How Fall Allergens Affect Inflammation and Autoimmune Conditions
- Dr. Teri Jaklin ND, IFMCP
- Sep 5
- 4 min read
As the summer begins to turn to fall, something different is floating around—a surge in environmental allergens like ragweed, mold spores, and leaf dust. Even if you're not sneezing or wiping a constant drip from your nose, these airborne antigens can aggravate inflammation and trigger autoimmune symptoms, especially for people living with chronic conditions like MS (multiple sclerosis), RA (rheumatoid arthritis), and AS (ankylosing spondylitis) . Even other generally inflammatory states can be aggravated - everything from inflammatory bowel stuff to depression.
Since this impacts almost all of us, let’s explore how it works—and more importantly, what you can do about it.
🦠 What Are Fall Allergens and Why Do They Matter?
Fall is peak season for:
Ragweed pollen
Mold spores from damp leaves
Dust stirred up by dry, windy weather
Particles from wildfire smoke in many areas this year!
These allergens are antigens—substances your immune system identifies as foreign invaders. For most people, they may cause mild seasonal allergies. But if you’re living with an autoimmune disease, your immune system is already dysregulated. Add in a spike of antigens from the environment, and your immune system can go from cautious to chaotic.
🔥 Autoimmunity and Inflammation: A Delicate Balance
Autoimmune conditions like MS, RA, and AS involve an immune system that’s already on high alert—mistaking the body’s own tissues for threats.
When extra environmental antigens enter the mix, they can:
Overwhelm immune tolerance
Increase systemic inflammation
Aggravate neurological or joint-related symptoms
Trigger fatigue, brain fog, and digestive distress
This can happen even without any typical allergy symptoms, making it harder to identify the cause of that “flare-y” feeling.
🦰 The Lung–Gut Connection: Breathing in, Flare Up
In Traditional Chinese Medicine (a foundation of Naturopathic Medicine), the lungs and large intestine are connected systems. Western research is now confirming that the gut-lung axis plays a central role in immune function.
Here’s how fall allergens play into it:
You breathe in mold spores or pollen or smoke.
The immune system reacts—especially in the lungs.
This response communicates with the gut lining.
Gut inflammation rises, impacting digestion, immune balance, and neurological function.
The result? A whole-body inflammatory response that can affect your symptoms, energy levels, mood, and even your mobility.
🧠 Why Fall Can Worsen Inflammation and Autoimmune Symptoms
If you've noticed you feel “off” in the fall—slower, stiffer, foggier—there’s likely a connection to what’s in the air.
Common fall-triggered symptoms in autoimmune conditions:
Fatigue and energy crashes
Muscle stiffness or joint pain
Increased brain fog or mood shifts
Digestive changes (bloating, constipation, gut discomfort)
Sleep disturbances
These symptoms may come on gradually, and you may not even realize they correlate with your environment. But paying attention can help you take action before they become a full-blown flare.
✅ How to Support Your Immune System During Fall Allergy Season
Whether or not you experience classic allergies, your body may still be reacting to increased antigenic burden. Here are some strategies to reduce inflammation and support immune balance this season.
1. Prioritize Gut Health to Regulate Immune Function
Your gut is the command center of your immune system. When it’s inflamed or imbalanced, your entire body becomes more reactive.
Support your gut this fall with:
Warm, easy-to-digest meals (soups, cooked veggies, bone broth)
Anti-inflammatory foods (ginger, turmeric, steamed leafy greens, flaxseed)
Probiotic-rich foods like sauerkraut, kimchi, or non-dairy kefir
Reduce or avoid refined sugar, simple carbohydrates - especially gluten-free baked goods, dairy, and ultra-processed foods
Pro Tip: If you suspect leaky gut or deeper dysbiosis, it may be time for a custom plan. (We can work on that together.)
2. Clean Up Your Indoor Air (Where You Spend 90% of Your Time)
Airborne allergens don’t stop at the front door. They settle in carpets, furniture, and air ducts.
To reduce indoor antigen exposure:
Use a HEPA air purifier in your bedroom, home office or main living space
Crack windows open daily for at least 10–15 minutes (not when wildfire smoke is about)
Vacuum with a HEPA filter and wet mop floors regularly
Remove shoes at the door
If you’re feeling sinus congestion, unexplained fatigue, or brain fog that doesn't lift, air quality might be a hidden trigger.
3. Support Your Lung–Large Intestine Axis
Fall is a great time to tune in to the rhythms of your respiratory and digestive systems.
Try these daily practices:
Diaphragmatic breathing (belly breathing)
Gentle movement outdoors (walking, yoga, tai chi)
Stay hydrated to support mucosal membranes
Use a netti pot or nasal lavage daily
Use your castor oil pack on your abdomen 30-60 mins per day
4. If You’re Struggling—Let’s Make a Plan
Sometimes your system needs more than a therapeutic self-care tune up. If you're experiencing heightened reactivity or inflammation this season, I’m here to help you:
Assess your current inflammatory load
Support your gut, detox, and immune pathways
Build a personalized fall health strategy
Whether you’re living with MS, RA, AS, or any other health condition, we can get ahead of the curve and reduce seasonal flares before they escalate.
🧘♀️ Final Thought: You’re Not Overreacting—Your Immune System Might Be
If your symptoms feel more intense this time of year, it’s not just in your head. Your body is likely responding to a very real increase in antigenic stress.
But the great news is, you’re not powerless. By supporting your gut, lungs, and nervous system, you can create a calmer internal environment—even when the air outside is anything but.
🌿 Here's to feeling strong and steady through the season.
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