Is Your Gut Messing with Your Immune System?

Here’s What You Need to Know About Digestion and Autoimmunity

These days, gut health is everywhere—and for good reason. More and more research (and real-life experience) shows that a happy gut doesn’t just help with digestion… it plays a huge role in immune health too.

If you're dealing with fatigue, skin flare-ups, constant bloating, joint or muscle pain, or those frustrating mystery symptoms no one seems to be able to explain—your gut might be trying to tell you something. Especially if you have an autoimmune condition or suspect something’s off with your immune system.

Let’s take a look at how gut health can impact immune function—and more importantly, what you can do to support both.

1. Leaky Gut: When the Barrier Breaks

You’ve probably heard the term “leaky gut.” It’s not just wellness-world hype—it’s a real thing.
Your gut lining is meant to be a strong but selective barrier. When it gets damaged (from things like stress, medications, processed foods, or infections), it can become too porous. That means undigested food particles, toxins, and bacteria can sneak into your bloodstream.

Your immune system sees these as intruders and launches an inflammatory response. Over time, this chronic immune activation can contribute to the development or worsening of autoimmune conditions.

2. Molecular Mimicry: When the Immune System Gets Confused

Some bacteria in your gut actually resemble your body’s own cells. So when your immune system attacks these bacteria, it can get confused—and start attacking your own tissues too.

For example, in rheumatoid arthritis, certain bacterial proteins mimic joint tissue. This may cause your immune system to go after your joints, mistaking them for foreign invaders.

3. Chronic Inflammation & Immune Overload

When your gut microbiome (the community of microbes in your digestive system) becomes imbalanced, your immune system can get stuck in “high alert” mode.

This constant state of inflammation disrupts immune tolerance—your body’s ability to know the difference between self and non-self. And to make matters worse, the beneficial bacteria that normally produce calming, anti-inflammatory compounds start to disappear.

The result? More inflammation, more immune confusion, and more risk for autoimmune flares.

4. T-Cell Imbalance: When the Immune System Goes Rogue

Your gut is home to a huge portion of your immune system—including immune cells like T-cells.

Regulatory T-cells (T-regs) are like the peacekeepers of your immune system. They help prevent the body from attacking itself. But when dysbiosis (gut imbalance) occurs, T-regs decrease while inflammatory cells like Th1 and Th17 rise.

This imbalance can tip your immune system into self-destructive mode. In autoimmune conditions like multiple sclerosis, for example, overactive Th17 cells may target nerve cells.

5. Missing Microbes, Missing Signals

Your beneficial gut bacteria do more than help you digest food—they also create powerful compounds like butyrate, which help regulate immune function and reduce inflammation.

When these good microbes are missing or out of balance, your body misses out on these protective signals. That leaves your immune system more likely to misfire.

Common Gut-Related Root Causes of Autoimmunity

Here are a few of the most frequent patterns I see in my practice:

• Low stomach acid (hypochlorhydria): This leads to poor digestion and sets the stage for bacterial overgrowth and inflammation.

• Sluggish motility: When the digestive system slows down, it can cause bloating, constipation, and contribute to SIBO (small intestinal bacterial overgrowth).

• Antibiotic overuse or extreme diets: These can wipe out beneficial microbes and reduce diversity—key to immune regulation.

• Environmental toxins, such as mould, pesticides, or other exposures, can damage the gut lining and trigger the release of inflammatory cytokines.

• Stress and trauma can both disrupt gut-brain signalling, impairing digestion, immune balance, and nervous system regulation.

My Story: From Autoimmune Chaos to Gut-Rooted Healing

Before I ever became a practitioner, I was a patient—dealing with the confusion and frustration of a body that felt like it was working against me.

I was diagnosed with Juvenile Rheumatoid Arthritis as a child, and later with Rheumatoid Arthritis and Lupus. I spent years on a carousel of medications, flares, and symptoms that didn’t make sense.

No one ever mentioned my gut.
No one warned me how repeated rounds of antibiotics could wipe out the diversity of my microbiome.
And no one talked about how the medications I was given could impact my hormones, either.

As I got older, I started struggling with hormonal symptoms too—things that were dismissed or brushed off as “just stress.” But the truth was, my immune system, my gut, and my hormones were all speaking the same language… I just didn’t know how to listen yet.

Learning about the gut-autoimmune connection changed everything for me.
It gave me a roadmap—and hope. And now, it's what I help others with every day.

At-Home Gut Check: 3 Gentle Ways to Tune In

Here are a few simple tools you can try at home to start listening to your gut:

1. The Lemon Water Test

Drink a glass of warm water with fresh lemon juice 10–15 minutes before meals.
If your digestion feels smoother (less bloating, more regularity), it may be a sign that your stomach acid is on the low side and could use support.

2. Track Bloating + Stool Patterns

Over 3 days, jot down:

• When you feel bloated (after meals? or late afternoon?)

• How often do you go?

• What your stool looks like (you can use the Bristol Stool Chart)

This can help identify whether sluggish motility or gut dysbiosis may be present.

3. Tongue Check

Look at your tongue first thing in the morning:

• A white coating? May indicate fungal or microbial overgrowth.

• Cracks? This could suggest dehydration or mineral deficiencies.

These aren’t diagnoses—but they are helpful clues you can bring into a deeper conversation with a practitioner.

Autoimmune Conditions Often Tied to Gut Imbalance:

Hashimoto’s Thyroiditis
Rheumatoid Arthritis
Lupus
Psoriasis
Type 1 Diabetes
Multiple Sclerosis
Crohn’s Disease & Ulcerative Colitis

What You Can Do to Support Gut + Immune Health

The good news: your gut is incredibly responsive to care. Healing doesn’t have to be extreme—it just takes consistency, patience, and a thoughtful plan.

Here are some gentle ways to begin:

• Focus on a whole-food, anti-inflammatory diet

• Avoid refined sugar and ultra-processed foods

• Support digestion (slow down, chew well, consider bitters or enzymes)

• Manage stress—your gut feels it

• Prioritize consistent, restorative sleep

• Move your body in ways that feel nourishing

• Work with a practitioner to explore deeper testing or targeted supplementation

Want Help Figuring It Out?

If this sounds like your story—and you’re ready to explore the gut-immune connection—I’d love to support you.

Together, we can build a personalized plan to reduce inflammation, support digestion, and help your immune system find more balance.

Kathi
Wholemade Nutrition & Wellness