Food Intolerances – Part I: what’s really going on in your gut?

  • Why would your gut start reacting to foods that you were once able to eat with no trouble?
  • Why can some people get away with eating ANYTHING while others have multiple food intolerances?
  • What if you feel like you’re reacting to EVERYTHING you eat? What’s actually happening here? And more importantly, what can we do about it?!


Food intolerances really seem to be on the increase. In Part I of this post I’ll summarise for you exactly what is happening in the gut when we are no longer tolerant of multiple foods. In Part II I’ll provide you with the essential steps to start supporting healthier gut immune function to calm down food reactions. And don’t worry, if you don’t want the details, you can just skip ahead to the infographics which give you the key points! 



The Gut Immune System


Food intolerances are the result of an imbalanced gut immune response. 

The immune system is what protects us from pathogens (disease-causing micro-organisms like bacteria and viruses), toxins and allergic substances.


A well-functioning immune system is able to distinguish between self and non-self, so that it mounts an appropriate immune response when it comes into contact with something harmful and does not mount an immune response to its own tissue or harmless substances.


When the immune system detects a foreign substance (known as an antigen), it produces immune cells such as T cells, B cells, antibodies and cytokines to start attacking and eliminating the potential pathogen in order to keep us safe.

The gut immune system is the largest immune organ in the body and protects us from pathogens via:

  • A physical barrier – the gut lining is made up of tightly packed cells known as tight junctures which provide a physical defence against foreign invaders
  • A mucus lining that traps pathogens and contains immune cells to attack invaders
  • The gut microbiota – the collection of micro-organisms (bacteria, yeast and other organisms) that naturally live in our gut and shape our immune response. A healthy immune system allows us to tolerate these organisms without mounting an immune response.


The immune system is programmed to tolerate food antigens so that we don’t treat the food we eat like a potential pathogen. To do so would result in chronic inflammation in the gut.


This immune programming is shaped by the early development of our immune system when we are an infant, from birth onwards and possibly even whilst still in the womb.

Briefly, factors which shape the development of our immune system include:

  • How we were born: vaginal delivery vs c-section delivery: the former exposes us to bacteria needed to colonise our gut to establish an immune system, the latter does not expose us to the same type of bacteria and can delay the development of our immune system
  • Breastfeeding: breastmilk contains immune regulating substances such as immunoglobins and prebiotic and probiotic bacteria that colonise the gut
  • Our mother’s health during pregnancy including diet, nutritional deficiencies, medication and genetics
  • Exposure to antibiotics in infancy. Early use of antibiotics can impair the development of a healthy gut immune system by interfering with the colonisation of healthy gut bacteria
  • The timing and dosing of food antigens in infancy (i.e. when and how we are weaned onto solid food)
  • The exposure to microbes within the environment we grow up in. The “hygiene hypothesis” suggests that allergies and immune disorders have increased in recent decades because of reduced exposure to microbes in infancy due to more sterile living conditions and the use of antibiotics


“Oral tolerance” is the suppression of an immune response to food so that we can tolerate the food we eat. So what causes a loss of oral tolerance?


When we have become intolerant to foods there is an imbalance in the gut immune system and one or more of the following has usually occurred:


  • The gut barrier lining has become weakened. The tight junctures between the cells that line the gut “open up” and allow substances through the gut lining into the bloodstream, substances which should otherwise stay inside the gut. This is known as “intestinal hyper-permeability”. This can result in increased inflammation in the gut and the whole body. Gluten in particular can cause intestinal hyper-permeability due to the effect it can have on weakening the tight junctures


  • The gut mucus lining has been compromised and weakened. The mucus lining is home to an important immune substance known as secretory IgA (an anti-inflammatory antibody) which defends us from pathogens, preventing the penetration of dangerous substances and has an anti-inflammatory effect in the gut, allowing for tolerance of food antigens and gut bacteria. A thin mucus lining and reduced secretory IgA result in our immune system becoming hyper-responsive to food and the micro-organisms living in our gut


  • The gut microbiota has become imbalanced, known as gut dysbiosis where there are fewer healthy organisms and more pathogenic organisms living in the gut. This can be caused by an inflammatory diet (high in sugar, refined carbohydrates and saturated fat), medications which disrupt the gut microbiota, chronic stress or an infection such as food poisoning, a parasite or a yeast or bacterial overgrowth. Genetically modified foods may also disrupt gut microbiota.


All of the above factors can result in an imbalanced and overactive gut immune system, leaving us more reactive to anything that our gut comes into contact with – even if it’s a harmless food or the harmless bacteria that live in our gut.


Intestinal hyperpermeability, reduced gut mucus lining and gut dysbiosis can all result in an overactive immune response in the gut and consequently, multiple food intolerances. 


Impaired digestion (i.e. not being able to properly break down the food we eat) is a common side effect of dysregulated immune function in the gut. This is because the increased inflammation damages the intestinal lining which is critical for the production of digestive enzymes which break down fats, proteins and carbs into their smaller constituents (lipids, amino acids and sugars). Impaired digestion can lead to malabsorption of nutrients which can contribute to other extra-intestinal symptoms such as fatigue, low moods, muscle cramps and skin conditions as well as exacerbating a dysfunctional immune system – compounding the very problem we are trying to resolve! We need key nutrients to repair and heal the gut and regulate our immune response.



What causes the gut to become intolerant to food?



So how do we repair the gut lining, rebalance the gut microbiota and normalise our immune response so that we don’t overreact to food?

Head over to Part II of this blog post to find out! 

N.B.  I am not referring to food allergies in this post, which are different types of food hypersensitivity. Food allergies often develop in early infancy or childhood. Food allergies generally involve a much stronger immune response (involving IgE antibodies) with more immediately severe symptoms such as difficulty breathing, swelling of the lips, face and eyes, itchy skin, abdominal pain and dizziness. In contrast, food intolerances involve IgG antibodies, and often develop later in life and result in the delayed onset of less severe (life-threatening) symptoms such as digestive symptoms (bloating, stomach pain, diarrhoea etc.), headaches, fatigue and joint pain.

I am also not referring to Coeliac disease which is an autoimmune condition where the immune system attacks the gut lining when gluten is ingested. In Coeliac disease, all gluten-containing grains must be eliminated and avoided for life.


Belkaid, Y and Hand, T., 2015. Role of the Microbiota in Immunity and inflammation. Cell, 157(1), pp.121–141.

Brandtzaeg, P., 2010. RevIews Food allergy : separating the science. Nature Publishing Group, 7(7), pp.380–400.

Chaplin, D.D., 2010. Overview of the Immune Response David. Journal of Allergy, 125.

Singh, R.K., Chang, H.W., Yan, D., et al, 2017. Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, pp.1–17.