What is IBS? Symptoms, causes and a functional medicine approach

Irritable bowel syndrome (IBS) is a chronic digestive condition where recurring abdominal pain, bloating, and changes to bowel habit occur without any structural damage to the gut. The gut looks normal on standard investigation, but the bacterial environment, the integrity of the gut lining, and the way the gut and brain communicate can all be affected.

Around one in five Australians experience IBS at some point, and it is more common in women. For most people, more than one thing is driving the syndrome, and the combination looks different from one person to the next.

Symptoms of IBS

IBS symptoms include recurrent abdominal pain, bloating, and changes to bowel habits, including diarrhoea, constipation, or both. A diagnosis is confirmed using the Rome IV criteria when pain has occurred at least one day a week over three months, alongside two or more of the following:

• Relief or worsening of pain with bowel movements
• A change the frequently of bowel movements
• A change in the consistency or appearance of stool

Symptoms need to have been present for at least six months before the three-month diagnostic window. IBS is, by definition, a persistent condition.

Beyond the formal criteria, people with IBS commonly report:

• Bloating and visible distension, often worse as the day progresses
• A sudden, urgent need to rush to the toilet
• A feeling of incomplete evacuation
• Mucus in the stool
• Reflux or nausea
• Abdominal cramping that changes in location and intensity
• Headaches or migraines in some cases

IBS subtypes

IBS is classified into five subtypes based on the predominant bowel pattern:

• IBS-C: constipation predominant
• IBS-D: diarrhoea predominant
• IBS-M: mixed, with alternating diarrhoea and constipation
• IBS-U: unspecified, when symptoms don’t clearly fit the other categories
• Post-infectious IBS: develops following a gut infection or a course of antibiotics, and is discussed further under causes

Subtype can change, which is one reason symptoms can be difficult to manage consistently.

What causes IBS?

IBS most commonly develops when the bacterial environment of the gut, the way the gut and brain communicate, and the gut lining’s ability to act as a barrier are all affected, often at the same time.

Gut bacteria and the microbiome
Changes to the gut’s bacterial population are seen consistently in IBS, but it’s not simply a matter of having fewer beneficial bacteria. What matters is which bacteria are present, where they are, and how varied the population is.

Chronic stress reduces the diversity of bacteria that help keep inflammation low in the colon, including species like Roseburia and Eubacterium rectale. When their numbers fall, the inflammatory environment in the gut worsens, and symptoms tend to become more severe.

Stress also changes the gut pH, or acidity of the gut, affects how bile breaks down fat, and reduces how well carbohydrates are absorbed. Each of these changes creates conditions that further alter bacterial populations.

SIBO
SIBO (small intestinal bacterial overgrowth) is a common finding alongside IBS. Bacterial species that normally reside in the large intestine, including Enterococcus, E. coli, and Klebsiella, migrate into the small intestine and ferment food before digestion can occur normally. The fermentation produces hydrogen or methane gas, causing bloating, distension, changes to how quickly food moves through the gut, and abdominal pain. Because SIBO and IBS share so many symptoms, SIBO is frequently missed without specific testing. You can read more in our SIBO guide.

A key reason SIBO develops (and recurs after treatment) is impaired motility. The migrating motor complex (MMC) is a wave-like muscle contraction that sweeps through the small intestine between meals, clearing bacteria and debris. When the MMC is thrown off by chronic stress, low stomach acid, or a dysregulated stress response, bacteria are able to accumulate where they shouldn’t. Addressing why the MMC isn’t working properly is as important as treating the overgrowth itself.

The gut-brain connection
In IBS, gut-brain communication is altered in a way that makes the gut hypersensitive to normal amounts of gas and movement, a state called visceral hypersensitivity. This happens because the gut has its own extensive nerve network, and it communicates constantly with the brain through the vagus nerve and shared chemical signals.

This goes further than the gut simply being sensitive. Repeated pain signals can change the way the nervous system reads gut activity, so that sensations that would normally go unnoticed start to register as pain. Immune cells in the gut lining can make this worse by releasing substances that keep the surrounding nerves on alert. This is why some people experience significant pain even without an obvious trigger like stress or a food reaction.

Chronic stress, anxiety, and low mood reinforce this sensitivity and can directly alter how quickly food moves through the gut, speeding it up or slowing it down, which is why bowel habits can be so unpredictable.

Intestinal permeability and food reactivity
When the gut lining becomes more permeable than it should be, partially digested food particles can pass into the bloodstream and trigger an immune response, creating food sensitivities that weren’t there before. A more permeable gut lining is consistently linked to more severe pain and less predictable bowel habits across the range of ways IBS can present.

As more foods begin to provoke reactions, the list of apparent triggers grows. People can find themselves in a cycle of increasing intolerance without understanding why.

