Hay Fever and Gut Health: Gut Microbiome, Immunity and Probiotic Research Explained

Each spring, many people experience hay fever, with symptoms such as sneezing, a runny or blocked nose, and itchy or watery eyes.

Hay fever causes symptoms mainly in the nose and eyes, but in recent years researchers around the world have also been investigating the relationship between the gut microbiome, immunity and allergic conditions.

So why are an allergic condition affecting the nose and a completely different part of the body—the gut—being studied together?

In this guide, we explain how hay fever and allergic rhinitis develop, how the gut microbiome interacts with the immune system, where probiotic research currently stands, how probiotics differ from prebiotics and fermented foods, and practical ways to think about diet and everyday pollen-season management.

What Are Hay Fever and Allergic Rhinitis?

Allergic rhinitis occurs when the immune system reacts to allergens such as pollen or dust mites.

When the trigger is pollen that appears during particular seasons—such as Japanese cedar or cypress pollen in Japan—the condition is commonly called hay fever.

Common symptoms include:

• Sneezing
• Runny nose
• Nasal congestion
• Itchy eyes
• Red eyes
• Watery eyes

What Happens in the Body When Pollen Enters?

Two important parts of the allergic response are IgE antibodies and mast cells.

In people who have become allergic to a particular pollen, IgE antibodies that recognise that allergen bind to the surface of mast cells.

When the allergen is encountered again, this can trigger the release of chemical mediators such as histamine and leukotrienes.

These substances act on nerves, blood vessels and other tissues in the nose, contributing to symptoms such as sneezing, a runny nose and nasal congestion.

Quick Fact: What Does “Sensitisation” Mean?

A term often used in allergy research is sensitisation.

It refers to a state in which the immune system has recognised a particular allergen and has developed an immune response to it, including the production of allergen-specific IgE antibodies.

The development of hay fever is influenced by several factors, including genetics, individual susceptibility, environmental exposure and the amount of pollen encountered over time.

How Are Gut Health and Immunity Connected?

The gut is often thought of mainly as the place where food is digested and nutrients are absorbed.

However, it is also one of the body's major contact points with food components, microorganisms and substances from the outside environment.

For this reason, the gut contains extensive immune-related structures, including gut-associated lymphoid tissue (GALT), along with many immune cells.

What Is the Gut Microbiome?

The human gut is home to a vast community of microorganisms.

This community is commonly referred to as the gut microbiota or gut microbiome.

The term “gut flora” is also widely used, reflecting the idea of many different microorganisms living together like a diverse ecosystem.

Gut microorganisms use components of our diet and produce a wide variety of substances, while interacting with the intestinal lining and the immune system.

Short-Chain Fatty Acids Produced from Dietary Fibre

One group of substances receiving considerable research attention is short-chain fatty acids (SCFAs).

Some types of dietary fibre pass through the small intestine without being fully digested and reach the large intestine, where they can be used by gut bacteria.

This process can produce short-chain fatty acids such as:

• Acetate
• Propionate
• Butyrate

Short-chain fatty acids are being studied for their interactions with the intestinal lining, immune cells and other physiological processes.

Quick Fact: Gut Bacteria Are Increasingly Studied as a Whole Community

Many people are familiar with the simple idea of “good bacteria” and “bad bacteria.”

This can be a useful way to introduce the subject, but modern microbiome research looks at a much more complex picture.

Researchers increasingly examine the overall composition and diversity of the gut microbiota, interactions between microorganisms, and the metabolites they produce.

Even microorganisms belonging to the same species may have different characteristics at strain level, which is why the whole microbial ecosystem is becoming an important research focus.

What Research Is Showing About Hay Fever and the Gut Microbiome

So what might the gut microbiome have to do with an allergic condition affecting the nose?

In recent years, researchers have increasingly investigated the relationship between the gut microbiome and allergic rhinitis.

Some studies comparing people with allergic rhinitis with those without it have reported differences in gut microbial composition or diversity.

