Autoimmune Flares May Start in the Gut

Why Your Autoimmune Flares May Start in the Gut

Have you ever had days when your body just doesn’t feel right?

Maybe your joints hurt. Or your skin gets red and itchy. Maybe you feel so tired that even getting out of bed is hard. These symptoms may be signs of something called an autoimmune flare — a time when your immune system gets confused and attacks parts of your own body.

It might sound strange, but many of these flares don’t start in your muscles, your skin, or even your blood.
They start in your gut.

Let’s talk about what that means — and why taking care of your gut may be one of the most important things you can do for your health.

Your Gut: The Immune System’s Secret Headquarters

Your gut is more than just a place where food is digested. It’s like a busy city filled with tiny workers — mostly bacteria — who help your body in many important ways. These good bacteria help you:

• Break down food

• Make vitamins

• Keep harmful germs away

• Train your immune system to know what’s dangerous and what’s not

In fact, about 70% of your immune system lives in your gut. That’s more than anywhere else in your body! So if your gut is unhappy, your immune system can get confused.

Imagine if a security team in a building gets bad training. They might start chasing after the wrong people, even your friends. That’s kind of what happens in autoimmune disease — your immune system starts attacking your own body by mistake.

What Is Leaky Gut — And Why Does It Matter?

Your gut has a special lining that acts like a tight filter. It lets in the good stuff (like nutrients from food) and keeps out the bad stuff (like bacteria, toxins, and undigested food particles).

But when the gut lining gets damaged, it becomes like a leaky bucket — stuff that’s not supposed to escape starts leaking into your bloodstream. This is called leaky gut or intestinal permeability.

Your immune system notices this and goes into attack mode.
The problem is: over time, it may start attacking your own tissues too — like your joints, thyroid, brain, or skin.

This is how many autoimmune conditions begin or get worse.

What Causes Leaky Gut?

There are several things that can damage the lining of your gut, including:

• Highly processed foods (especially sugar, seed oils, and artificial additives)

• Food sensitivities (like gluten, dairy, soy, or corn)

• Chronic stress (stress hormones can weaken the gut lining)

• Antibiotics and other medications (they can kill off good bacteria)

• Infections (like candida, parasites, or harmful bacteria)

• Toxins from mold, pesticides, or heavy metals

You might not feel gut pain at all. But if you’re having joint pain, fatigue, rashes, or brain fog, your gut might still be the hidden cause.

Common Signs Your Gut Might Be Behind Your Autoimmune Flares

Even if your stomach feels okay, your gut could still be in trouble.
Look for signs like:

• Feeling puffy or inflamed

• Digestive problems (like gas, bloating, or constipation)

• Feeling tired all the time

• Skin issues like eczema or psoriasis

• Trouble focusing or remembering

• Food cravings (especially for sugar or carbs)

• Autoimmune conditions like Hashimoto’s, lupus, or rheumatoid arthritis that get worse suddenly

If these sound familiar, your gut may be asking for help.

How Functional Medicine Looks at the Gut-Autoimmune Connection

Unlike regular medicine that often just treats symptoms, Functional Medicine looks at the root cause.
Instead of just asking “What’s wrong with you?” we ask “Why is this happening in the first place?”

When it comes to autoimmune flares, one of the first places we look is the gut.

Functional medicine uses tools like:

• Stool testing to see what bacteria are living in your gut

• Food sensitivity testing

• Organic acids tests to check for gut imbalances

• Anti-inflammatory nutrition plans

• Targeted supplements to repair and support the gut lining

By healing the gut, many people see major changes in their autoimmune symptoms — fewer flares, more energy, less pain.

What You Can Do Today to Help Your Gut

You don’t have to wait to start feeling better. Here are a few easy steps you can begin right now:

1. Eat More Whole Foods

Think: vegetables, fruits, clean protein, healthy fats, and fiber-rich foods. These feed the good gut bacteria and calm inflammation.

2. Avoid Gut-Damaging Foods

Cut back on processed snacks, sugary drinks, fried foods, and anything that makes your symptoms worse.

3. Add Gut-Friendly Support

Try foods like bone broth, fermented veggies (like sauerkraut), and foods high in glutamine (like cabbage) to support healing.

4. Lower Your Stress

Stress affects your gut just as much as food. Simple things like deep breathing, gentle walks, or laughter can help more than you think.

5. Work with a Functional Medicine Coach

The gut is complex. You don’t have to figure it out alone. A functional medicine coach can help guide you, support you, and create a plan that’s just right for your body.

Ready to Feel Better? Let’s Start with Your Gut.

Autoimmune flares don’t happen out of nowhere. Your body is sending you signals — and the gut is often where those signals begin.

At Intentional Wellness, Inc., Shannon helps clients uncover the real reasons behind their autoimmune symptoms and teaches them how to calm the fire — starting with the gut.

Whether you’ve been diagnosed with an autoimmune disease or just suspect something’s not right, Shannon will guide you through a whole-body healing process using functional medicine tools and personal support.

Don’t wait for another flare to take action.

Sign up today for a Functional Medicine Coaching session with Shannon at Intentional Wellness, Inc.
Your gut — and your entire body — will thank you.