Your gut does far more than digest food. It is home to a vast network of bacteria, viruses, fungi and other microorganisms, collectively known as the gut microbiome. These microbes have a significant impact on your immune system and overall health. 

Insights in this article are provided by Vivere's Head of Nutrition, Yusra Serdaroglu Aydin, a registered dietitian with a background in nutrition, food engineering and culinary arts. Her approach is grounded in science and shaped by a strong understanding of personalised nutrition and the human microbiome, making her guidance especially relevant for those looking to support their immune system through gut health.

Here are the five biggest takeaways from this article about the link between your gut and immune system:

• The gut and immune system are closely connected, with around 70% of immune cells located in the gut.

• A balanced gut microbiome can help regulate immune responses and reduce inflammation.

• Diet, stress management, sleep quality and regular exercise all play a role in supporting gut health.

• Probiotics and prebiotics can help nourish beneficial gut bacteria and strengthen immune defences.

• Avoiding excessive use of antibiotics and highly processed foods can help maintain microbiome balance.

The gut is not just a tube where food is broken down. It is a highly active and complex system that constantly communicates with your immune system. The gut-associated lymphoid tissue (GALT) is one of the largest immune organs in the body [1]. Around 70% of your immune cells are in this area, where they encounter microbes, dietary components and environmental triggers every day.

A healthy gut microbiome works with the immune system to distinguish between harmful invaders and harmless substances like food particles or friendly bacteria. When the microbiome is imbalanced, known as dysbiosis, the immune system can become overactive, leading to inflammation and increased susceptibility to illness.

Your gut microbiome trains your immune cells from early life, helping them recognise pathogens and respond appropriately [2] [3]. Beneficial bacteria produce short-chain fatty acids (SCFAs) such as butyrate, propionate and acetate, which help regulate inflammation and strengthen the gut lining. A robust gut barrier prevents harmful bacteria and toxins from entering the bloodstream.

On the other hand, an imbalanced microbiome can weaken this barrier, leading to a “leaky gut” and triggering chronic inflammation [4] [5]. This has been linked to a range of conditions, including allergies, autoimmune diseases and metabolic disorders.

What you eat directly affects the diversity and stability of your gut microbiome. A diet rich in fibre from fruits, vegetables, legumes, nuts, seeds and whole grains provides the fuel for beneficial bacteria. These plant fibres act as prebiotics, encouraging the growth of healthy microbes.

Probiotic foods like yoghurt, kefir, sauerkraut, kimchi and miso introduce live beneficial bacteria into the gut. Combining probiotics with prebiotics creates a synergistic effect, sometimes referred to as synbiotics, which can enhance microbiome diversity and function.

It is also important to limit ultra-processed foods high in sugar, refined carbohydrates and artificial additives. These can feed less beneficial bacteria, promoting inflammation and potentially reducing microbiome diversity.

• High-fibre fruits and vegetables such as apples, pears, carrots, broccoli and leafy greens [6]

• Fermented foods, including natural yoghurt, kefir, sauerkraut and kimchi [7]

• Whole grains like oats, brown rice and barley [8]

• Legumes such as lentils, chickpeas and beans [9]

• Nuts and seeds for fibre, healthy fats and micronutrients [10]

While diet is essential, lifestyle factors also play a significant role in gut and immune health.

Chronic stress can disrupt the gut microbiome and impair immune responses. Practices such as mindfulness meditation, breathing exercises and gentle yoga can help reduce stress levels [11] [12] [13].

Poor sleep can alter the composition of the microbiome and increase inflammation. Aim for seven to nine hours of restorative sleep each night [14] [15] [16].

Moderate exercise, such as brisk walking, swimming or cycling, supports a healthy microbiome and enhances immune function [17]. Avoid excessive high-intensity training without adequate recovery, as it may have the opposite effect [18] [19] [20].

Antibiotics can wipe out both harmful and beneficial bacteria. Only use them when prescribed, and discuss with your healthcare provider whether probiotic support would be helpful afterwards [21] [22] [23] [24].

While whole foods should be the foundation of your nutrition, certain supplements can be beneficial, especially if your diet is lacking in specific areas.

May help restore balance after illness or antibiotic use, particularly strains such as Lactobacillus and Bifidobacterium [25] [26].

Often derived from inulin, fructo-oligosaccharides (FOS) or galacto-oligosaccharides (GOS), which help feed beneficial bacteria [27].

Supports immune regulation and may influence microbiome diversity. In the UK, supplementation is often recommended during autumn and winter [28] [29] [30].

Found in oily fish, they help modulate inflammation and support immune health [31] [32].

Supplements including herbal extracts such as curcumin, ginger, elderberry and saffron and be used to help support immunity.

