The gut-immune axis: 8 things that scientists know (so far!)

Picture your gut as a bustling little city of microbes, immune cells and signalling molecules all working together. Similar to a medieval market square where merchants, messengers, guards and citizens all chatter, work and trade. Your immune system isn’t some distant garrison; it lives in the gut, patrols it, and cooperates with microbial neighbours. Scientists call this the “gut-immune axis” – the constant two-way conversation between your intestines and immune defences. When that dialogue runs smoothly, your whole body benefits. When it breaks down, inflammation and illness can follow.

Below are eight key insights into what researchers currently understand about this axis and what you can do to keep the peace inside your microbial city.

1. Around 70% of your immune system lives in your gut

Roughly 70% of your immune cells live in your gut-associated tissue, like Peyer’s patches, the lamina propria and lymph nodes near your intestines. Your gut lining, a single layer of cells protected by a thin, slippery mucous membrane, acts like a city wall. If that barrier becomes compromised and permeable, bits of bacteria or toxins such as LPS can slip through, triggering inflammation throughout the body. When your microbial “citizens” are out of balance (a state called dysbiosis), the immune system can become chronically agitated. A strong gut barrier and balanced microbiome are essential for keeping your immune system calm and well-regulated.¹ Think of the merchants, messengers, guards and citizens we spoke of before – if there is an imbalance of them, or even worse, the city walls become compromised, that can quickly escalate to chaos! Maintaining a healthy gut barrier is not just about digestion; it’s about keeping your immune system sane.

2. Microbes send messages to your immune system

The microbes in your gut don’t just sit there. They are busy chemists – fermenting, breaking down fibres, and producing substances that act like signals. These include short-chain fatty acids (SCFAs), like butyrate, propionate and acetate, which we measure in our Gut Microbiome Test. These compounds:

Feed your gut lining cells
Strengthen the gut barrier
Help create regulatory T-cells (Treg), the peacekeepers that stop your immune system from overreacting, a common characteristic of many autoimmune conditions.

Other microbial products, such as tryptophan and bile acid metabolites, act as immune messengers. Some new studies show that these metabolites can influence how gut cells handle stress and cell death in inflammatory bowel disease (IBD). ² Microbes are not passive residents; they are biochemical diplomats influencing immune policy.

3. Your gut talks to every organ in the body

The gut-immune axis doesn’t stop in your belly; it connects to nearly every organ:

Gut-lung axis: Microbes can shape how your lungs respond to infection or asthma.³
Gut-skin axis: Gut imbalances are linked to skin issues such as eczema, acne and psoriasis.⁴
Gut-brain axis: Immune signals from the gut affect mood, stress, and even the risk of neurodegenerative diseases.⁵
Gut-metabolism and cardiovascular axis: Changes in the gut-immune axis can raise the risk of hypertension and heart disease.⁶

And the list doesn’t end there. Your gut-immune axis has also been shown to be connected with your liver, bladder, spleen, kidneys, hormones, etc. You name it! All these routes are connected through immune cells, nerves, and blood vessels – a superhighway of information running through your body.

4. Gut immune cells can affect your brain and mood

Research shows that certain immune cells in the gut can influence behaviour and stress responses:

At Johns Hopkins, scientists found that intestinal γδ T cells affect stress and depression-like behaviour, through a receptor called dectin-1 on immune cells.⁷
Other work suggests stress can make the gut more permeable, allowing immune molecules like IL-22 to reach the brain and alter activity in regions that control anxiety.⁸
In Alzheimer’s models, gut immune cells can even migrate along the gut-brain axis, and a high-fibre diet (which feeds gut bacteria) helps reduce disease frailty.⁹

So, immune cells in the gut are not isolated defenders; they can dispatch signals, travel or affect distant tissues and organs.

5. Diet, probiotics and prebiotics shape the axis

What can you do?

Probiotics (beneficial bacteria, e.g. in kefir) can rebalance your microbiome and calm inflammation.¹⁰
Prebiotics (fibres that feed good microbes) help them thrive and produce SCFAs. ¹¹
Synbiotics (combined probiotics + prebiotics) are showing promise in supporting both the microbiome and immune system. You can read more in our Scientific Lead Advisor, Dr. Amrita Vijay’s, latest research paper here, which investigates our synbiotic treatment (kefir + Complete Preb i otic).
Diets rich in fibre, plants, and fermented foods are linked to a higher microbial diversity, lower inflammation and healthier immunity.¹²

6. Healing your gut barrier with collagen and nutrients

If your gut barrier is damaged (by stress, infection, poor diet, toxins, or inflammation), it needs repair. Collagen peptides provide amino acids like glycine and proline that support tissue rebuilding and mucous production. While human studies are still limited, combining collagen and mucosal nutrients (like glutamine, zinc, and vitamins A & D) can help maintain a strong gut barrier. This is why collagen is one of our key recommendations on our Gut Health Protocol, alongside the kefir and Complete Prebiotic.

7. Natural anti-inflammatories: Boswellia and curcumin

Botanical extracts can help cool inflammation while the gut heals. Boswellia serrata (Indian frankincense) blocks inflammatory enzymes (5-LOX) and has shown up to 82% improvement in ulcerative colitis (UC) symptoms in trials. Curcumin, from turmeric, works through other anti-inflammatory routes (NF-κB and COX2), making the two great partners.¹³ These and similar anti-inflammatories can be a strategic “fire-hoe” to dampen inflammatory responses while the gut-immune axis recalibrates.

8. Epigenetics, stress and adaptation

Think of epigenetics as the “software” of your gut-immune axis. Your genes aren’t fixed switches – they can turn on or off in response to diet, sleep, toxins, or stress. These epigenetic changes affect how your gut barrier and immune system behave.¹⁴ Chronic stress, including circadian disruptions, can throw this system off balance, leading to inflammation, altered mucosal immunity, increased gut permeability and microbial shifts.¹⁵ Managing stress, sleep, and circadian rhythm is vital for long-term gut-immune harmony.

A simple gut-immune support plan

Here’s a simple step-by-step gut health protocol to help strengthen your gut-immune axis:

Kefir – adds beneficial bacteria to your gut ecosystem.
Complete Prebiotic – feeds your good microbes so they can produce protective metabolites.
Collagen – can help protect, support and repair your gut barrier.
Boswellia serrata – can modulate inflammation during flare-ups.
Ashwagandha – and mindfulness practices to help manage stress, sleep and circadian rhythms, calming the gut-brain axis.

Monitor, adjust and personalise! Track your progress and pay attention to your digestion, skin, mood, and energy over time.

The gut isn’t just a digestive tube; it’s the command centre of your immune system. A healthy gut-immune axis means balanced microbes, a strong barrier, and a calm immune response that protects you without overreacting. Nourish your microbes, repair your gut lining, manage stress, and let your inner city thrive.

Any questions? Contact one of our Nutritional Therapists via live chat, weekdays from 8 am to 8 pm.