The truth about food intolerances and gut issues
Photo by NATHAN MULLET on Unsplash
If you're living with unexplained gut issues, constipation or a need to rush to the loo, you've probably wondered whether certain foods are to blame. Maybe you've tried cutting out gluten, dairy, or other suspected culprits, only to find yourself still struggling, or confused about what you can actually eat.
The relationship between food and gut issues is real, but it's far more nuanced than most people realise. Let me walk you through what's actually going on, and why the approach matters just as much as identifying the trigger foods.
Understanding the different types of food reactions
First, let's clear up some confusion. When people talk about ‘food intolerances’, they're often lumping together three very different types of reactions:
Food allergies: These involve your immune system producing IgE antibodies and can happen when your immune system reacts to something that it sees as serious or life-threatening, like a peanut, eggs or dairy. It hits the panic button. Reactions happen quickly (within minutes to two hours) and can be severe. Think hives, swelling, difficulty breathing, or anaphylaxis. These are relatively rare but require immediate medical attention. Food allergies are usually diagnosed through specific allergy testing with your GP.
Food intolerances: These aren’t immune reactions and are more about digestion. Food intolerances occur when your body lacks the enzymes needed to digest certain foods properly. The classic example is lactose intolerance. Here, your body doesn't produce enough lactase enzyme to break down the lactose in dairy. The undigested food then ferments in your gut, causing bloating, pain, gas, and diarrhoea. These reactions are dose-dependent (a little might be fine, a lot causes problems) and delayed (symptoms can appear hours later).
Food sensitivities: Food sensitivities do involve your immune system, but it’s more ‘irritated’ than ‘panicked’ – and involves a different pathway to allergies (IgG antibodies rather than IgE). They can also involve chemical reactions to compounds in foods (like histamine, salicylates, or FODMAPs). Symptoms, like bloating, headaches, joint pain and skin issues, are often delayed by 24-72 hours, which makes them incredibly difficult to identify without proper investigation.
It’s not just about the food you’re eating
Here's what many people don't realise: gut issues aren’t just about the food you're eating. It's about the state of your gut when that food arrives – gut barrier integrity, inflammation levels, microbiome balance, stress, and digestive function.
When your gut is inflamed or compromised in some way, foods that wouldn't normally cause problems can suddenly trigger discomfort – not because you're ‘intolerant’ to them, but because your gut is in a reactive state.
This is why you may be fine eating a specific food on one day, but on another, the same food causes you problems.
Why generic food intolerance tests aren’t really that helpful
You've probably seen them advertised – home testing kits that claim to identify your food intolerances by testing your blood for IgG antibodies to hundreds of foods.
But here's the problem: IgG antibodies to foods are actually a normal response. They show that you've eaten that food before and your immune system has recognised it – not necessarily that it's causing you problems. Having IgG antibodies to a food doesn't automatically mean you need to eliminate it.
These tests often come back showing reactions to 20, 30, or even 50 foods – ones that you eat regularly – leaving you wondering what you’re actually going to eat. Then you eliminate them all, leaving you with an impossible-to-handle, restrictive diet that can actually make things worse by reducing dietary diversity and starving beneficial gut bacteria.
A better type of food reactivity testing
However, there is a more sophisticated approach to food reactivity testing that I use in clinic: the FIT176 test from KMBO Diagnostics.
This test measures IgG antibodies (showing which foods your immune system has encountered), but it goes one crucial step further by also measuring complement C3d – a marker of active inflammation.
Think of it like this:
IgG alone = "I’ve seen this food before"
IgG + complement C3d = "This food started a fire"
When both markers are elevated, it's far more likely that the food is actively causing inflammation and contributing to your symptoms – not just something you've eaten recently. This makes the list of 'reactive' foods much smaller and easier to prioritise.
The FIT176 test also assesses gut barrier integrity by measuring zonulin and occludin (markers of leaky gut) and checks for candida overgrowth. This gives us valuable insight into the state of your gut lining and whether it's allowing food particles to cross into the bloodstream where they shouldn't be.
Functional stool testing: the other piece of the puzzle
The other comprehensive testing option is functional stool testing, which tells us what's happening inside your gut:
Inflammation markers
Digestive enzyme production
Gut microbiome composition (beneficial and harmful bacteria)
Presence of parasites or pathogenic bacteria
Markers of gut barrier integrity
Which test is right for you depends on your specific symptoms and clinical picture. The key is having a clear understanding of what's actually going on, rather than randomly eliminating foods.
The problem with DIY elimination diets
I completely understand the temptation to just cut things out and see what happens. When you're in discomfort, you want answers fast.
But here's what I see happen time and time again:
You eliminate too many things at once. When you cut out gluten, dairy, eggs, and soy all at the same time, and your symptoms improve, which one was the problem? Or was it all of them? Or none of them. Maybe you just gave your gut a break from overeating?
