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What’s Wreaking Your Gut? 3 Causes of Bacterial Dysbiosis

bacterial dysbiosis
September 8, 2025

Living with autoimmune disease can feel like stepping into a plot with zero foreshadowing. Suddenly, your immune system swings from defender to saboteur, leaving you dealing with fatigue, joint pain, raging inflammation, and a symptom list longer than a grocery store receipt. Truth is, the body doesn’t rebel for no reason, and that reason often boils down to the state of your gut flora. At Dr. Autoimmune, we’re pulling back the curtain on the real root of autoimmune disease, aka bacterial dysbiosis, and how it can nudge your immune system past the tipping point.

@drautoimmune #dysbiosis is caused by #diet #antibiotics #trauma - #autoimmunedisease ♬ original sound - drautoimmune

Why Your Gut Might be Ground Zero for Autoimmune Disease

What is dysbiosis? Simply put, bacterial dysbiosis means that the gut microbiome has become unbalanced. The protective, friendly species go MIA, and the intrusive, disease-triggering ones move in and multiply. That power shift stirs up inflammation, production of leaky gut proteins, and a misdirected immune response that can mistake your own body for the intruder.

What are the Causes of Bacterial Dysbiosis?

There are several culprits behind gut imbalances and autoimmunity, and we want to dive deeper into 3 of them:

1. Standard American Diet (SAD)

SAD diet

It's right there in the name: the way most Americans eat creates conditions for gut misery. The SAD diet is typically loaded with processed foods, refined carbohydrates, and artificial chemicals and preservatives, which feed the wrong types of gut bacteria instead of the good bacteria that keep your immune function in check. Eventually, this imbalance results in inflammation and autoimmune disease.

Gut health tip: Roll your cart past the flashy boxes and load up on whole foods instead (rainbow veggies, high-fiber greens, smart fats like avocado and olive oil, and fermented foods like sauerkraut and kefir that fortify your microbiome.

2. Early Exposure to Antibiotics

Sometimes antibiotics rescue us from serious infections, frequent colds, or preventable cavities. The problem? They don’t discriminate between good and harmful gut bacteria. Taking antibiotics early in life levels the microbiome; it’s like bulldozing a thriving garden and expecting it to grow back exactly the same as it was before. But it won’t. Instead, antibiotic use can set the stage for bad bacteria to dominate, the gut lining to thin, and an immune system that can suddenly overreact to harmless food.

Gut health tip: steering clear of unnecessary antibiotics is a win for your microbiome. If you need them, pairing with a quality probiotic can help your gut bounce back faster.

3. Traumatic Experiences

This may surprise you, but childhood emotional trauma can literally change your gut microbiome. Trauma activates the autonomic nervous system, sending ripples of change through your digestive tract. A persistent stress response leads to gut inflammation and tilts the microbiome toward dysbiosis. It’s important to view adverse childhood experiences not only through a psychiatric lens but also as a potent, underappreciated risk factor for autoimmune disease decades later.

Gut health tip: A food plan alone won’t heal you if the emotional and mental health remain unaddressed. Professional therapy, consistent mindfulness, and deliberate nervous system regulation can help you restore the entire web of mind and gut.

Next Steps

If you’re battling an autoimmune condition and dysbiosis, the first question you need to ask is: What is going on in my gut? Understanding the root causes of bacterial overgrowth can help you:

30 day reset program

  • Improve digestion
  • Reduce inflammation
  • Rebalance your immune system
  • Finally feel like yourself again

We offer a 30-Day DIY Reset Program to help people with bacterial dysbiosis achieve symptom improvement through diet, lifestyle changes, supplements, and more. Learn more about the Dr. Autoimmune online program and take control of your gut health today!

Disclaimer: This blog does not constitute medical advice and is for informational purposes only. Always seek the opinion of your doctor or other qualified health providers with any questions regarding a medical condition.

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