Always Congested? Your Microbiome Holds the Secrets to Better Breathing

Do you often find yourself struggling with a chronic stuffy nose? Is your nose constantly blocked, making it difficult to breathe? If this is you, you're one of a growing number of people who suffer from chronic sinus congestion. Sinus symptoms like sneezing or a runny nose are often the result of allergens or irritants in your home or environment. In this post, we will discuss the integrative and functional medicine approach to clearing sinus congestion, and what role your microbiome plays in your ability to breathe freely. We will explore the various causes of chronic nasal congestion and provide tips on how to get relief!

The most common cause is allergens

Whether you're stepping out into the park, cuddling with your dog, or fluffing your pillows at night, you're constantly exposed to potential allergens. Pet dander, pollen, those annoying dust bunnies—they're everywhere! And up to 30% of adults and 40% of children experience respiratory symptoms as a result (1).

But it's not the presence of these allergens that’s the problem—it’s actually how your immune system reacts to these potential triggers that are the difference between whether or not you develop symptoms.

Common allergens that irritate your sinuses around the ear, nose, and throat are things like:

  • Mold spores. Moist air and damp environments are the preferred places for mold, commonly found in basements, bathrooms, and other areas with low ventilation.
  • Pet dander. Our furry friends that share our spaces leave behind microscopic irritants that can cause nasal congestion.
  • Pollen, grass, or other seasonal plants are blooming. During the summer, spring, and fall, a variety of plants release tiny particles that can attach to your hair, skin, and clothing and cause sinus congestion.
  • Dust mites. Tiny creatures that thrive in warm, humid environments—like your bed! Symptoms include waking up with a stuffy nose or itchy eyes.

These are just some of the more common allergens that cause symptoms in nasal tissues. But, why then, do some people react so severely to allergens, and others seem to breeze through with nary a sniffle? The real answers may be hiding in your gut.

Read more: The Functional Medicine Guide to Seasonal Allergies

It's a microbes thing

Your microbiome, or the collection of beneficial bacteria that inhabit your gut, also regulates your immune system.

We often hear about this bacteria only in the gut, but every surface on your body is colonized by different types of beneficial bacteria. This includes internal systems like your gut, lungs, and nasal passages. And instead of causing sickness, these good microbes essentially “teach” your immune system how to tell the difference between harmful pathogens, and everyday items like foods, pet dander, or grass (2).

Because humans have never been able to completely avoid interaction with microorganisms, our immune system has had to learn which ones are harmful, and which ones aren't. Researchers have found that people with respiratory allergies have different gut bacteria than people who don’t experience allergies (3)

How does this process happen? Researchers and integrative practitioners alike are still working to fully understand this complex interaction, but evidence indicates that exposure—and not avoidance—is a crucial factor.

Shop high-quality, powerful probiotics.

Training your immune system

In modern times, our relationship with bacteria has changed. In that, we seem to try to avoid our microbial neighbors at all costs. Disinfecting wipes, hand sanitizer, and antibiotics are more commonplace now than ever before, but is that really a good thing?

All this sanitizing disrupts the microbiome and is the basis for what is commonly referred to as the ‘hygiene hypothesis’. This theory suggests that our push for cleanliness and reduced exposure to a diverse array of environmental microbes deprives our bodies of immune stimulation, therefore hindering this immune learning process results in an increased risk for allergic disease.

To support this hypothesis, your gut, lungs, and nasal passages all make up your microbiome, and studies have shown that disruption to that microbiota is linked to many chronic diseases (4). Several interesting studies have also provided support for the hygiene hypothesis. For example:

  • People who own indoor pets have been shown to have a lower incidence of allergic disease (5).
  • Children who grow up on farms are also less likely to have allergies (6).
  • Frequent antibiotic use is linked to reduced microbiome diversity (7)

Early-life experiences such as formula feeding vs. breast milk and c-section births also impact microbiome development (8,9).

Related: Healing Your Gut to Boost Immune Function

Want to learn more?

Histamine worsens the problem

Our microbiome is also responsible for producing histamine, which is the first chemical messenger that works to shuttle those pesky allergens out of the body. It’s histamines you can thank for the sniffling, sneezing, itchy eyes, and runny nose.

Histamine does play an important role in overall health, but just like inflammation—a certain amount is necessary but too much can be a problem. This is known as histamine intolerance.

Many microbes that reside in the human gut are capable of producing histamine because they make it from amino acids (specifically, histidine) present in the proteins you eat. The more of these histamine-making microbes you have, and the more histidine in your diet, the more histamine you can potentially produce in your gut. All this histamine manufactured by your microbiome can then be absorbed by different cells and sent around your body.

Basically, more histamine can mean worsening allergy symptoms.

