The Nasal Microbiome: Why Your Sinus Health Starts with Bacteria

When people think about the microbiome, they almost always think about the gut. Probiotics, fermented foods, fiber — the gut microbiome has dominated health conversations for a decade. But there's another microbial ecosystem that's arguably just as important for your daily health, and almost nobody is talking about it: the nasal microbiome.

Your nose is not just a passive air filter. It's a living ecosystem where hundreds of bacterial species compete, cooperate, and directly determine whether you stay healthy or develop sinusitis, respiratory infections, and even dangerous hospital-acquired infections. Two groundbreaking studies published in 2025 have finally given us an unprecedented look at this hidden world — and the findings are reshaping how scientists think about sinus bacteria health and infection prevention.

In this article, we'll break down what the nasal microbiome is, what these landmark studies found, which bacteria protect you (and which put you at risk), and how you can actively support a healthier nasal microbiome with practical, evidence-based strategies — including the role of nasal irrigation in maintaining microbial balance.

What Is the Nasal Microbiome?

The nasal microbiome refers to the entire community of microorganisms — bacteria, fungi, viruses, and archaea — that live inside your nasal passages and sinuses. Just like the gut has trillions of microbes that influence digestion and immunity, your nose has its own microbial ecosystem that serves as your body's first line of defense against airborne pathogens.

Every time you breathe, you inhale approximately 10,000 liters of air per day along with bacteria, viruses, allergens, dust, and pollution. Your nasal microbiome is what stands between those invaders and your lungs.

The Key Players in Your Nose

While hundreds of bacterial species can be found in the nose, research has consistently identified several dominant groups:

• Staphylococcus epidermidis — The most common skin bacterium, generally protective and associated with healthy nasal passages.
• Corynebacterium species — Abundant in healthy noses, these bacteria are associated with lower infection risk and may produce antimicrobial compounds.
• Dolosigranulum pigrum — A lesser-known species that recent research has identified as a key protector against pathogenic bacteria.
• Staphylococcus aureus — The most studied nasal pathogen, carried by about 30% of people. While often harmless, it can cause serious infections if it enters the bloodstream through wounds or surgical sites.
• Moraxella catarrhalis — Common in children, sometimes pathogenic but also associated with competitive exclusion of worse pathogens.

The balance between these populations — which species dominate, which are suppressed — determines your susceptibility to everything from common colds to life-threatening hospital infections.

The 2025 Sanger Institute Study: Largest-Ever Nasal Microbiome Analysis

In December 2025, researchers at the Wellcome Sanger Institute, University of Cambridge, University of Birmingham, and Imperial College London published the largest study of the human nasal microbiome ever conducted. Their findings, published in Nature Communications, fundamentally changed how scientists understand bacterial communities in the nose.

Key Finding 1: Persistent Carriers Have a Depleted Microbiome

The study found that people who persistently carry Staphylococcus aureus have a distinctly different nasal microbiome than non-carriers. Specifically, persistent carriers showed:

• An abundance of S. aureus dominating the bacterial community
• Significantly fewer species of other bacteria
• Notably low levels of S. epidermidis, Dolosigranulum pigrum, and Moraxella catarrhalis

In other words, the noses of persistent S. aureus carriers look like a monoculture rather than a diverse ecosystem. This mirrors a well-established pattern in ecology: diverse ecosystems are more resilient, while monocultures are vulnerable.

Key Finding 2: Certain Bacteria Block S. aureus Colonization

Perhaps the most exciting finding was that specific bacterial species appear to actively prevent S. aureus from establishing itself. Non-carriers had significantly higher levels of Staphylococcus epidermidis, Dolosigranulum pigrum, and Moraxella catarrhalis — suggesting these species create a competitive environment that keeps S. aureus out.

Key Finding 3: "Intermittent Carriers" Don't Really Exist

For decades, scientists classified people into three groups: persistent S. aureus carriers, intermittent carriers, and non-carriers. This study overturned that framework. The researchers found that so-called "intermittent carriers" are really just non-carriers who temporarily picked up S. aureus from their environment — not a distinct biological category. This has significant implications for hospital screening protocols and infection risk assessment.

