When you experience bloating, skin issues, fatigue, or discomfort after eating, you’ve probably wondered whether a specific food might be to blame. While a growing number of at-home tests are now available, from food allergy and sensitivity tests to gut microbiome analysis, not all of them function the same way or offer results based on the same principles.

In this article, we explore the key differences between these types of testing, their scientific foundations, and when each might be useful. The insights come from Yusra Serdaroglu Aydin, Vivere’s Head of Nutrition. Yusra is a registered dietitian with a background in nutrition, food engineering, and culinary arts. Her approach combines rigorous science with a deep understanding of personalised nutrition and the human microbiome, helping people address food-related symptoms safely and effectively using scientifically validated solutions.

Here are the five key takeaways from this article on allergy, intolerance, and gut microbiome testing:

• Food allergy tests identify rapid, immune-driven reactions that can be life-threatening. These require IgE testing or skin prick diagnostics.

• Food sensitivity and intolerance tests, such as IgG blood tests or hair analysis, lack strong scientific backing.

• Gut microbiome analysis offers deeper insights into microbial balance and health, associated health risks, along with personalised nutrition recommendations.

• Approximately 70% of your immune cells reside in your gut, making microbiome balance essential for reducing food reactions and supporting immune tolerance.

• Symptoms like bloating, rashes, fatigue, or diarrhoea may result from allergies, intolerances, or gut dysbiosis, each requiring a different approach.

Food allergies involve the immune system misidentifying a food protein as dangerous. This triggers an immediate IgE-mediated response, often within minutes of ingestion [1]. Several factors can contribute to the development of food allergies, including genetic predisposition, gut barrier dysfunction (such as leaky gut), imbalances in the gut microbiome, and early-life exposures that affect diet and immune system development [2].

• Swelling of the lips, throat or face

• Hives or itchy skin

• Wheezing, coughing or difficulty breathing

• Nausea, vomiting or abdominal pain

• Anaphylaxis (a life-threatening reaction requiring emergency care)

• Peanuts

• Tree nuts

• Milk

• Eggs

• Fish and shellfish

• Wheat

• Soy

• IgE Blood Tests – Measure levels of allergen-specific Immunoglobulin E in the blood [5].

• Skin Prick Tests – Introduce small amounts of allergen to the skin to check for a raised reaction [6].

• Oral Food Challenge – Administered under medical supervision to confirm or rule out allergy [7].

These methods are medically validated and essential for diagnosing true food allergies.

Food intolerances and sensitivities do not involve the immune system in the same way as allergies. They typically cause delayed or mild-to-moderate symptoms and are often linked to digestion, enzyme function, or gut health [8]. Common contributing factors include enzyme deficiencies, which affect the efficient digestion of these ingredients, increased gut lining permeability, imbalances in gut bacteria, excess intake or impaired detoxification pathways, as well as chronic stress and inflammation [9].

• Bloating, wind or cramping

• Fatigue or brain fog

• Skin rashes

• Mood swings

• Diarrhoea or constipation

• Headaches

• Lactose – from dairy

• Gluten – found in wheat, barley and rye

• Histamines – found in aged cheese, wine, fermented foods

• FODMAPs – fermentable carbohydrates

• Caffeine and alcohol

• Sulphites, salicylates and MSG

• IgG Blood Tests – Measure IgG or IgG4 antibodies, which often indicate tolerance, not intolerance [11].

• Hair Analysis – Claims to detect intolerances based on bio-energetic signals or mineral patterns in hair, but lacks scientific support [12].

• Other Tests – Unproven methods that assess reactions through live blood or electrical signals [12].

Many companies now offer food sensitivity or intolerance tests examining for IgG or IgG4 levels in blood, but according to important bodies and professionals, these tests aren’t backed up by strong scientific research, and the results may be controversial [13]. The reliable ways to investigate food intolerance is through a clinician-guided elimination diet and symptom tracking, blood, breath and stool tests that check for individual intolerance or sensitivities [14].

Gut microbiome analysis uses advanced DNA sequencing to identify and assess the microbial communities in your gut. Unlike allergy or sensitivity tests, microbiome testing looks at how your body functions at a foundational level [15].

About 70% of your immune cells are in your gut, where they constantly interact with your microbiota [16]. When your gut microbiome is imbalanced, which is called dysbiosis, it can lead to chronic inflammation, weakened immune tolerance, increased sensitivity to safe foods, as well as skin problems, fatigue, mood changes, and digestive issues.