Histamine intolerance can occur either when you’re producing a lot of histamine in your gut, or you have a deficiency in the enzyme required to properly break it down. Two types of beneficial bacteria—Bifidobacterium infantis and Saccharomyces boulardii—may help degrade histamine (10).

Read more: The Benefits of Quercetin and Other Natural Antihistamines

The gut-lung connection

Until relatively recently, it was believed the lungs were sterile, but now we know they harbor a very “distinct” kind of microbiome (11).

The gut and the respiratory system are obviously very different, but they are both made up of membrane-bound mucosal surfaces that harbor tiny but beneficial bacteria. Interestingly, inflammation tends to happen in both the gut and the lungs in people with chronic airway diseases (12). While we have a lot more information about the gut microbiome, due mostly to the simple ease of obtaining samples, there may be similar processes affecting microbial balance in the lungs as there is within the digestive tract. Similar to the intestinal microbiome, microbial communities likely have a major impact on the proper functioning of the lung and respiratory tissue.

As allergy season rolls around, it’s a good time to remember that the microbes that inhabit our body have a very important role to play and that our rigorous disinfecting doesn’t distinguish between harmful pathogens and beneficial bacteria. There may be a point that we need to consider the balance of healthy bacteria as a strategy worth protecting in our defense against environmental pathogens.
It may be likely that supporting a balanced immune response and reducing inflammation is the way to go for long-term success against allergies.

Browse: Functional allergy supplements.

Other underlying causes of chronic congestion

Chronic nasal congestion isn’t always caused by allergies. There are actually a number of underlying causes that can contribute to this problem.

Nasal polyps. These growths aren’t cancerous and can occur in the nose or sinuses. If large enough, they can physically obstruct the passages in your sinuses, which can make you feel like your nose is constantly blocked. It’s also not uncommon to have a diminished sense of smell or taste. Polyps are most likely to crop up in people who have allergies, asthma, or chronic sinus infections.

Pregnancy. Around 20 percent of pregnant women experience congestion or a stuffy nose, a condition called pregnancy rhinitis (13).

Low thyroid (hypothyroidism). Nasal congestion is a lesser-known symptom of hypothyroidism, a condition in which your body either doesn’t produce or can’t properly utilize thyroid-stimulating hormone (TSH).

Irritation. Vasomotor rhinitis tends to occur when your nasal passages are irritated by something in your environment. Think cigarette smoke, cleaning products, or dry air.

Related: The 7 Best Essential Oils to Relieve Children’s Allergy Symptoms

At-Home steps to improve allergies and congestion

  • Neti pot or nasal sprays. Gently flushing out irritants or allergens from your nasal passages can be a big relief for your sinuses. Then, provide some soothing support for the tissues inside your nose by running a humidifier or taking a hot shower with plenty of steam.
  • Eat pre and probiotic foods. Fiber, fermented foods, and probiotics can help recalibrate your microbiome and bring balance to your immune reactions.
  • Fuel a balanced immune response. Vitamin C, zinc, and other essential nutrients support a balanced immune response to allergens and other environmental invaders.
  • Heal your gut. Work with a functional provider to address any underlying infections, and focus on a nutrient-dense diet to support your microbiome.
  • Resolve underlying intestinal inflammation by getting tested for allergies or food sensitivities.

Read: Guide to Natural Antihistamines

Functional medicine for allergy treatment near me

So, what can you do to get relief from your allergies? The answer may be as simple as taking care of your microbiome. You can improve your symptoms by eating a balanced diet that includes plenty of probiotics and prebiotics and maintaining an overall healthy immune system. If you’re still struggling with allergy symptoms despite following these tips, it’s time to see a functional medicine doctor who can help. They can help you find the right treatment for you based on the specific allergens you are reacting to. With the right plan in place, you should start feeling better in no time!


  1. https://www.frontiersin.org/articles/10.3389/fcimb.2021.650893/
  2. https://clinicalmolecularallergy.biomedcentral.com/articles/10.1186/s12948-020-00120-x
  3. https://www.karger.com/Article/FullText/510536
  4. https://www.nature.com/articles/s41430-021-00991-6
  5. https://pubmed.ncbi.nlm.nih.gov/12190366
  6. https://pubmed.ncbi.nlm.nih.gov/22625206
  7. https://pubmed.ncbi.nlm.nih.gov/21233272
  8. https://www.nature.com/articles/s41598-020-72635-x
  9. https://www.frontiersin.org/articles/10.3389/fmicb.2020.02099/full
  10. https://journals.sagepub.com/doi/full/10.1177/1179552217752679
  11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765541/
  12. https://www.frontiersin.org/articles/10.3389/fimmu.2020.02144/full
  13. https://pubmed.ncbi.nlm.nih.gov/26365758/


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