Why the Microbiome Matters for Autoimmune Health

Why the Microbiome Matters for Autoimmune Health [Watch the full conversation: YT Link]

How Gut Health Connects the Dots Between Infections, Inflammation, and Wellbeing

When it comes to autoimmune health, the microbiome is the missing link many of us have been searching for. Recently, I (Dr. Amigues) had the privilege of sitting down with infectious disease specialist Dr. Coulter for a fascinating conversation about how the trillions of microorganisms that live within and around us shape our immunity, inflammation, and risk for chronic disease.

A Meeting of Minds: Rheumatology Meets Infectious Disease

Both rheumatology and infectious disease have long focused on the immune system—how it defends, how it sometimes overreacts, and how it can lose its way in autoimmune conditions. But the microbiome is now emerging as the bridge connecting infection, inflammation, and autoimmunity. It’s not just a trend—it’s a revolution in how we understand and support health.

What Exactly Is the Microbiome?

The microbiome is the vast, invisible world of bacteria, fungi, viruses, and other microbes living in and on our bodies—especially in the gut, but also on the skin, in the mouth, lungs, and beyond. These microbes aren’t just along for the ride; they help us digest food, regulate our immune system, and produce key molecules that affect metabolism, hormones, and even mood.Think of your microbiome as a thriving ecosystem: when it’s diverse and healthy, you’re more resilient. When it’s depleted or out of balance, inflammation can take hold.

The Gut–Joint Connection

Gut health and joint health are more connected than most people realize. Conditions like IBD-related arthritis and ankylosing spondylitis show how gut inflammation can drive joint inflammation. Research (including at NYU) has shown that certain bacterial imbalances in the gut can actually trigger or worsen autoimmune responses. The gut is an immune “training ground”—and when its microbial balance is off, the immune system can lose its sense of what’s “self” and what’s “threat.”

How Modern Life Disrupts Our Microbial World

Modern farming and widespread antibiotic use have transformed our microbial landscape. Dr. Coulter shared an “aha” moment: the same bacteria being lost from our soils are also crucial for our bodies. Industrial agriculture—through tilling, fertilizers, and pesticides—destroys soil diversity, which then affects the diversity of the foods we eat and, ultimately, our own gut microbiome. The health of our planet’s soil mirrors the health of our own bodies.

The Antibiotic Balancing Act

Antibiotics are life-saving, but they’re also powerful disruptors of the microbiome. Every course not only wipes out infection, but also reduces helpful gut bacteria that protect us. The new best practice? Shorter, targeted antibiotic courses—enough to treat infection, but gentle on the gut.

How to Heal the Gut—Naturally

Restoring gut health starts with food, not pills. Fermented and fiber-rich foods help repopulate beneficial bacteria and support a healthy gut ecosystem. Some of the best natural probiotics and prebiotics include:

• Sauerkraut, kimchi, and fermented pickles

• Kombucha and miso

• Yogurt and kefir

• Fermented salsas like pico de gallo These foods deliver both the good bacteria and the fiber they feed on—helping your gut flourish from the inside out.

Are We Too Clean?

Our modern obsession with sterility may actually be harming our immune systems. Kids who grow up on farms or spend more time in nature have lower rates of asthma and eczema. Exposure to diverse microbes—through soil, animals, and natural environments—helps “train” the immune system to respond appropriately. While hygiene is important (especially in healthcare), overuse of antibacterial products can deprive us of beneficial microbial exposures.

Food, Culture, and Connection

How we eat matters as much as what we eat. Cultures that prioritize shared meals, slow eating, and whole foods often have fewer inflammatory diseases. In contrast, highly processed, rushed meals deprive our microbiome—and our minds—of nourishment. Simple, local, seasonal, and colorful foods still hold the key to a thriving gut and a resilient body.

The Next Frontier: The Microbiome in Post-Infectious Syndromes

We also discussed post-infectious syndromes like post-COVID and chronic Lyme. These conditions are characterized by lingering symptoms—fatigue, brain fog, pain—even after the initial infection is gone. The emerging view: the microbiome and its relationship with immune regulation may play a key role in why some people recover quickly and others don’t.

The Takeaway: Protecting Your Microbiome, Protecting Your Health

The microbiome isn’t just a buzzword—it’s central to understanding autoimmune disease, recovery from infection, and lifelong health.

Protecting your microbiome means:

• Using antibiotics only when necessary, and as briefly as possible

• Eating a diverse, minimally processed, fiber-rich diet

• Embracing nature and microbial diversity—get outside, garden, play in the dirt!

• Slowing down for meals and connection—nourishing both gut and soul

Just as the soil needs care to sustain the planet, your microbiome needs care to sustain your body. Both are living systems that thrive on diversity, balance, and respect for the natural world.

Ready to support your gut—and your health? Start with one small change today.

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