Foods that contain short-chain carbohydrates like fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) are well-recognised triggers in IBS. But the reason some people react strongly to fermentable carbohydrates while others do not often comes back to the state of the gut lining and microbial environment, not the foods themselves.

Histamine and hormonal influence
Poor clearance of histamine can worsen IBS symptoms by triggering immune reactivity in the gut. This becomes particularly relevant during perimenopause and menopause. Falling progesterone levels can reduce the body’s ability to clear histamine, an immune chemical involved in allergic and inflammatory reactions, meaning even ordinary exposures to food or environmental triggers can produce a stronger reaction than they would have previously. Conversely, high oestrogen or unopposed oestrogen states can also aggravate levels of histamine and cause irritation.

Post-infectious IBS
For some people, IBS begins after a gut infection or a course of antibiotics. The infection may have cleared, but the gut doesn’t always return to how it was. The gut lining can be damaged during a significant infection, the gut’s bacterial population is often significantly disrupted, and the immune system can remain mildly activated long after the original illness has cleared.

Sometimes these changes don’t correct themselves without support. This is why symptoms can persist and why addressing what changed in the gut environment is central to recovery in this group.

Other contributing factors
Several additional factors can increase the likelihood of developing IBS or worsen existing symptoms:

• A genetic predisposition to IBS
• Low stomach acid, which impairs early digestion, reduces the barrier against bacterial migration into the small intestine, and contributes to food protein reactivity
• Antibiotic use, which alters the composition of gut bacteria
• Pathogenic parasites such as Giardia
• A diet low in fibre or high in processed foods
• Poor sleep, low physical activity, and high alcohol intake

How is IBS investigated and assessed?

IBS is diagnosed based on symptom history using the Rome IV criteria, after other conditions have been ruled out. Inflammatory bowel disease (Crohn’s disease and ulcerative colitis), coeliac disease, and colorectal conditions are typically excluded first through blood tests, stool analysis, and in some cases endoscopy or colonoscopy.

Your GP will usually check inflammatory markers, thyroid function, and coeliac antibodies as a starting point. In many cases this will identify or rule out conditions that need to be addressed first.

Where standard testing returns normal results but symptoms persist, functional testing can provide a more detailed picture of what is happening in the gut. Depending on the presentation, this may include:

• SIBO breath testing to detect bacterial overgrowth in the small intestine, though breath testing has known limitations in IBS
• Comprehensive microbiome stool analysis to assess microbial diversity, pathogenic organisms, and markers of gut inflammation and immune activity
• Food sensitivity testing to identify immune-mediated reactivity
• Organic Acids Test, which assesses how well cells are producing energy and whether certain microbes are generating waste products that affect how you feel
• Nutritional assessment to identify deficiencies affecting gut repair or nervous system function
• Mould and mycotoxin testing in complex or treatment-resistant presentations

Test results are most useful when we read them alongside everything else going on for you: when your symptoms started, what came before them, which medications or antibiotics you’ve taken, and how stress or lifestyle changed around the same time. A stool test or breath test on its own doesn’t paint the whole picture.

Why IBS can persist after treatment

IBS often persists after treatment because the microbial environment, intestinal permeability, and gut sensitivity all remain unchanged, meaning symptoms return when treatment stops or a trigger reappears.

Conventional treatments include:

• Antispasmodics, to reduce cramping and abdominal pain
• Laxatives or antidiarrhoeal agents, to regulate bowel habit
• Low-FODMAP dietary protocols, to reduce fermentable carbohydrates that produce gas
• Psychological therapies such as CBT, to address the gut-brain component of symptoms

Antispasmodics reduce cramping by relaxing gut muscle directly but do not address why the gut is hypersensitive or inflamed in the first place. Laxatives can help regulate bowel movements, but used for too long they can gradually reduce the colon’s ability to contract on its own. Antidiarrhoeal agents slow transit but prolonged use can create rebound constipation, adding to the original problem.

A low-FODMAP diet reduces the fermentable carbohydrates that increase gas production. But prolonged restriction also removes the prebiotic fibre that beneficial bacteria depend on, so bacterial diversity can fall during extended use. Recent microbiome research supports this, showing that while a low-FODMAP diet reliably reduces symptoms, it can noticeably reduce beneficial bacterial populations during prolonged restriction.

Psychological therapies such as CBT show genuine benefit for visceral hypersensitivity. They work by changing how the brain reads pain signals and reducing the stress response that keeps the gut on high alert. But they are unlikely to resolve IBS where a disturbed microbial environment, a more permeable gut lining, or histamine reactivity are central to what is maintaining symptoms.

For some people, one or more of these approaches can ease symptoms considerably and keep them manageable long-term. For others, particularly those with post-infectious IBS, a significantly altered gut microbiome, or hormonal contributors, standard treatment addresses the surface without changing what is producing the problem.

