What Causes IBS, Leaky Gut, IBD, and Bloating?

Figure 1. Difference between IBS, IBD, leaky gut, and bloating

What causes IBS?

IBS does not have one confirmed cause [1], making diagnosis difficult in some cases. It likely develops due to changes in how the gut and brain communicate through a complex, bidirectional pathway known as the gut-brain axis, as well as changes in gut sensitivity, bowel movements, immune signalling, and the gut microbiome. 

Factors such as infection, stress, genetics, and early-life experiences may increase susceptibility to IBS, but no single factor explains every case of irritable bowel syndrome. Instead, it is likely caused by a combination of different factors.

IBS is classified as a disorder of gut-brain interaction, meaning the digestive tract and brain may not communicate or respond to signals as expected [2]. There are several mechanisms that could be contributing to an altered gut-brain axis. They include:

• Altered gut–brain communication: The brain and digestive system exchange information through nerves, hormones, immune signals, and chemicals produced by gut microbes. In IBS, altered signalling may affect bowel movements, digestive secretions and how the brain processes sensations from the gut [3].

• Visceral hypersensitivity: Some people with IBS have unusually sensitive nerves within the intestines. A normal amount of gas or stool may therefore produce pain, urgency, or uncomfortable pressure [4].

• Changes in bowel movement: If intestinal muscles contract too quickly, the bowel may absorb less water, contributing to diarrhoea, particularly in IBS-D (irritable bowel syndrome with diarrhoea). Slow movement allows more water to be removed from stool, contributing to constipation in IBS-C (irritable bowel syndrome with constipation).

• Microbiome differences: Studies have identified differences in the gut microbiota of some people with IBS, including reductions in Lactobacillus and Bifidobacterium and increases in Enterobacteriaceae [5]. These may affect fermentation, gas production, immune activity, and gut–brain signalling. However, there is no single microbial pattern that causes every case.

• Previous gastrointestinal infection: IBS can begin after food poisoning or another intestinal infection. Known as post-infectious IBS [6], this may involve lingering changes in intestinal nerves, immune activity, the gut barrier, or microbiome, and can affect between 5% and 32% of people.

• Psychological stress: Stress does not make IBS imaginary, but the body’s stress response can change intestinal contractions and sensitivity [7]. The relationship works in both directions, as persistent digestive symptoms can also increase stress.

Although not directly inherited, IBS sometimes runs in families [8], which may reflect shared genes, diets, environments, and microbiomes. Antibiotic exposure, difficult early-life experiences and certain dietary triggers are also being investigated. These factors may increase risk or trigger symptoms without being the sole cause of IBS.

What causes a leaky gut?

A leaky gut, more formally known as increased intestinal permeability, develops when inflammation, infection, disease, medication, or other physical stress disrupts the gut barrier lining and its tight junctions. Although not a recognised medical condition itself, leaky gut is associated with several recognised conditions.

The gut lining is selectively permeable because it must allow water and nutrients to enter the bloodstream while preventing the passage of pathogenic microbes, toxins, undigested food particles, and other unwanted substances [8]. 

Neighbouring intestinal cells are connected by protein structures called tight junctions. These junctions help control what can move through the barrier. When the intestinal lining or tight junctions become disrupted, more material may cross the barrier than usual.

Factors associated with increased intestinal permeability include:

• gastrointestinal infections

• Crohn’s disease and ulcerative colitis

• coeliac disease

• severe illness, burns or physical trauma

• prolonged or heavy alcohol exposure

• certain medicines, including non-steroidal anti-inflammatory drugs

• inflammation affecting the intestinal lining

• changes in the composition or activity of gut microbes

The relationship between permeability and disease is complicated. Inflammation can weaken the intestinal barrier, exposing the immune system to more microbial material and contributing to further inflammation.

A review of research on intestinal permeability describes it as a two-way relationship. Scientists are still working to establish whether altered permeability is a cause, a consequence, or both in different conditions.

What causes inflammatory bowel disease?

Although the exact cause of inflammatory bowel disease (IBD) is unknown, it’s believed that a combination of abnormal responses from the immune system, genetics, gut microbes, and environmental triggers is responsible [9]. IBD is not caused by IBS, stress, or a particular food, but these factors may influence symptoms in someone who has already been diagnosed.