Key Finding 4: Machine Learning Can Predict Infection Risk

Using machine learning algorithms, the researchers were able to predict with high accuracy who was a persistent S. aureus carrier based solely on their overall bacterial community profile. As Dr. Dinesh Aggarwal, lead author and Clinical Lecturer at Imperial College London, explained: "By identifying the bacterial profiles that protect against S. aureus colonization, our findings could inform new, microbiome-based strategies to reduce infection risk without relying on antibiotics."

The SSI Study: How Nasal Bacteria Prevent Dangerous Infections

Just months later, in mid-2025, a separate international research team led by Statens Serum Institut (SSI) in Denmark published their own landmark nasal microbiome study in Cell Reports, examining over 1,500 individuals across Denmark and Germany.

The Competition Between S. aureus and S. epidermidis

This study confirmed and extended the Sanger findings. The nose is typically dominated by either S. aureus or S. epidermidis — and these two species appear to be in direct competition. When one dominates, the other is suppressed. Both species showed remarkable stability over time, meaning once a dominant species establishes itself, it tends to maintain its position.

Dolosigranulum and Corynebacterium: Natural Infection Fighters

A particularly striking finding was that the presence of S. aureus decreased significantly when bacteria such as Dolosigranulum and Corynebacterium were also present in the nose. As lead author Anna Cäcilia Ingham explained: "We can now see the nasal microbiome in much higher resolution than before. This means we can distinguish between different bacterial compositions and better understand why some bacteria persist while others come and go."

Co-author Marc Stegger, department head at SSI, added: "We see a clear pattern where some bacteria establish themselves and remain dominant, while others vary more over time. This has implications for how we understand infection risk — and potentially also how we can influence it."

What Influences Your Nasal Microbiome?

The SSI study also identified several factors that influence which bacterial species dominate your nose:

• Age — The nasal microbiome shifts as you get older, with certain species becoming more or less common
• Sex — Men and women tend to have somewhat different nasal bacterial profiles
• Smoking status — Smoking significantly disrupts the nasal microbiome and may promote pathogenic colonization
• Overall bacterial composition — The existing community influences which new species can establish themselves

Why the Nasal Microbiome Matters for Sinus Health

These studies aren't just academic exercises. The nasal microbiome directly impacts several conditions that millions of people deal with every day:

Chronic Sinusitis

People with chronic sinusitis consistently show reduced microbial diversity in their sinuses compared to healthy individuals. The same pattern identified in the 2025 studies — pathogen dominance plus reduced diversity — is a hallmark of chronic sinus disease. Supporting bacterial diversity may be just as important as treating acute infections.

Post-Surgical Infections

S. aureus is the leading cause of surgical site infections. Hospitals routinely screen patients before major surgeries, particularly orthopedic procedures like joint replacements. The Sanger study's finding that S. aureus carriage can be predicted by the broader bacterial community offers a potentially faster, more accurate screening method that could prevent thousands of infections annually.

Antibiotic Resistance

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most feared antibiotic-resistant bacteria. According to the Global Burden of Disease Study, S. aureus infections cause roughly one million deaths per year worldwide, and MRSA strains are making these increasingly difficult to treat. Understanding how the nasal microbiome naturally suppresses S. aureus opens the door to antibiotic-free prevention strategies.

Allergic Rhinitis and Hay Fever

Emerging research suggests the nasal microbiome also influences allergic responses. Certain bacterial profiles are associated with higher rates of allergic rhinitis and hay fever. A balanced nasal microbiome may help modulate the immune response to allergens.

How Nasal Irrigation Supports Nasal Microbiome Health

If microbial diversity is key to nasal health, how do you protect and promote it? This is where nasal irrigation — an ancient practice now backed by modern science — plays a critical role.

Some people worry that rinsing the nose with saline might "wash away" good bacteria. The reality is more nuanced and, ultimately, more encouraging.