Because studies differ in age groups, geography, diet, season, lifestyle and analytical methods, current research is focused on identifying whether there are reproducible microbiome patterns associated with allergic rhinitis across larger and more diverse populations.

Researchers are also examining the intestinal barrier, immune responses and metabolites produced by gut microbes to better understand how these systems may interact.

The “Gut–Airway Axis”

One concept receiving increasing attention is the gut–airway axis.

Although the gut and respiratory tract are physically separate, researchers are studying how they may communicate indirectly through immune signalling and microbial metabolites.

This provides one possible framework for understanding why scientists are interested in the gut when studying conditions that primarily affect the nose and airways: the immune system functions as a connected, body-wide network.

Probiotic Clinical Research Is Also Expanding

A growing number of clinical trials have investigated probiotics in people with allergic rhinitis.

A 2026 meta-analysis included 29 randomised controlled trials involving a total of 2,078 participants.

Across these studies, statistically significant differences were reported in some measures of nasal symptoms and quality of life between probiotic and control groups.

At the same time, the probiotic strains, doses, duration of use, participant characteristics and outcome measures varied considerably between studies.

Research is therefore moving towards understanding which specific strains and study conditions are associated with particular outcomes.

For this reason, probiotics and allergic rhinitis are best viewed as an emerging research area exploring the relationship between the microbiome and immunity alongside established approaches to hay fever management.

Quick Fact: “Lactic Acid Bacteria” Is Not Enough to Identify a Study

An important concept in probiotic research is the strain.

Even microorganisms belonging to the same species of Lactobacillus or Bifidobacterium may have different characteristics at strain level.

When reading probiotic research, it is therefore useful to look at the exact strain, the amount used and the duration of the study rather than only the general type of bacterium.

Probiotics, Prebiotics, Synbiotics, Postbiotics and Fermented Foods

When reading about gut health, several similar terms frequently appear:

• Probiotics
• Prebiotics
• Synbiotics
• Postbiotics
• Fermented foods

They describe different concepts, so it helps to separate them clearly.

Quick Fact: How Are Fermented Foods Different from Probiotics?

Fermented foods and probiotics are sometimes discussed as if they were the same thing because both involve microorganisms.

Fermented foods are foods produced through controlled microbial growth and enzymatic activity.

Probiotics, however, have a specific scientific definition: live microorganisms that provide a demonstrated health benefit when given in adequate amounts.

Some fermented foods may also be heated or processed after fermentation, meaning that live microorganisms may no longer be present.

A useful distinction is therefore: fermentation describes how a food is produced, while “probiotic” describes a specific live microorganism with demonstrated health benefits.

Quick Fact: Postbiotics Mean More Than Simply “Dead Bacteria”

The term postbiotic also has a specific scientific definition.

It refers to a preparation containing inanimate microorganisms and/or their components that has been shown to confer a health benefit on the host.

Simply inactivating a microorganism does not automatically make the resulting material a postbiotic.

The preparation itself and the evidence supporting its use are important parts of the definition.

With Probiotics, Look at the Strain

When learning about probiotics, the strain can be just as important as the species.

Two strains belonging to the same species may have different characteristics.

This is why strain identification is an important detail when comparing probiotic research.

Everyday Diet and Lifestyle for Gut Health

The composition of the gut microbiome varies considerably from person to person.

It is influenced by many factors, including diet, age, environment, physical activity, sleep and medication use.

For this reason, a practical approach to gut health is to focus on the overall pattern of everyday eating rather than relying on one particular food.

Include Dietary Fibre from a Variety of Foods

Dietary fibre includes food components that are not fully digested and absorbed in the small intestine and can reach the large intestine.

Some types of fibre are used by gut microorganisms and are involved in the production of short-chain fatty acids.

Foods containing dietary fibre include:

• Vegetables
• Fruit
• Legumes
• Whole grains
• Potatoes and other root vegetables
• Mushrooms
• Sea vegetables

Combining a variety of plant foods can provide different types of dietary fibre and a broad range of nutrients.

Fermented Foods Can Be Part of Everyday Eating

Fermented foods such as yoghurt, natto, miso and kimchi have long been part of food cultures around the world.

