Catherine Clark

Unravelling IBS

The SIBO, ISO, IMO, Secondary Hyperoxaluria, Histamine Intolerance, Trauma and Chronic Stress, Methylation and IBS Connection

Irritable bowel syndrome (IBS) is a common gut disorder causing abdominal pain, bloating, and changes in bowel habits, like diarrhea or constipation. 

Classified as a disorder of the gut-brain axis, effective treatment requires addressing both digestive dysfunction and the miscommunication between the gut and the brain. 

 

This article explores some common underlying issues that should be identified and addressed to manage and potentially resolve IBS completely.

SIBO (Small Intestinal Bacterial Overgrowth)

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Emerging research increasingly links SIBO with IBS, particularly in post-infectious IBS, IBS-D (diarrhoea predominant), and IBS-M (mixed type). 

SIBO occurs when bacteria normally confined to the large intestine migrate into the small intestine, where they ferment food too early in the digestive process. This can lead to gas, bloating, abdominal pain, and altered bowel habits.  

Because SIBO closely mimics and exacerbates IBS symptoms, it is often overlooked. Fortunately, reliable testing and treatment is available.

ISO (Hydrogen Sulfide Overgrowth)

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ISO occurs when there is an excess of hydrogen sulphide-producing bacteria in the small or large intestine. This can lead to symptoms like diarrhea, bloating, abdominal pain, sulphur food intolerance (e.g., eggs, garlic, onions), and gas with a characteristic “rotten egg” smell. 

ISO is increasingly recognised as a contributing factor in IBS, particularly in diarrhea-predominant (IBS-D) cases. Although there is currently no standardised test for diagnosing ISO, it can often be identified through a combination of symptoms and stool testing. 

If you find you avoid eggs, garlic and onion because they just don't seem to agree with you, then ISO may be the reason. 

IMO (Intestinal Methanogen Overgrowth)

IMO occurs when methanogens, microbes from the archaea family (not bacteria), overgrow in the small and/or large intestine. These organisms produce methane gas as a by-product of their metabolism. 

Methanogens are normally present in a healthy colon, especially the distal colon, where methane helps slow gut motility, which aids water and electrolyte absorption and the formation of solid stool. However, under certain conditions, methanogens can proliferate, leading to excessive methane production. This slows gut transit time too much and can contribute to constipation-predominant IBS (IBS-C), along with symptoms like bloating, discomfort, and straining.  

Excess methane in the small and/or large intestine can lead to constipation

Secondary Hyperoxaluria

Secondary hyperoxaluria occurs when oxalates are excessively absorbed from the gut into the bloodstream, resulting in elevated levels in the urine. This is often triggered by digestive disturbances commonly seen in IBS, such as fat malabsorption, dysbiosis, intestinal inflammation, and increased intestinal permeability (leaky gut). 

Under these conditions, oxalates are less likely to bind to calcium (and other minerals) in the gut, which increases their absorption into the bloodstream (general circulation). 

Unbound oxalate crystals are sharp and abrasive, and when they accumulate in the gut, they can irritate the intestinal lining leading to inflammation, increased intestinal permeability (leaky gut), heightened visceral sensitivity (worsening pain), and can activate immune cells further driving abdominal pain, cramping and loose stools (urgency). 

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When oxalates enter systemic circulation, they can contribute to a wide range of symptoms, including kidney stones/pain, urinary issues, joint pain and stiffness, fibromyalgia-type muscle and fascia pain, brain fog, and oxidative stress (just to name a few!). 

This creates a vicious cycle where gut dysfunction drives oxalate overload, and excess oxalates, in turn, worsen both gut and overall health.  

The good news is that oxalate issues can be identified through symptom patterns and stool testing, and confirmed with urine testing, and it is highly treatable. 

If you’ve ever felt worse after eating a ‘healthy’ diet high in leafy greens, nuts, or chocolate, oxalate overload may be a contributing factor. 

