We spoke to Registered Nutritional Therapist Lillian Klein about the growing confusion between food intolerances and gut health issues. Drawing on her expertise in personalised nutrition and the microbiome, Lillian shared her insights into what a food intolerance really is, how it differs from a food allergy, and why your gut might be the missing piece of the puzzle.
A food intolerance occurs when your digestive system struggles to process certain foods properly. This is different from a food allergy, which triggers an immune reaction [1]. If you're wondering why a food intolerance is different from a food allergy, the key distinction is that intolerances involve the digestive system, while allergies involve the immune system. With intolerances, the problem is often linked to enzyme deficiencies (like lactase, needed to digest lactose) or sensitivities to natural food chemicals (like histamine).
Symptoms of food intolerances tend to develop gradually, mostly hours after eating and are often dose-dependent. In other words, a small amount of the food may cause no reaction, but larger portions can trigger symptoms.
Gut dysbiosis refers to an imbalance in the trillions of bacteria living in your gut. Ideally, these microbes work in harmony, supporting digestion, nutrient absorption, immune function, and even mood. However, factors like poor diet, stress, antibiotics, and lack of fibre can disrupt this balance [2].
When dysbiosis occurs, digestion can suffer, the gut lining may become more permeable, and inflammation can increase. This can all make your gut more sensitive to foods you previously tolerated with ease. Common gut dysbiosis symptoms include bloating, irregular bowel movements, fatigue after eating, and even skin issues.
Here’s where it gets tricky: the symptoms of food intolerance and gut dysbiosis can look almost identical. Both can cause:
Because of this overlap, many people cut out foods unnecessarily, assuming they have an intolerance when in fact their gut health may just need some attention. For example, if you're experiencing a bloated feeling after eating, it might be due to gut dysbiosis rather than a specific food sensitivity.
Gut bacteria play a crucial role in helping us break down and process food. If these microbes are out of balance, it can affect enzyme production, impair digestion, and increase gut sensitivity [3].
This means that foods triggering symptoms may not be the root cause. Instead, they may simply be highlighting an underlying gut imbalance. In many cases, supporting your gut, rather than permanently cutting out foods, can significantly improve symptoms.
Whether you’re dealing with suspected intolerances or just want to improve digestion, focusing on gut health is a smart place to start. Helpful strategies include:
If you’re unsure whether your symptoms stem from a true food intolerance or from a gut imbalance, it’s worth seeking advice and, where needed, getting tested. Breath tests for lactose intolerance or SIBO (small intestinal bacterial overgrowth), or comprehensive stool tests, can provide valuable insights.
If you're debating gluten sensitivity vs intolerance, testing and professional guidance can help clarify whether you're reacting to gluten itself, or if your gut is simply inflamed or imbalanced.
By taking a balanced, evidence-based approach, it’s often possible to improve tolerance and broaden your diet over time - which is ultimately better for both your gut and overall health.
The next time digestive symptoms strike, don’t be too quick to blame the food. Instead, consider whether your gut might need a little extra care. By focusing on gut health, you may not only ease symptoms but also build long-term digestive resilience, allowing you to enjoy a more varied, balanced diet with confidence.
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