having enough soluble fibre.

Eat a diverse diet focused around whole foods in their natural forms as this ensures your natural microbiome will be diverse, numerous and protective.

I hope you have found this video helpful, please do leave a comment if you did or have a question! And yes SIBO is a complex condition but it is entirely treatable. If you are suffering please don’t do so in silence, more information on my clinical services can be found at lieblinghealth.com.