Gut Health & Your Immune System: Why It All Starts in the Gut

I’m writing this while fighting off a cold — herbal tea in hand! Being a naturopath, unfortunately, doesn’t give me superpowers. But I will say this: since improving my gut health, I don’t get sick nearly as often as I used to.

And that’s no coincidence.

Around 70–80% of your immune system lives in your digestive tract. If your gut health is struggling, your immune function likely is too.

In clinic, I often see people with lingering infections, slow recovery, or autoimmunity – and when we look deeper, their gut is inflamed, imbalanced, or under-functioning. The immune system is trying its best, but it’s operating without the foundations it needs.

Let’s look at why gut health is so key for immunity – and how to support both naturally.

Your gut: your immune system’s headquarters

Your gut isn’t just about digestion – it’s home to an entire immune landscape called the GALT (gut-associated lymphoid tissue). This includes specialised immune cells, protective secretions like secretory IgA, and your gut lining itself, which acts as both a filter and a barrier.

Even more fascinating? Your microbiome (the trillions of bacteria in your gut) plays a huge role in training and regulating your immune system. The right microbes help calm inflammation, defend against pathogens, and maintain immune tolerance — basically teaching your body what to react to and what to ignore.

When your gut lining becomes damaged (think leaky gut), or your microbiome gets thrown out of balance (dysbiosis), your immune system can become either sluggish and under-responsive… or over-reactive and inflamed.

Signs your immune system and gut might both be struggling

• Frequent colds, flus or infections

• Ongoing sinus, ear, throat, or chest infections

• Slow recovery after illness

• Food sensitivities or intolerances

• Autoimmune conditions (e.g. Hashimoto’s, coeliac, rheumatoid arthritis)

• Skin issues like eczema or hives

• Digestive symptoms – bloating, reflux, constipation, diarrhoea

• Histamine intolerance or allergies

• Low energy or post-viral fatigue

These aren’t always just immune issues — they’re red flags that your gut may need some love too.

What your pathology results might reveal

If you’ve had bloods done recently, they can offer important clues. Often, I see people with “normal” results that are technically in range, but not optimal – and that can be enough to affect both gut and immune function.

Some common patterns include:

LOW White blood Cells (WBCs)

WBCs are integral to fighting off infections. Low neutrophils can be a key indicator that your immune system is under functioning.

Check: Full blood count in pathology.

Low zinc

Zinc is crucial for both gut lining repair and immune cell function. Even a mild deficiency can increase infection risk and slow wound healing.

Check: plasma zinc or serum zinc.

Low vitamin D

This sunshine vitamin modulates immune responses and supports healthy microbial balance. Deficiency is common, especially in winter.

Check: 25-OH vitamin D.

Low iron or ferritin

Iron supports oxygen delivery and immune cell proliferation – and is often low in menstruating women or people with gut inflammation.

Check: iron studies, especially ferritin.

Low B12 or folate

Needed for cell repair and energy, and often affected by low stomach acid or gut malabsorption.

Check: serum B12 and folate.

Elevated CRP or ESR

Markers of inflammation that can reflect chronic immune activation or gut-driven inflammation.

Check: CRP and ESR.

Lab work isn’t everything, but when paired with symptoms, it can paint a powerful picture – especially if we’re looking for the root cause of poor immune function.

How to naturally support your gut–immune connection

If your immune system feels like it’s always under fire, start by nourishing your gut. Here’s how:

Focus on whole, anti-inflammatory foods

Think rainbow veg, healthy fats, bone broth, fermented foods, and fibre-rich meals that feed your microbiome.

Hydrate & support digestion

Bitters, herbal teas (like ginger or chamomile), and mindful eating can all help digestion and absorption.

Rebuild your microbiome

Probiotic foods like sauerkraut, kefir and miso can help restore balance – but sometimes a tailored probiotic supplement is needed too.

Prioritise rest & nervous system support

Stress impairs gut barrier function and immune resilience. Breathwork, slow walks, journalling, or seeing a therapist can help your gut too.

Test, don’t guess

If you’ve been unwell for a while, a comprehensive stool test can show what’s happening with your microbes, gut lining, inflammation levels and immune markers like secretory IgA. I love using Co-Biome!

What about supplements?

There’s no one-size-fits-all here – but in clinic, I often see beautiful results from nutrients like:

• Zinc (if deficient)

• Vitamin D (especially through winter)

• Vitamin C for histamine balance and antioxidant support

• L-glutamine to help heal the gut lining

• Medicinal mushrooms like reishi and cordyceps for immune modulation

• Echinacea and andrographis (short-term) for acute immune support

But again – personalised care is key. Taking the wrong thing at the wrong time can aggravate symptoms or delay healing. Please get a naturopath on board to guide you in your personalised approach.

Final thoughts

If you’ve been focusing on boosting your immune system without looking at your gut, it might be time to shift gears.

A healthy gut creates a balanced, resilient immune system – one that can defend you from infection and avoid unnecessary inflammation. Whether you’re getting sick all the time, struggling with allergies or autoimmune issues, or just want to feel stronger – start with your gut.

Need help decoding your bloods or getting to the root of poor immunity?

I’d love to support you with personalised testing, treatment and care.

Hit the button below to find out how we can strengthen your gut–immune connection from the inside out.

Blog author: Talitha

I specialise in gut health (IBS, IBD, microbiome testing), women's health (preconception, fertility, hormone balance), and mental health (depression, stress, anxiety). I am a degree- qualified naturopath who LOVES helping people transform their health stories!!