What Saline Rinsing Actually Does to Nasal Bacteria

1. Physically removes excess pathogenic bacteria and biofilms. Bacterial biofilms — sticky colonies that antibiotics struggle to penetrate — are a major driver of chronic sinusitis. Saline irrigation physically disrupts these biofilms, reducing pathogenic bacterial load. A 2024 study on xylitol-enhanced rinses showed particularly strong biofilm disruption.
2. Clears inflammatory debris and mucus. Excess mucus traps bacteria and creates an anaerobic environment that favors pathogens over beneficial species. By clearing this debris, saline rinsing creates conditions that favor aerobic, protective bacteria.
3. Restores mucociliary clearance. The cilia — tiny hair-like structures that line your nasal passages — beat in coordinated waves to sweep pathogens out. Infection, dehydration, and inflammation impair this system. Saline irrigation rehydrates the mucosa and restores ciliary function, supporting the nose's natural self-cleaning mechanism.
4. Creates a more hospitable environment for commensal bacteria. By reducing inflammation, flushing out excess pathogens, and maintaining optimal moisture levels, regular rinsing supports the conditions under which protective species like S. epidermidis and Dolosigranulum thrive.

A 2024 study published in The Lancet Respiratory Medicine involving over 11,000 participants demonstrated that regular nasal saline irrigation reduced illness duration by approximately two days and significantly reduced antibiotic use. This suggests that saline rinsing supports the nose's natural defenses rather than undermining them.

The Right Way to Rinse for Microbiome Health

Not all rinsing practices are equal when it comes to supporting your nasal microbiome. Here's an evidence-based protocol:

1. Use isotonic saline for maintenance. Isotonic (0.9%) saline most closely matches your body's natural fluid balance. This concentration cleanses without excessively disrupting the microbial environment. ATO Health sinus rinse packets are pre-measured to provide the correct isotonic concentration every time — eliminating guesswork and ensuring consistency.
2. Rinse 1–2 times daily during normal conditions. This frequency supports mucociliary clearance and reduces pathogenic biofilm accumulation without over-disrupting commensal populations.
3. Increase to 2–3 times daily during infections or high-allergen periods. During acute illness, more frequent rinsing helps physically remove viral and bacterial load. The COVID clinical trials used protocols of up to 4–6 rinses per day during active infection.
4. Always use distilled or previously boiled water. Tap water can introduce harmful organisms, including Naegleria fowleri (the brain-eating amoeba) in rare cases. Using sterile water protects the delicate nasal environment.
5. Use pharmaceutical-grade saline packets. Consistent salt concentration matters. Too much salt (hypertonic) can damage mucosal tissue with prolonged use; too little (hypotonic) can cause discomfort and swelling. Pre-measured packets like those from ATO Health ensure you get the right concentration every time.

The Future: Nasal Probiotics and Microbiome-Based Treatments

Both the Sanger Institute and SSI research teams have explicitly stated that their next goal is to explore whether the nasal microbiome can be intentionally manipulated to prevent infections. As Anna Cäcilia Ingham of SSI noted: "The next step is to explore how we might promote the bacteria that naturally suppress S. aureus. This could ultimately lead to new ways to protect against infection — and over time reduce the need for antibiotics."

What's Coming

• Nasal probiotic sprays — Researchers are investigating whether spraying beneficial bacteria like S. epidermidis or Dolosigranulum pigrum into the nose could protect high-risk patients before surgery.
• Microbiome-based screening — Instead of just testing for S. aureus, hospitals may analyze the entire nasal bacterial community to predict infection risk with much greater accuracy.
• Personalized decolonization — Rather than the one-size-fits-all approach of applying antibiotic ointment (mupirocin) to everyone before surgery, treatments could be tailored based on individual microbiome profiles.
• Synbiotic nasal rinses — Combinations of prebiotics (nutrients for beneficial bacteria) with saline rinses could become a standard approach to maintaining nasal health.

Until these advanced therapies become available, the most practical thing you can do is maintain the nasal environment that lets your existing good bacteria thrive — and the evidence is clear that regular saline nasal irrigation is the single best tool for that job.

