Food Allergy or Intolerance?

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Food reactions can sometimes be glaringly obvious. But for many of us, they are more subtle and hard to figure out. The biggest thing that will impact your gut is the food that you eat. But how do you know what the right thing is?


There are many different ways that we can react to food. We may have a flat out intolerance, where every time we try to eat the food the body does not digest it and tries to expel it from our body (as is the case with lactose intolerance). 

We may react to foods at one time, but then other times it is fine. 

And we may not have any immediate reaction at all, but over time we begin to feel unwell, with increasing amounts of bloating and indigestion. 

It can be tricky to figure out what is what, so here is some info that may help you to get closer to understanding these intolerances and what to do about them. 


When it comes to food intolerance, the two most common culprits by far are wheat and dairy. Dairy intolerance is common not only because many people have issues with digesting lactose, the sugar from milk, but also because casein (the dominant protein in dairy) is large and hard to digest by a human stomach. 

Cows have 4 stomachs, humans have one. It is not surprising that so many of us have issues with digesting milk and milk products. Common symptoms include diarrhoea (check lactose intolerance), bloating and irregular bowel movements. 

The other issue is gluten, which is mostly found in wheat products like bread, pasta, crackers, cookies and noodles. Again, gluten is a large protein and is quite difficult to digest. Gluten intolerance symptoms vary but can include bloating, constipation, diarrhoea, wind and reflux. 

Before going into any other food intolerance explorations, stop consuming these two things and see if your symptoms reduce. 


Another type of food reaction can occur when you eat normal ‘healthy’ foods that contain specific fibres that may react with your body in certain ways. These fermentable are ‘eaten’ by your gut bacteria, which in turn create gasses that can lead to bloating, burping, wind and irregular bowel movements. 

The problem with these types of reactions doesn’t really lie with the food but with your body’s reaction to otherwise healthy food. 

One of the treatment strategies for this is using a low FODMAPs diet – this essentially eliminates most of the fermentable compounds from the diet which leads to less fermentation and fewer symptoms. The problem with this is while it may provide relief short term, your bacteria actually NEED these fermentable fibres to thrive, and it can detriment your microbiome in the long term to stay on this type of diet. 

If you’re reacting to fermentable foods, it’s time to check in with a naturopath to conduct some testing to see what the state of your microbiome is. 


Often people misunderstand the difference between a food allergy and food intolerance. This often leads to expensive testing that doesn’t really get to the root of the problem. Let us simplify this for you.

A food ALLERGY is when your immune system lodges a response to a certain food. This leads to the production of antibodies to the food, which means when you eat it creates an inflammatory reaction.  Common food allergy reactions are hives, itchy skin, anxiety and excessive mucus production (even sinus issues). 

A food INTOLERANCE is when you have a reaction to a food, but it’s local to the gut (not a systemic reaction). Food intolerance can indeed cause systemic symptoms like fatigue however generally it is a reaction at the gut wall that is the main issue. A common food intolerance sign would be when you eat a food and become bloated afterwards. As mentioned earlier, it could be an intolerance to a component of the food (like the fibre or protein) or just generally to the food itself (like every time you eat capsicum you get reflux)


One of the things that we commonly see at Shift, is patients that have completed a food allergy test (usually at the recommendation of someone) to find out why they are reacting to foods. This is NOT something we recommend as standard practice as Shift because…

  • Normally it’s an intolerance causing the issue, not a food allergy.
  • It tells us nothing about fermentation reactions, and which bacteria are causing them.
  • When the microbiome is damaged, it can lead to an over-reactivity of the immune system to all kinds of food. This means normal healthy foods will react. What is most important here, is to treat the gut and microbiome. This will then stop the overreactivity and often there is no need to permanently remove the food (although sometimes there will be). 
  • The cost of this test is much better spent on a high-quality stool analysis to look at the health of the microbiome, digestive capability and immunity of the gut. Once you sort out the issue here, you may want to look at Ig testing for foods, however in most cases after-treatment of the gut you will not need to go down this pathway. 

Lastly, the best way to get clues as to what you are reacting to is to remove gluten and dairy and keep a diet and symptom diary for a few weeks to track what you eat, how your gut symptoms are (bloating and bowel habits) and how you feel. And if you’re still stuck see one of our naturopaths and we would be happy to help.

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Your ability to digest food and absorb nutrients determines your health, and your microbiome (the bacteria that live inside you) are so important for preventing disease.

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