Choosing foods that suit your usual eating pattern and including them as part of a varied diet can make them easier to enjoy consistently.

Microbial Diversity Is Also a Research Focus

One area of microbiome research is microbial diversity—the presence of many different types of microorganisms within the gut ecosystem.

In everyday eating, this can be approached by including a variety of vegetables, legumes, grains, mushrooms, sea vegetables and fruit.

Adding variety to the foods you eat can also make meals more nutritionally diverse.

Sleep, Physical Activity and Daily Routine Matter Too

Gut health is influenced by more than diet alone.

Physical activity, sleep and regular daily routines are also part of the broader lifestyle picture.

Rather than changing one part of your diet dramatically, thinking about eating, movement and sleep together can provide a more practical everyday approach.

Hay Fever Season: Practical Management and How to View Gut Research

Research into the gut microbiome and allergic conditions is an interesting and rapidly developing field.

At the same time, during pollen season it is also useful to focus on reducing the amount of pollen reaching the eyes and nose.

Reduce Pollen Exposure in Everyday Life

Depending on local pollen conditions, practical measures may include:

• Using a mask or glasses outdoors
• Choosing clothing materials that pollen is less likely to cling to
• Removing pollen from clothing before entering the home
• Washing the face and rinsing the mouth after returning home
• Adjusting ventilation according to pollen levels
• Cleaning indoor spaces regularly

Combining several simple measures can help reduce everyday exposure to pollen.

There Are Several Established Treatment Options

Treatment for hay fever and allergic rhinitis can vary according to the symptoms and their severity.

Common approaches include:

• Antihistamines
• Intranasal corticosteroids
• Leukotriene receptor antagonists
• Allergen immunotherapy

The most appropriate option depends on the pattern and severity of symptoms, personal preferences and other health considerations, so treatment can be discussed with a doctor or pharmacist.

Quick Fact: Hay Fever Management Can Start Before Symptoms Become Severe

For people who experience hay fever at roughly the same time each year, treatment can sometimes be started before peak pollen exposure or when symptoms are still mild.

Speaking with a doctor or pharmacist before the main pollen season can make it easier to plan an approach suited to that year's conditions.

What Is Sublingual Immunotherapy?

Allergen immunotherapy involves giving controlled amounts of the relevant allergen over time under medical supervision.

In Japan, sublingual immunotherapy is available for Japanese cedar pollen allergy.

It is a long-term treatment carried out under medical supervision, and a treatment period of around three to five years is generally recommended.

For people whose hay fever significantly affects daily life each year, it is one of the options that can be discussed with an appropriate medical professional.

Gut Health and Hay Fever Remain an Active Area of Research

The relationship between the gut microbiome, immunity and allergic conditions has become an increasingly active area of research.

Current evidence shows that the gut microbiome and immune system interact closely and that many studies are now exploring how these interactions may relate to allergic rhinitis.

Probiotic research is also becoming more detailed, with increasing attention paid to specific strains, dosage, duration of use and participant characteristics.

In everyday life, a varied diet containing fibre-rich foods and fermented foods can be combined with regular sleep and physical activity as part of a broader approach to gut health.

During pollen season, reducing pollen exposure and using appropriate evidence-based treatment can be considered alongside those general lifestyle habits.

Rather than viewing the gut, nose and immune system as completely separate topics, looking at diet, lifestyle, environmental exposure and established allergy management together provides a useful way to understand this developing area of research.

Reference Information

• Japan Ministry of Health, Labour and Welfare – information on hay fever and allergic rhinitis
• Japanese Society of Allergology – Allergy Portal
• International Scientific Association for Probiotics and Prebiotics (ISAPP) – Consensus Definitions
• Wang Z, Lu Y. Efficacy of probiotics on immunological and clinical outcomes in allergic rhinitis: an umbrella review and updated meta-analysis of RCTs in children and adults. BMC Immunology. 2026.
• Recent systematic reviews and meta-analyses examining the gut microbiome and allergic rhinitis