Always consult a qualified healthcare professional before starting any supplement, especially if you have existing health conditions or take medication.

If your gut and immune system are not working in harmony, you may notice signs such as:

• Frequent colds or infections

• Ongoing digestive issues like bloating, diarrhoea or constipation

• Food intolerances or sensitivities

• Unexplained fatigue

• Skin issues such as eczema or acne

If these symptoms persist, it may be worth seeking medical advice and considering gut microbiome testing for a more personalised approach.

• Eat a varied, plant-rich diet to increase microbiome diversity.

• Incorporate fermented foods regularly.

• Manage stress with relaxation techniques.

• Prioritise quality sleep.

• Stay active with regular moderate exercise.

• Limit processed foods and unnecessary medications.

• Consider probiotic and prebiotic support when appropriate.

“Your gut and immune system are deeply connected, and caring for one means supporting the other. Through a balanced diet rich in fibre and fermented foods, a healthy lifestyle and mindful use of supplements, you can nurture your microbiome and strengthen your immune defences. Small, consistent changes can have a lasting impact on your health and resilience.”

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] Diet induced changes in the microbiota and cell composition of rabbit gut associated lymphoid tissue (GALT) | Scientific Reports

[2] How the early life microbiome shapes immune programming in childhood asthma and allergies - ScienceDirect

[3] Childhood Development and the Microbiome: The Intestinal Microbiota in Maintenance of Health and Development of Disease During Childhood Development - PMC

[4] Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review - PMC

[5] Intestinal barrier permeability: the influence of gut microbiota, nutrition, and exercise - PMC

[6] Fruit‐Based Diet and Gut Health: A Review - Maqsood - 2025 - Food Science & Nutrition - Wiley Online Library

[7] High fiber fermented foods - Stanford

[8] Why whole grains are protective: biological mechanisms - PubMed

[9] Health Benefits of Plant-Based Nutrition: Focus on Beans in Cardiometabolic Diseases - PMC

[10] Potential Prebiotic Properties of Nuts and Edible Seeds and Their Relationship to Obesity - PMC

[11] Stress, depression, diet, and the gut microbiota: human–bacteria interactions at the core of psychoneuroimmunology and nutrition - PMC

[12] Neurobiological Implications of Chronic Stress and Metabolic Dysregulation in Inflammatory Bowel Diseases - PMC

[13] Stressed to the Core: Inflammation and Intestinal Permeability Link Stress-Related Gut Microbiota Shifts to Mental Health Outcomes - PMC

[14] Sleep Deprivation and Gut Microbiota Dysbiosis: Current Understandings and Implications - PMC

[15] Severe, short-term sleep restriction reduces gut microbiota community richness but does not alter intestinal permeability in healthy young men | Scientific Reports

[16] Gut microbiota and sleep: Interaction mechanisms and therapeutic prospects - PMC

[17] Physical Exercise and the Gut Microbiome: A Bidirectional Relationship Influencing Health and Performance - PMC

[18] Sports and Immunity, from the recreational to the elite athlete - ScienceDirect

[19] Effect of Intensity and Duration of Exercise on Gut Microbiota in Humans: A Systematic Review - PMC

[20] The Connection Between Physical Exercise and Gut Microbiota: Implications for Competitive Sports Athletes - PMC

[21] Impact of antibiotics on the human microbiome and consequences for host health - PMC

[22] Antibiotics promote the growth of antibiotic-resistant bacteria in the gut | Imperial News | Imperial College London

[23] The effect of antibiotics on the composition of the intestinal microbiota - a systematic review - ScienceDirect

[24] Facing a new challenge: the adverse effects of antibiotics on gut microbiota and host immunity - PMC

[25] Probiotics and gut health - BDA

[26] Elucidating the role of diet in maintaining gut health to reduce the risk of obesity, cardiovascular and other age-related inflammatory diseases: recent challenges and future recommendations - PMC

[27] Elucidating the role of diet in maintaining gut health to reduce the risk of obesity, cardiovascular and other age-related inflammatory diseases: recent challenges and future recommendations - PMC

[28] Vitamin D and the Host-Gut Microbiome: A Brief Overview - PMC

[29] Gut-vitamin D interplay: key to mitigating immunosenescence and promoting healthy ageing - Immunity Ageing

[30] Vitamin D and Microbiome: Molecular Interaction in Inflammatory Bowel Disease Pathogenesis - ScienceDirect

[31] Elucidating the role of diet in maintaining gut health to reduce the risk of obesity, cardiovascular and other age-related inflammatory diseases: recent challenges and future recommendations - PMC

[32] Impact of Omega-3 Fatty Acids on the Gut Microbiota - PMC