You don't eliminate for long enough – or you eliminate for too long. True food reactions need 4-6 weeks of complete elimination to see results. But keeping foods out longer than necessary can actually reduce your tolerance to them and limit your nutritional intake unnecessarily.
You reintroduce incorrectly. Reintroduction is just as important as elimination. It needs to be systematic, one food at a time, with proper observation periods. Rush it, and you'll miss the trigger. Do it wrong, and you might blame the wrong food.
You ignore the underlying issues. Eliminating foods might reduce symptoms temporarily, but if you're not addressing why your gut became reactive in the first place – leaky gut, low stomach acid, SIBO, dysbiosis, chronic stress – you're just putting a plaster over a wound that needs stitches.
What actually causes food-related gut issues?
In my clinic, when someone comes to me with gut issues they believe are food-related, we investigate these common root causes:
Low stomach acid: Counter-intuitively, many people with reflux and upper gut discomfort actually have too little stomach acid, not too much. This means food isn't properly broken down, leading to fermentation, bloating, and discomfort.
Leaky gut (intestinal permeability): When the gut lining becomes damaged, partially digested food particles can cross into the bloodstream, triggering immune reactions and inflammation.
Small Intestinal Bacterial Overgrowth (SIBO): Bacteria that should be in your large intestine migrate into the small intestine, where they ferment foods (especially carbohydrates) and produce gas, causing pain, bloating, and altered bowel habits.
Dysbiosis: An imbalance in gut bacteria – too many harmful bacteria, not enough beneficial ones, or a lack of diversity. This affects how well you digest food and how your immune system responds to it.
Enzyme deficiencies: Not producing enough digestive enzymes (from the pancreas, small intestine, or liver/gallbladder) means food doesn't break down properly.
Motility issues: If food moves too slowly (constipation) or too quickly (diarrhoea) through your system, it affects digestion and can cause discomfort.
Stress and nervous system dysregulation: Your gut slows down or speeds up depending on whether your nervous system is in ‘rest and digest’ or ‘fight or flight’ mode. Chronic stress = chronic digestive dysfunction.
The right way to investigate food triggers
If you suspect food is contributing to your gut issues, the truth is there's no one-size-fits-all approach. Every client is different, and the way we investigate depends on your symptoms, health history, and what feels right for you.
Here's how I typically work with clients, though the exact path we take together will be unique to you:
Understanding what's going on: We start by really understanding your symptoms, health history, and what you've already tried. Sometimes patterns become clear just from this conversation. Other times, testing gives us valuable insight, but it's not always necessary, and budget is always a consideration.
Testing. Options include the FIT176 Food Reactivity Test (if we suspect specific food triggers), comprehensive stool testing (if we need to understand your overall gut health), sometimes both, sometimes neither. Testing can fast-track answers, but there are other ways to get to the root cause through careful observation, symptom tracking, and targeted dietary approaches if budget doesn’t allow.
Supporting your gut: Whether we test or not, we usually start by supporting your digestive function. This might mean addressing low stomach acid, supporting enzyme production, or reducing gut inflammation. Often, symptoms improve at this stage alone.
Investigating food triggers (if needed): If food reactions are still an issue, we might use a structured elimination and reintroduction protocol. This is always tailored to your situation. What we eliminate, for how long, and how we reintroduce depends on your symptoms, test results (if you've had them), and what feels manageable for your life.
The ongoing work: Throughout this process, we're addressing the underlying issues that made your gut reactive. The goal is always the same: healing your gut so you can enjoy food without fear, discomfort, or endless restrictions.
The key thing to understand? There's no single ‘right’ way to do this. The best approach is the one that fits your body, your budget, and your life – and that's what we figure out together.
When to seek professional support
You should consider working with a qualified nutritional therapist or functional medicine practitioner if:
You've been living with unexplained gut issues for months or years
Your GP has ruled out serious conditions but offered no solutions beyond "it's IBS"
You've tried eliminating foods on your own without lasting improvement
You're already avoiding multiple foods and your diet is becoming restrictively limited
Your gut symptoms are affecting your quality of life, social activities, or mental health
You're experiencing other symptoms alongside the gut discomfort (fatigue, skin issues, joint pain, brain fog) that might be connected
The bottom line
Food can absolutely contribute to gut issues, but it's rarely as simple as ‘this food is bad for you’. Your gut is a complex ecosystem, and discomfort is usually a sign that something in that ecosystem is out of balance.
Rather than endless restriction and guesswork, the goal is to understand:
What's causing your gut to be reactive
Which specific foods (if any) are genuine triggers for you
How to heal your gut so you can expand your diet again
Because you deserve to eat without fear, discomfort, or confusion. And with the right investigation and support, that's entirely possible.
Ready to get to the root of your gut issues?
If you’re tired of guessing why you don’t feel your best, I can help you find a way forward that works for you – whether that includes testing or not.
Why not book a free and informal chat. We'll talk through your symptoms, what you've already tried, and explore what might be the right next step for you. No pressure, no hard sell – just an honest conversation about whether working together makes sense.