The human body hosts trillions of microorganisms, including bacteria, viruses, and fungi, which collectively form the microbiome. A significant portion of these microbes resides in the gut, where they contribute to various bodily functions. Allergies are an overreaction of the immune system to substances that are normally harmless, such as pollen or certain foods. Recent scientific investigations reveal a connection between the health of the gut microbiome and the likelihood of developing allergic conditions, suggesting our internal microbes can influence how our immune system responds.
How the Microbiome Trains the Immune System
Developing a balanced immune response is a learning process called immune tolerance, the mechanism by which the immune system is taught to recognize and ignore harmless substances. A large part of this education happens in the gut, where approximately 70-80% of the body’s immune cells are located. Constant exposure to dietary components and microbial residents helps train these immune cells to differentiate between harmful pathogens and innocuous compounds.
This educational process is heavily guided by the gut microbiome. A diverse and balanced microbial community presents the immune system with a wide range of signals that help calibrate its responses. Think of the microbiome as a training academy for immune cells like T-cells. Exposure to different microbes and the substances they produce helps these cells learn to stand down in the presence of harmless allergens.
When the microbiome lacks diversity or is imbalanced—a state known as dysbiosis—this training can be incomplete. Without sufficient microbial input, the immune system may not develop proper tolerance, leading to heightened sensitivity. This misguided defensive response is the foundation of an allergic reaction, where the body mistakenly identifies a harmless allergen as a threat and mounts an inflammatory attack.
An imbalanced gut microbiota can also affect the integrity of the intestinal barrier. This can lead to increased permeability, sometimes called a “leaky gut,” which allows allergens to pass more easily into the bloodstream. This increased exposure can further provoke the immune system, contributing to the development and severity of allergic responses.
Early Life and Microbiome Development
The foundation for an individual’s microbiome is laid during infancy and early childhood, a formative period for immune system development. The method of birth is one of the first factors to influence a newborn’s microbial makeup. During a vaginal delivery, an infant is exposed to the mother’s vaginal and fecal microbes, including beneficial strains like Lactobacillus, which helps establish a healthy gut community from the start.
In contrast, infants born via Cesarean section miss this initial exposure and are instead colonized by microbes from the hospital environment and skin contact. This can result in a less diverse initial microbiome, which may affect the normal trajectory of immune system maturation. Studies show this difference in early microbial colonization can be a factor in the later development of allergic diseases.
The method of infant feeding also has a profound effect on the developing microbiome. Breast milk contains nutrients, beneficial bacteria, and specialized prebiotics called human milk oligosaccharides (HMOs). These HMOs are not digested by the infant but serve as food for beneficial gut bacteria, such as Bifidobacterium, promoting their growth. Formula, while a nutritious alternative, does not contain this same complex array of microbial components.
The use of antibiotics in early life can also alter the developing microbiome. While often necessary for treating bacterial infections, antibiotics are not selective and can wipe out beneficial bacteria along with harmful ones. This disruption can reduce microbial diversity when the immune system is still learning, and this alteration has been associated with an increased risk of developing allergies.
The Role of Diet and Environment
Beyond early life, diet and environmental exposures continue to shape the gut microbiome and its influence on allergic responses. A diet rich in dietary fiber from a variety of plant-based sources, such as fruits, vegetables, and whole grains, provides prebiotics that nourish beneficial bacteria. These microbes ferment the fiber, producing compounds like short-chain fatty acids (SCFAs), which help maintain the gut barrier and regulate immune function.
Conversely, a diet high in processed foods, which are low in fiber and high in sugar and unhealthy fats, can reduce microbial diversity. This type of diet can favor the growth of less beneficial bacteria, leading to dysbiosis and a pro-inflammatory state in the gut. Including fermented foods that contain live cultures, such as yogurt and kefir, can introduce beneficial microbes (probiotics) directly into the digestive system.
The environment in which a person lives also contributes to their microbial exposures. The “hygiene hypothesis” suggests that living in overly sterile environments may limit exposure to a wide range of microbes, which can hinder the proper education of the immune system. Exposure to diverse environmental microbes, such as those found in soil or on pets, can help build a more robust and diverse microbiome.
This concept is sometimes referred to as the “old friends” mechanism, where regular contact with a variety of harmless microorganisms helps to maintain immune balance. For instance, children who grow up on farms or with pets tend to have a lower incidence of allergies, thought to be due to their greater microbial exposure. A less diverse urban environment may offer fewer opportunities for this type of beneficial interaction.
Specific Allergic Conditions Linked to the Microbiome
The connection between an imbalanced microbiome and immune dysregulation has been observed in several specific allergic conditions. Eczema, or atopic dermatitis, is often one of the first allergic diseases to appear in infancy. Research has pointed to a “gut-skin axis,” indicating that the health of the gut can directly influence the health of the skin. Infants who develop eczema have been found to have different patterns of gut bacteria, suggesting an early imbalance may contribute to the skin inflammation seen in this condition.
Respiratory allergies, such as asthma and allergic rhinitis (hay fever), are also linked to the microbiome through the “gut-lung axis.” This concept describes how the gut microbiota can influence immune responses in the airways. Alterations in gut microbial composition can affect the development of inflammation in the lungs. For example, lower levels of certain beneficial bacteria in the gut during early life have been associated with an increased risk of developing asthma.
The microbiome’s role in food allergies is also becoming clear. The development of oral tolerance—the ability to eat food without an allergic reaction—is dependent on a healthy gut microbiome. Specific gut microbes are thought to signal to the immune system that food proteins are harmless. A lack of these particular bacteria may impair this process, leading the immune system to mount an attack against certain food proteins, resulting in a food allergy.