• Bloating or irregular bowel movements

• Skin flare-ups, including eczema and acne

• Fatigue

• Food cravings

• Frequent illness or slow recovery

• Low resilience to stress or dietary changes

• Antibiotic use

• Processed or low-fibre diet

• Stress and poor sleep

• Environmental toxins or medication use

• Lack of microbial diversity

• qPCR (Quantitative Polymerase Chain Reaction) – Detects and quantifies specific known DNA sequences for targeted microbes or genes with high sensitivity. Not suitable for broad microbiome profiling [19].

• 16S rRNA Gene Sequencing – Sequences the 16S rRNA gene to identify dominant bacterial groups at the genus level and estimate their relative abundance. Limited to bacteria and lower resolution [20].

• Shotgun Metagenomic Sequencing – Sequences all DNA in the sample, identifying bacteria, fungi, viruses, and more with high resolution. Enables both taxonomic and functional microbiome profiling [20].

Gut microbiome testing helps pinpoint microbial imbalances and guides nutrition, supplementation and lifestyle changes to improve tolerance, digestion and immune function.

Food allergy testing is important for detecting acute immune responses, and elimination diets can help manage known intolerances. However, these approaches often fail to uncover the root causes or offer lasting solutions.

Microbiome analysis provides deeper insights, though results can vary depending on the testing method and the depth of bioinformatics or AI-driven interpretation. While many providers offer limited, static reports without actionable insights, Vivere goes further. 

We perform an in-depth analysis of your gut microbiome, evaluating the complex relationships between your gut ecosystem and the foods you eat to generate a comprehensive score for each food.

Vivere’s gut microbiome analysis empowers you to:

• Assess bacterial balance and diversity

• Understand specific metabolisms linked to your microbiome

• Identify elevated health risks driven by microbiome imbalances

• Support the microbiome through personalised nutrition and supplements

• Reintroduce foods previously associated with intolerances or sensitivities with more tolerance

• See measurable improvements within weeks, as demonstrated in clinical studies

• Achieve a healthier microbiome and thus, better overall health over time

Bothersome symptoms like bloating, irregular bowel movements, gas, or fatigue after eating can be frustrating, especially when they persist or become chronic. While food allergy tests are essential for identifying acute immune reactions, the scientific backing for many food sensitivity and intolerance tests remains limited.

Instead of relying solely on elimination, a more effective and sustainable approach begins with understanding your gut microbiome, the ecosystem at the core of your digestion, immunity, and overall well-being.

Microbiome testing goes deeper, identifying imbalances that may be driving symptoms and revealing how your gut microbes interact with specific foods. This insight allows for a personalised nutrition plan tailored to your unique profile, helping you improve your health from the inside out naturally, holistically, and sustainably.

Vivere helps you take control of your health with personalised insights from state-of-the-art gut microbiome testing, nutritional guidance, science-backed supplements and expert support. Sign up today and start living better, for longer.

[1] Food Allergies - NIH

[2] Host-microbiome interactions in atopic and allergic diseases - Science Direct

[3] Food Allergy - NHS

[4] Food allergies around the world - Frontiers

[5] IgE allergy diagnostics and other relevant tests in allergy, a World Allergy Organization position paper - PMC

[6] Role of Skin Prick Test in Allergic Disorders: A Prospective Study in Kashmiri Population in Light of Review - PMC

[7] Will Oral Food Challenges Still Be Part of Allergy Care in 10 Years’ Time? - PMC

[8] Food allergy vs. food intolerance: What's the difference? - Mayo Clinic

[9] Food Intolerances - PMC

[10] Food intolerance - NHS

[11] Blood testing for sensitivity, allergy or intolerance to food - PMC

[12] Unproven Diagnostic Tests for Adverse Reactions to Foods - Science Direct

[13] The Myth of IgG Food Panel Testing - AAAAI

[14] The Differential Diagnosis of Food Intolerance - PMC

[15 Current understanding of the human microbiome - PMC

[16] The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimizing Treatment Strategies - PMC

[17] Gut microbiota dysbiosis in functional gastrointestinal disorders: Underpinning the symptoms and pathophysiology - PMC

[18] Gut Microbiota Dysbiosis: Triggers, Consequences, Diagnostic and Therapeutic Options - PMC

[19] Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling - PMC

[20] Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing - Science Direct