What You Can Do Today to Support Your Nasal Microbiome

You don't need to wait for nasal probiotics. Based on the current research, here's a practical daily protocol for supporting a healthy nasal microbiome:

Daily Nasal Microbiome Support Protocol

1. Morning rinse: Irrigate with isotonic saline using ATO Health sinus rinse packets and distilled water. This clears overnight mucus buildup and resets your nasal environment for the day.
2. Evening rinse: A second rinse before bed clears the pollutants, allergens, and pathogens accumulated during the day. This is especially important during allergy season or if you live in a high-pollution area.
3. Stay hydrated: Adequate hydration maintains the mucus layer that protective bacteria depend on. Dehydrated nasal passages become inflamed and favoring pathogenic species.
4. Avoid unnecessary nasal antibiotics: Overuse of topical nasal antibiotics (like mupirocin) can devastate your nasal microbiome, similar to how oral antibiotics disrupt gut flora. Only use them when specifically prescribed by your doctor.
5. Don't smoke: The SSI study confirmed smoking significantly alters the nasal microbiome. If you smoke, this is one more powerful reason to quit.
6. Manage allergies proactively: Chronic nasal inflammation from untreated allergies disrupts the microbial environment. Address allergies with appropriate treatments to maintain a balanced microbiome.

Common Misconceptions About Nasal Bacteria

Misconception 1: "All bacteria in the nose are bad"

This is the biggest misconception. The 2025 studies prove that many nasal bacteria are actively protective. Trying to eliminate all nasal bacteria (with antibacterial sprays or excessive antibiotic use) can actually increase your infection risk by removing the species that keep pathogens in check.

Misconception 2: "Nasal irrigation kills good bacteria"

Saline irrigation doesn't sterilize the nose. It physically removes excess mucus, debris, and free-floating pathogens. The commensal bacteria that adhere to nasal tissue and form stable communities are largely unaffected by gentle saline rinsing. In fact, by reducing biofilm-forming pathogens and inflammation, irrigation creates better conditions for beneficial bacteria.

Misconception 3: "Oral probiotics improve nasal health"

While gut health influences overall immune function, oral probiotic supplements do not directly change the bacterial composition of your nasal passages. The nasal microbiome is a distinct ecosystem that requires direct interventions — like nasal irrigation and potentially future nasal probiotic sprays — to modify.

Misconception 4: "If S. aureus is in my nose, I need antibiotics"

Carrying S. aureus is normal for about 30% of the population and does not typically require treatment. Antibiotic decolonization is generally only recommended before specific surgeries or for healthcare workers in certain settings. Indiscriminate antibiotic use against nasal S. aureus contributes to resistance without providing benefit for most people.

Frequently Asked Questions

What is the nasal microbiome?

The nasal microbiome is the community of bacteria, fungi, and other microorganisms that naturally live inside your nasal passages. A healthy nasal microbiome is dominated by beneficial species like Staphylococcus epidermidis, Dolosigranulum pigrum, and Corynebacterium, which help protect against infections by competing with harmful pathogens like Staphylococcus aureus.

Can nasal irrigation improve your nasal microbiome?

Yes. Saline nasal irrigation helps maintain a healthy nasal microbiome by physically flushing out excess pathogenic bacteria, reducing biofilm buildup, restoring mucosal moisture, and supporting the natural mucociliary clearance system. Studies show regular rinsing reduces Staphylococcus aureus colonization and supports the growth of protective bacterial species.

Does Staphylococcus aureus in the nose cause sinus infections?

Staphylococcus aureus lives harmlessly in about 30% of people's noses. However, persistent carriers have a significantly higher risk of post-surgical infections and complicated sinusitis. The 2025 Sanger Institute study found that persistent S. aureus carriers have fewer protective bacterial species in their nose, which may explain their higher infection risk.

What bacteria protect against sinus infections?

Research has identified several protective nasal bacteria including Staphylococcus epidermidis, Dolosigranulum pigrum, Corynebacterium species, and Moraxella catarrhalis. These species appear to inhibit colonization by Staphylococcus aureus and other pathogens through competitive exclusion and antimicrobial compound production.

How often should I rinse my sinuses to support nasal microbiome health?

For general nasal microbiome maintenance, once or twice daily with an isotonic saline solution is recommended. During active infections or high allergy seasons, you can increase to 2–3 times daily. Always use distilled or previously boiled water and pharmaceutical-grade saline packets for safety and consistency.