How to Get Your Microbiome Ready for Allergy Season

The Seed Digest

• Seasonal allergies can have many causes. Genetics, age, environment, and microbiome health can all affect the severity of symptoms.
• Are your allergies getting worse? It could be due to a mix of internal and external factors (hello, global warming). The microbiome of your gut, nose, and lungs may also play a sneaky role. 

Once spring hits and seasonal allergies flare, you might blame your scratchy eyes and stuffy nose on your neighborhood’s oak trees and ragweed. But your outdoor environment is just one part of the equation. Your ecosystems within—that is, your gut, nasal, and lung microbiomes—influence seasonal sniffles too. 

Here’s how the microbiomes of your body might affect your allergy risk and what you can do to ease symptoms. Plus, why climate change’s impacts on allergies are nothing to sneeze at.

Why You Suffer From Seasonal Allergies

Seasonal allergies (allergic rhinitis) occur when your immune system overreacts to airborne allergens, often pollen from trees, grasses, and weeds. 

When inhaled, these pollen particles land on the mucous membranes of the nose, eyes, and throat. Some people’s immune systems mistakenly identify them as harmful invaders and release immunoglobulin E (IgE) antibodies to fight them off.¹

These antibodies are safe for the body in low amounts. But, after repetitive exposure, they cause a cascade of uncomfortable localized symptoms, including sneezing, runny nose, itchy eyes, and congestion.

Some people breeze through allergy season without a sniffle, thanks to their genetics. Their upbringing likely plays a role, too. The hygiene hypothesis suggests that exposure to certain microorganisms early in life can help prevent allergies later. Exhibit A: Living in a farm environment during childhood has been shown to protect against allergy development.^2,3,4,5

Age also matters, to an extent. Seasonal allergies often kick in during childhood.⁶ However, shifts in environment, immune function, and microbial health can also trigger allergies later in life.^7,8

How the Microbiome Influences Allergies 

Seasonal allergies aren’t just about pollen. The microbiomes of the body—particularly in the gut, nasal passages, and lungs—may play a role in their progression.

Gut Microbiome

The gut microbiome and its compendium of bacteria, viruses, and fungi play a supporting role in your body’s immune responses. These microbiota are in constant communication with your immune system through a variety of pathways. 

When in a state of balance, the gut microbiome helps to prevent overreactions to harmless substances like pollen. It does so by balancing the activities of certain immune cells (Th1 and Th2), regulating the production and breakdown of histamines, and facilitating “cross-talk” between your intestinal and immune cells.^9,10,11 

The gut microbiome also acts as a security system for the rest of your body. When functioning properly, it maintains a tight intestinal barrier that prevents harmful substances from leaving the gut and entering the bloodstream. When compromised, the gut barrier may allow more irritants to pass through, potentially triggering an immune response and exacerbating allergies.¹² ​

Certain gut bacteria also produce short-chain fatty acids (SCFAs) like butyrate and acetate, which can help provide energy to immune cells, contribute to intestinal barrier integrity, and reduce inflammation associated with allergic reactions.¹³

It is now widely accepted that when your gut microbial communities are in a state of imbalance (dysbiosis), it can make you more susceptible to allergic reactions (as well as other conditions like autoimmune disorders, asthma, and inflammatory bowel disease).^13,14

Nasal Microbiome

Your nasal passageways are home to more than just snot. They’re teeming with bacteria that form a barrier from the germs, pollution, and other irritants you might breathe in daily. 

In times of health, nasal microbiota outcompete pathogens and keep them from traveling deeper into the respiratory tract.¹⁸ However, certain bacteria in the nose may be linked to increased nasal inflammation and allergy risk.¹⁹

One 2024 study found that children with allergic rhinitis tended to have higher levels of Staphylococcus bacteria in their nasal microbiomes than non-allergic kids.²⁰ Adults with allergies have also been shown to have greater amounts of Staphylococcus bacteria in their noses.²¹ 

These are early findings, and more research is needed before we can definitively say that any type(s) of nasal bacteria directly influence allergy symptoms.

Lung Microbiome

The lungs used to be considered “sterile” (free of microorganisms) in healthy states. However, unlocks in microbiome sequencing have revealed that the lungs do contain bacteria, viruses, and fungi, just in lower quantities than other organs.²² 

Your airways house bacteria like Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, which can affect health and disease risk. Namely, an increase in Proteobacteria in the lungs has been associated with allergies.^22,23

The lung microbiome tends to share characteristics with the oral microbiome, as material “migrates” from one to the other.²² Preliminary research also shows that the lung microbiome may share immunological functions with the gut.²³

Aerobiome

The air you breathe carries its own invisible hitchhikers. The aerobiome is made of bacteria, fungi, viruses, spores, and—you guessed it—pollen that it picks up from soil, vegetation, bodies of water, and human activities. The exact makeup of the aerobiome depends on factors like land use, vegetation cover, and pollution levels.^24,25,26 

Areas with diverse vegetation tend to have a more varied aerobiome, impacting the types and quantities of allergens present. In the spring, allergenic pollen released from plants like grasses and oak, maple, and birch trees can make up a major component of the aerobiome—hence why a trip to the park may set off your symptoms.²⁷ 

Air pollution can influence the structure and function of the aerobiome, too. According to fascinating ongoing research, airborne pollutants like particulate matter (PM) and nitrogen dioxide (NO₂) can make pollen more “allergenic,” or likely to cause an allergic reaction.²⁸

These pollutants—which can be emitted by gas cars, power plants, and even wildfires—alter the chemical composition of pollen grains, damaging their surface and causing them to release more pesky allergens into the air. 