The immune system normally attacks harmful organisms while tolerating the many harmless microbes that live in the digestive tract. In IBD, this balance breaks down. Immune activity continues when it should switch off, resulting in ongoing inflammation and tissue damage [10].

Researchers believe several factors interact to cause IBD:

1. Abnormal immune activity: The immune system may respond inappropriately to microorganisms or other contents of the digestive tract, potentially triggered by environmental factors, genes, or the gut microbiome itself [11].

2. Genetic susceptibility: IBD sometimes runs in families, and many genetic variations are associated with increased risk [12]. These genes often influence immune regulation, microbial recognition or intestinal barrier function.

3. Gut microbiome changes: People with IBD often have altered diversity and activity of their gut microbes [13]. These microorganisms may interact differently with the immune system in someone who is genetically susceptible.

4. Environmental exposures: Researchers are investigating how factors including infections, antibiotic exposure, smoking, dietary patterns, air pollution and aspects of industrialised living may influence IBD risk. Evidence is stronger for some factors than others, and an association does not prove that an exposure directly causes IBD in an individual [14].

Genes alone cannot fully explain IBD. Many people with associated genetic variations never develop the condition, while others develop it without having a close relative with IBD.

What causes bloating?

Bloating can be caused by swallowed air, microbial fermentation, constipation, slow digestive movement, food intolerance, or increased sensitivity to normal intestinal stretching. It can also accompany IBS, IBD, coeliac disease and other conditions. Importantly, feeling bloated does not always mean the intestines contain excessive gas.

Gas enters the digestive tract in two main ways. The first is swallowing air while eating, drinking, chewing gum, or talking. The second is fermentation, which occurs when bacteria in the large intestine break down carbohydrates that were not fully digested in the small intestine.

Other factors include:

• Poorly absorbed carbohydrates: Lactose, fructose, and certain fermentable carbohydrates can draw water into the bowel and be fermented by bacteria, producing gas.

• Constipation: Slow-moving stool gives microbes more time to ferment intestinal contents. Accumulated stool may also make it harder for gas to move through the bowel.

• Changes in digestive movement: Delayed stomach emptying or slow intestinal movement can cause prolonged fullness, pressure and visible swelling.

• Visceral hypersensitivity: People with sensitive intestinal nerves may experience discomfort from amounts of gas that would not bother others.

• Abdominal muscle responses: In some people, the diaphragm moves down while the abdominal wall relaxes. This can make the abdomen visibly expand without a major increase in intestinal gas.

• Hormonal changes: Menstrual cycle-related changes may affect fluid retention, bowel movements, and sensitivity, causing temporary bloating.

How are the gut microbiome and these digestive problems connected?

The gut microbiome may influence IBS, IBD, intestinal permeability, and bloating through fermentation, immune regulation, barrier maintenance, and gut–brain signalling. However, microbiome changes are not necessarily the original cause. They may precede a condition, develop because of it, or form part of a two-way biological relationship.

The microorganisms living in the gut produce compounds when they break down dietary substances. These compounds can interact with intestinal cells, immune cells, and nerves. Microbes can also influence how much gas is produced and how the intestinal barrier functions.

Research has identified differences in the microbiome among people with IBS and IBD [15]. However, findings vary considerably between studies and individuals. Diet, age, medicines, geography, infection, and the digestive condition itself can all affect microbial composition.

Summary: Understanding the causes behind digestive symptoms

Digestive symptoms usually arise from several interacting mechanisms rather than one universal trigger. IBS, IBD, increased intestinal permeability, and bloating may share connections with the microbiome and intestinal barrier, but they remain distinct problems. Understanding those differences can help prevent symptoms from being incorrectly attributed to a single food, microbe, or diagnosis.

IBS does not turn into IBD, and bloating does not automatically mean that the gut is “leaking”. Similarly, someone can have increased intestinal permeability as part of a recognised disease without having a separate condition called leaky gut syndrome. 

Need help managing the symptoms of IBS? Try our PureHMO® IBS Support with IBS Defend Probiotic that’s designed to target the root cause of IBS – an imbalanced gut microbiome.

---

Author details

Written by: Leanne Edermaniger, M.Sc. Leanne is a professional science writer who specializes in human health and enjoys writing about all things related to the gut microbiome. She has written extensively on inflammatory bowel disease, prebiotics, and microbiome research.

Her work focuses on translating complex medical science into evidence-based, practical health guidance.