Histamine Intolerance (HIT)

Histamine intolerance (HIT) and IBS are closely linked, as they share overlapping symptoms and often arise from similar underlying gut dysfunctions. 

HIT can mimic or worsen IBS symptoms such as bloating, abdominal pain, cramping, visceral hypersensitivity, diarrhea and anxiety, especially after consuming histamine-rich foods.

In many people with IBS, factors like gut inflammation, dysbiosis, or increased intestinal permeability (leaky gut) can reduce the activity of diamine oxidase (DAO), the main enzyme that breaks down histamine in the gut and bloodstream. Some individuals may also have reduced histamine-N-methyltransferase (HNMT) activity, an enzyme essential for breaking down histamine within the liver, brain and other tissues. 

When DAO and/or HNMT activity is impaired, histamine accumulates, triggering a wide range of symptoms. While histamine is a crucial compound involved in immune responses, digestion and neurotransmission, excess histamine can lead to symptoms commonly seen in IBS.

 

HIT can be identified through clinical assessment, dietary response, and targeted testing such as stool analysis or DAO activity testing. Fortunately, with the right approach, histamine intolerance can be effectively managed and often resolved over time. 

In some cases, what appears to be IBS may, in fact, be driven or exacerbated by histamine intolerance. 

Trauma and Stress

Trauma, especially early life trauma or chronic psychological stress, is strongly linked to both the development and persistence of IBS. 

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In these instances, the nervous system can get ‘stuck’ in a chronic or overreactive stress response, dominated by sympathetic (fight-flight-freeze) activation and reduced parasympathetic (vagal) tone. This imbalance alters the gut function in several ways:

• Gut motility and sensitivity shift, leading to visceral hypersensitivity (an exaggerated response to normal gut sensations).
• Digestive capacity decreases, with reduced secretion of digestive enzymes and stomach acid (increases risk of developing SIBO and digestive issues). 
• The gut microbiome becomes disrupted, favouring pathogenic or inflammatory microbes over beneficial species (dysbiosis).
• Intestinal permeability (“leaky gut”) increases, allowing food antigens and endotoxins to enter the bloodstream, triggering immune activation and systemic inflammation. 
• Suppression or dysregulation of the migrating motor complex (MMC) – rhythmic wave-like contractions that occur in the gastrointestinal tract that help clear out bacteria, food particles and waste between meals and is vital to maintaining gut health and preventing SIBO. 

Altogether, these changes predispose one to developing IBS in the first place and can create a vicious cycle that maintains and worsens IBS symptoms over time, making nervous system regulation and psychological support essential to treatment. 

Methylation

Methylation is a fundamental biochemical process that supports detoxification, neurotransmitter balance, immune function, and gut lining repair, all of which are essential for healthy digestion.

Optimal methylation plays a role in the prevention and management of every condition discussed in this article, and often underlies broader patterns of gut dysfunction. 

While the connections between methylation and issues such as IBS, IMO, ISO, Secondary Hyperoxaluria, Histamine Intolerance, and the impacts of stress and trauma are complex, they are clinically significant and should not be overlooked. 

Supporting healthy methylation, through nutrition, lifestyle, and, where needed, targeted supplementation, is a foundational strategy in restoring gut health and resilience.  

Multiple factors can contribute to the symptoms experienced by individuals with IBS, and several are likely present.  

If you've tried standard IBS therapies without relief, investigating and addressing these issues could be a game-changer.

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The information provided above is for general educational purposes only. It is not a substitute for personalised medical or health advice and does not take your individual circumstances into account. The content above is intended to inform and educate, not to promote or advertise any specific service.

Always consult your own qualified healthcare professionals regarding your individual situation before making decisions related to your health.

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Catherine Clark is a Naturopath, Nutritionist, and Medical Herbalist with a special interest in GIT health, hormones, mental health, and methylation. Catherine consults in person from Logan, Queensland and also online via Telehealth throughout Australia. 

If you are looking for tailored solutions that support your digestive system from the inside out - blending natural medicine, nutrition, and mind-body practices – Click the link below to get in touch.