Treating IBS: a functional medicine approach

A functional medicine approach to IBS starts by identifying what’s contributing to your symptoms, rather than applying the same protocol to everyone. That means reviewing your symptom history alongside standard and functional test results, to build a clearer picture of what’s changed in your gut, and why. Treatment is then built around your specific contributors, not just the symptoms they’re producing.

Strategies are personalised and may include:

• Gut microbiome support: assessment of bacterial diversity, pathogenic organisms, and markers of gut inflammation, with targeted probiotic and dietary support guided by what testing shows
• Motility and gut-brain support: identifying whether the gut’s natural clearing function is being affected by stress, nervous system dysregulation, or other factors, including strategies such as vagus nerve and breathwork practices, gut-directed hypnotherapy, and meal spacing to support the gut’s natural clearing rhythm
• Food tolerance assessment: distinguishing between foods that are genuinely problematic for you and those that are manageable with gut repair in place, moving beyond broad elimination toward something more sustainable
• Gut lining repair: where mucosal damage or permeability is contributing to ongoing reactivity, targeted nutrients, including zinc and glutamine, to support repair and reduce immune activity at the gut wall
• Dietary support: tailored to what you tolerate now, with the aim of expanding rather than restricting as gut function improves

When to seek support

See your GP or a practitioner if you have:

• Gut symptoms for more than a few weeks that haven’t resolved on their own
• A diagnosis of IBS without SIBO, gut microbiome health, or intestinal permeability assessed
• Symptoms affecting your ability to work, socialise, or eat without anxiety
• Ongoing use of medication to manage symptoms, without understanding what’s producing them
• Blood or mucous in the stool, unexplained weight loss, fever alongside gut symptoms, or a new change in bowel habits after age 50, which requires prompt medical review

Frequently asked questions

Is IBS the same as inflammatory bowel disease?

No. IBS and inflammatory bowel disease (IBD) are two distinct conditions. IBD refers to Crohn’s disease and Ulcerative Colitis, both of which involve visible structural inflammation and damage to the digestive tract. IBS involves no such overt structural changes. Because some symptoms overlap, IBD is typically ruled out before an IBS diagnosis is confirmed.

Can stress cause IBS?

Stress is one of the most significant contributors to IBS, though it rarely acts alone. The gut and brain communicate constantly through the vagus nerve and shared chemical messengers. Chronic stress alters gut motility, reduces microbial diversity, and increases gut sensitivity, meaning the gut registers normal amounts of gas and movement as significant discomfort.

Can IBS affect mood or mental health?

Yes, and the relationship runs in both directions. Gut bacteria produce most of the body’s serotonin, which affects how the gut moves and how pain is registered. When the bacterial population is disrupted, this can affect both gut function and mood. People with IBS have higher rates of anxiety and depression than the general population.

Is IBS a lifelong condition?

IBS is chronic by definition, but that does not mean symptoms are fixed or unmanageable. For many people, identifying and addressing what is contributing to symptoms, whether that is the microbial environment, the gut lining, the stress response, or hormonal factors, produces significant and lasting improvement.

Can IBS develop after a gut infection?

Yes, and this is a recognised subtype called post-infectious IBS. A significant gut infection or a course of antibiotics can disrupt the microbial environment in ways that trigger ongoing symptoms long after the original infection has resolved. Rebalancing the gut microbiome is often central to recovery in this subtype, which tends to have a clearer starting point than other presentations.

What is the best diet for IBS?

There is no single diet that works for everyone with IBS, but certain approaches have consistent evidence behind them. A low-FODMAP diet reduces fermentable carbohydrates that produce gas and is one of the most researched short-term interventions for symptom relief. A Mediterranean-style eating pattern supports microbial diversity and reduces inflammatory load and is better suited as a longer-term framework. Where histamine sensitivity or specific food reactivity is a factor, dietary adjustments are guided by those triggers rather than a standard template.

Does everyone with IBS have food sensitivities?

Food sensitivities are common in IBS but are not universal, and they are rarely true allergies. Reactions are more often a sign of what’s happening in the gut – bacteria fermenting food in the wrong place, an immune system reacting through a more permeable gut lining, or poor clearance of histamine. This is why the list of problem foods can change, and why broad elimination diets often fail to resolve the underlying issue. Identifying which foods are genuinely problematic requires careful assessment rather than removing entire food groups.

How long do IBS flare-ups last?

IBS flare-ups typically resolve within two to four days, but duration varies depending on what triggered the flare and how well the underlying gut environment is functioning. When triggers like stress, diet, or disrupted sleep are part of the picture, flare-ups can last longer. Addressing those factors tends to reduce both how often flare-ups happen and how long they last.