Why Your Allergies Are Getting Worse

If your allergies have been worse than usual lately, you’re not alone. It’s tough to track if seasonal allergies are getting more severe across the board since most symptoms don’t result in emergency room visits or medical care.²⁹ 

However, there is a consensus that climate change is making allergy season last longer. With spring temperatures rising due to human-caused greenhouse gas emissions, some plants are producing pollen earlier in the year. Meanwhile, fall temperatures are also warmer, extending the length of the growing season for plants like ragweed.³⁰ Between 1995 and 2021, ragweed pollen season across the U.S. and Canada lasted 1–3.5 weeks longer on average.³¹

At the same time, rising carbon dioxide concentrations in the atmosphere are also fueling allergens. Higher levels of CO₂ emissions and air pollutants can increase pollen production in plants, specifically ragweed and grasses.³² Many climate models predict that pollen production will continue to increase as the planet warms—potentially doubling by the end of this century.³³

5 Tips for Allergy Relief

While there is no “cure” for seasonal allergies, there are ways to ease symptoms—some of which tap directly into your body’s microbial defenses. Follow these tips to keep sniffles to a minimum this (seemingly infinite) allergy season and beyond:

1. Minimize your exposure. 

Allergy symptoms tend to be worse on dry, windy days when pollen levels are high and subside when rainy weather washes pollen out of the air. Check your area’s pollen forecast and, on high-pollen days, stay indoors and keep your windows shut. If you’re spending time outside, shower and change your clothes once home to prevent prolonged exposure. Using a HEPA filter in your home and car may also help reduce the amount of allergens you’re exposed to.^30,34 

2. Tend to your gut microbiome with probiotics. 

Reminder: A healthy gut microbiome can help regulate immune responses and reduce allergy severity. You can start to build gut diversity and resilience by eating a variety of fiber-rich plant foods. Research suggests that foods containing the flavonoid quercetin (such as onions, apples, grapes, and berries) may be especially effective at minimizing allergy symptoms.^35,36

Probiotics can also be a part of your game plan. Certain probiotic bacteria appear to regulate immune response and curb the production of inflammatory cytokines—signaling molecules produced by cells of the immune system that promote inflammation.³⁷ In turn, they’ve been shown to significantly reduce nasal symptoms and improve quality of life during peak hay fever season, per a 2016 systematic review and meta-analysis.³⁸ 

For example, certain Lactobacillus strains have been found to decrease allergic rhinitis symptoms such as congestion, itching, and sneezing.³⁹

3. Keep stress in check. 

Not only can chronic stress directly aggravate allergic conditions, but it can also disrupt the gut via the gut-brain axis, a two-way telephone line between the gut and nervous system.⁴⁰ And, as shown, imbalances in the gut ecosystem can further exacerbate allergies. Bake in self-care practices like diaphragmatic breathing, yoga, and journaling.

4. Try nasal irrigation. 

After being outdoors on high-pollen days, consider using a nasal irrigation device to help flush irritating allergens from nasal passageways with saline water. Make sure to use water that’s distilled, sterile, or previously boiled.⁴¹

5. Chat with your doctor.

Depending on your symptoms and individual needs, your healthcare provider may recommend an over-the-counter or prescription medication for allergies. 

Frequently Asked Questions (FAQs)

• How can I get rid of allergies? You can’t, but you can ease their symptoms by protecting your gut microbiome with probiotics and fiber-rich foods, reducing the amount of time you spend around your triggers, keeping your nasal passageways clear, and consulting your doctor if needed. 
• Are allergies genetic? Yes, to an extent. People with a family history of allergies have a higher risk of developing them. That said, your specific triggers may shift depending on your environment.⁴² 
• What causes allergies? Allergies are complex. Genetics, age, and the environment you grew up in vs. the environment you now spend time in can all affect your risk. Imbalances in the gut, lung, and nasal microbiomes may also contribute to allergies, though we need more research before we can say exactly how. And a final PSA: Climate change is making allergy season longer, and it will likely continue to do so as long as greenhouse gases continue to accumulate in the atmosphere. 

The Key Insight

It’s not in your head: Allergy season is getting longer and more severe due in part to climate change and air pollution. The microbiomes of your body can help support your immune system wage defense against pesky pollutants. Tend to your microbial health and support efforts to combat climate change to help ease symptoms now and down the road.