Autoimmunity doesn’t begin with symptoms or a blood test. It unfolds quietly, often over years or even decades, long before a symptom is felt or a diagnosis made. By understanding what drives this process, we can often change the outcome.
Autoimmune diseases are increasing at an alarming rate. We know there is a genetic predisposition involved, and we do have better lab tests, but neither can account for a nearly 20 percent increase yearly. Something else is happening. Or many things, simultaneously.
Ultimately, for autoimmune as well as for most chronic diseases, the root cause is the same. We are asking our biology to function in an environment it was not designed for. Simultaneously, we deprive our biology of the tools to adapt to and survive our environment.
The environment and our lifestyle choices both contribute to the chronic diseases that are all too common and are affecting younger and younger people. Processed food, toxic exposure, chronic stress, poor sleep, lack of movement and connection, reduced microbial diversity, the list goes on. In fact, much about our modern life makes it hard to stay healthy, and ill health often starts with our immune system staying overactivated.
Life Hits Hardest in the Gut
If there’s one place where modern life hits hardest, it’s the gut, the home and school of the immune system.
Your gut is not just a digestive tube. It’s an immune organ, a sensory organ, another brain, and home to trillions of bacteria that are trying to protect and heal you. Young immune cells learn discernment here. A healthy microbiome helps maintain a thick, protective mucus layer, lining the intestines. This barrier is critical to a healthy gut, immune system, and brain.
But when the microbiome becomes imbalanced – through poor diet, antibiotics, toxins, stress, lack of plant fiber diversity, or just our modern life – that barrier begins to weaken. If the nutrients that sustain and feed the microbiome are not provided, it can’t maintain the barrier, that mucus layer that keeps the contents of the gut separate from the rest of us.
When the mucus barrier fails, tiny molecules and particles that should stay inside the gut start slipping out of the gut. Your immune system notices immediately. That’s its job. It asks, “Why is this here? This doesn’t belong here.” And it reacts.
First, this response is appropriate. But if this continues day after day, month after month, the immune system remains activated. And a constantly activated immune system becomes dysregulated. If the underlying causes are not addressed, the system can become increasingly reactive over time.
At this point, some people start to experience symptoms. Food sensitivities may start or escalate. GI symptoms develop or increase. In general, chronic low-grade inflammation makes us feel off, just not right. Brain fog and irritability are common.
Early, subtle signals matter – fatigue that doesn’t resolve, new sensitivities, changes in digestion, sleep disruption, or mood shifts. These are not random or disconnected issues; they are often early expressions of imbalance. Learning to recognize and respond to these signals gives us a window of opportunity to intervene before deeper dysfunction takes hold.
Healing, then, is less about fighting the body and more about creating the conditions for it to recalibrate. The immune system is not broken – it is responding to the inputs it receives. When we begin to change those inputs consistently, the system can shift. This requires patience and curiosity rather than urgency and fear. Small, sustained changes – how we eat, sleep, move, think, and connect – compound over time. And while there is no one-size-fits-all approach, there is a common principle: when we align our daily lives more closely with what our biology needs, the body has an extraordinary capacity to restore balance.
Immune Tolerance
If the immune system stays stuck in overactivation, the threshold that determines “this is a problem” gets lower until, eventually, the immune system starts reacting indiscriminately. At that point, discerning self from non-self is no longer the immune system’s top priority.
When that discernment, called immune tolerance, starts to fail, we have a problem. Because once tolerance is lost, the immune system doesn’t just react to food proteins or bacterial fragments. It can start reacting to your own tissues, as if you are the threat. And that is the start of an autoimmune disease.
Thyroid. Joints. Skin. Brain. In time, this is diagnosed as Hashimoto’s, rheumatoid arthritis, psoriasis, and multiple sclerosis. The list is long. Each type of tissue involved has its own named disease.
Chronic immune overactivation, especially in folks with a genetic predisposition, is the underlying cause of autoimmune disease. But instead of asking, “What drug matches this disease?” Functional medicine asks, “Why did this happen to this person, now?” We look at gut health, microbiome diversity, nutritional status, toxic burden, stress physiology, sleep, connection, and all that goes into living a fulfilling life – because these are the inputs shaping immune behavior.
Sometimes autoimmune disease starts differently, starts much faster. Infections and toxic exposures, anything that activates or confuses the immune system can contribute. Viral infections, medications, environmental toxins like mold or pesticides, toxic smoke, and heavy metals can all trigger loss of immune tolerance and autoimmunity. As can severe or chronic stress, which shifts immune balance. It is not uncommon to develop symptoms of rheumatoid arthritis six months or so following severe emotional trauma. Sleep deprivation impairs immune regulation and repair.
Psychoneuroimmunology
Grief, trauma, chronic overwhelm – these are not just emotional experiences. They are biological events that shape immune behavior. This is what psychoneuroimmunology is about – the interplay between your mind, your two brains and nervous system, and your immune system. You cannot separate them.
Here’s the empowering part:
This process is modifiable. Not always reversible – but often improvable. And sometimes dramatically so.
To reduce autoimmune risk, start with the gut. Clean up the diet (less processed, more real food). Increase plant diversity; colorful plant foods are required to feed the microbiome. Prioritize sleep, move more, and spend time in nature. Minimize toxin exposures. Address stress at all levels-not just intellectually but emotionally, spiritually, and in your body. Nurture connections and gratitude.
If you have a diagnosed autoimmune disease, please learn about the benefits of low-dose naltrexone, the only medical treatment I am aware of that safely rebalances a part of the underlying immune system’s dysfunction.
Nutrition, sleep, movement…all this lifestyle advice is not organ- or disease-specific. All our biology, our physiology, is built on the foundation of our nutrition and our lifestyle choices. Genetic potential is shaped by context; genes are expressed or silenced within the environment we create.
For good or bad, the choice is ours to make every day.
Tamara Sachs, MD, is a Mount Sinai–trained physician who completed her Internal Medicine training in New Haven, CT. She began her career in molecular biology, followed by years in emergency and primary care medicine. Since 2003, she has focused exclusively on Functional Medicine, seeing patients and lecturing frequently.
Functional Medicine & Integrative Care LLC. 1 Booth House Lane, New Milford, CT 06776. Call 860.354.3304, email: mail@tsachsmd.com, and visit: tsachsmd.com to learn more.
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