The Gut Microbiome Connection to Food Allergies

The Gut Microbiome and Food Allergies

The gut influences so many key processes in the body. Research over the past 40 plus years has increasingly pointed to just how important a healthy gut microbiome is in understanding the risk for food allergies. It’s also shown us how we can better support a baby’s gut microbiome in those crucial early days, and potentially lead to exciting future therapeutics aimed at allergic diseases.

food allergy diagnosis can be life altering for a family. It can leave parents feeling helpless and overwhelmed as they try to coexist with the allergy and build a new normal for their affected child and family. But emerging research exploring the connection between food allergies and the gut microbiome could spark hope and prove beneficial in the treatment and prevention of food allergies in the future.

What Does the Gut Microbiome Have to Do with Food Allergies?

I spoke with Dr. Elisa Song, integrative pediatrician and functional medicine expert, to learn more about this connection. We know that 70–80% of the immune system is located in your gut. Food allergies occur when your immune system mistakenly treats a certain food as a harmful substance and responds by releasing histamine.

She explained that the gut microbiome has much to do with our immune system not interpreting these foods appropriately. According to Dr. Song, “The way our gut microbiome develops, even from the time [our babies] are inside our bodies, from the moment that they’re born, we can see the effects of the gut microbiome on their future risk for developing not just food allergies, but any allergic disease.”

Research has shown that gut dysbiosis, which is an abnormal array of gut microbes in the intestines, precedes the development of food allergies. “So anything that increases our children’s risk of gut dysbiosis can increase our risk for food allergies,” she says. Furthermore, studies have shown that individuals with food allergies have a different gut microbiome composition compared to those without food allergies, further proving the gut’s influence over allergy risk.

“Anything that increases our children’s risk of gut dysbiosis can increase our risk for food allergies.”

Why are Food Allergies on the Rise?

There are many related factors contributing to this rise in food allergies in Western cultures. Before we take a look at lifestyle changes, it’s important to understand how these factors affect the gut and gut bacteria. It is thought that the rise in allergies may be influenced by the microbes we are or aren’t exposed to in early life.

David Strachan’s 1980 “hygiene hypothesis” proposed that exposure to microorganisms in the early years of life protected against allergic diseases and that our ultra clean modern lifestyle may be a contributing risk to developing allergies for babies. In 2003, Graham Rook and his team developed the “old friends’’ hypothesis as an evolution of this earlier notion.

The “Old Friends” Hypothesis

“[The ‘old friends’ hypothesis] suggests that early and regular exposure to harmless microorganisms—‘old friends’ present throughout human evolution and recognized by the human immune system—train the immune system to react appropriately to threats,” according to literature from Proceedings of the National Academy of Sciences on the subject. “It’s not that children in developed countries aren’t subject to enough infections when they are young,” the article noted, “but that their exposure to the microbial world is far more circumscribed than it once was.” 

Furthermore, “Exposure to nonpathogenic microbes activates a variety of immune processes, including Treg cells, to regulate the immune system appropriately. So, with fewer old friends to learn from, our immune systems grow up to be trigger-happy.” In short, when we are exposed to too few of the old “friendly” germs that assist in training our immune systems how to correctly respond, our immune systems may be more prone to treat something harmless as an enemy.

Research has shown that the prenatal and early infancy time periods are crucial in the development of one’s gut microbiota. A baby’s gut colonization can be influenced by how they were delivered (vaginal versus cesarean section), through breastfeeding, by contact with other family members, and more.

Antibiotics, Dr. Song shares, are a contributor to gut dysbiosis in modern society. To be clear, antibiotics are lifesaving and appropriate in multiple healthcare situations, but it’s important to only use them when necessary. Because antibiotics indiscriminately kill off bacteria, no matter if it’s considered “good” or “bad” bacteria,  supporting a healthy gut before, during, and after use is imperative.

How to Support Your Child’s Gut 


Advice from an integrative pediatrician

  • Introduce fermented foods like kombucha, kefir, and miso soup into their diets. For those with wider palates, you can also try sauerkraut and kimchi.
miso fennel chicken soup
Miso Fennel Chicken Soup
  • Offer a wide variety of fiber-rich foods including whole fruits and vegetables, beans, and whole grains.
  • Opt for minimally processed foods.
  • Supplement with a prebiotic and probiotic, especially when antibiotics are used. 
  • Prioritize sleep.
  • Spend time in nature; let your littles get dirty.

These recommendations are not only suggested for the child but also for the mother, starting before pregnancy.

Protective Measures Against Food Allergies

“The Role of the Microbiome in Food Allergy”, a study that looked at multiple trials and analysis over a 20-year period, confirms that, “Children growing up with older siblings have a lower incidence of allergic disease, compared with children from smaller families, likely due to their early exposure to environmental microbes in the home. Additionally, factors associated with a decreased risk of developing allergic disease later in life include being born via vaginal delivery, being breastfed during the first four months of life, pet ownership, and the absence of early antibiotic exposure. By contrast, growing up in an urban, Westernized environment is associated with increased rates of asthma, atopic dermatitis and food allergy.” 

How to Support Your Child Nutritionally with Food Allergies

Following guidance on how to support a healthy gut is paramount to supporting your child’s overall health. While some individuals may outgrow food allergies, there is currently no cure. For kids who have been diagnosed with food allergies, a parent’s top priority will be to keep them from accidental exposure or ingestion of the allergic food. Beyond this, though, Dr. Song suggests a few nutritionally supportive areas to focus on that may reduce the histamine reaction if exposed. 

She explains that a type of white blood cell called a mast cell is responsible for releasing an inappropriate amount of histamine when an allergen attaches to it. To stabilize and support these mast cells, she recommends eating foods that are rich in quercetin. Doing so, she says, may lessen the histamine released upon exposure to an allergen. “The more quercetin we have in our system, the more ideal it is, not just with food allergies, but for kids where histamine is a problem with asthma, eczema, or hay fever.” There are many foods rich in quercetin that you may already be feeding your kids or can readily add to their diet. 

Dr. Song has also pointed to both zinc and iron, two common nutrient deficiencies for babies, as important parts of the nutritional puzzle. She explains that zinc is also a natural mast cell stabilizer and can help support a healthy gut lining. Protein offers a rich source of both nutrients and she recommends animal protein, shellfish, seeds, and legumes as avenues to get the proper amounts. Lastly, she highlights the importance of a high-fiber diet because it feeds the gut microbiota, which in turn supports a healthier gut.  Fiber can be found in fruits and vegetables, whole grains, beans, chickpeas, and lentils.

healthy family gut microbiome

Dr. Song’s Top Quercetin-Rich Foods


Raw onions
Red apple, with skin
Red grapes
Kale
Spinach
Capers
Watercress
Cherries
Berries
Broccoli
Tomatoes
Asparagus
Green tea
Black tea
Red leaf lettuce
Chili peppers

The Future Therapeutic Possibilities 

As the connection between food allergies and the gut microbiome have come into clearer view over decades of research, there are exciting prospects for treatment being explored. Dr. Song cautions that it can take as long as or longer than 17 years for research to translate into clinical practice. “Food Allergy and the Microbiome: Current Understandings and Future Directions” a cohort study exploring the relationship between allergies and the microbiome and potential therapies states that, “Diet, probiotics, prebiotics, synbiotics, and fecal microbiota transfer represent potential microbial therapeutics for food allergy prevention and treatment.”

While fecal microbiota transfers are on the distant horizon, focusing on diet, probiotics, and prebiotics now is something families can do that may have potential benefits without causing harm, explains Dr. Song.

You can hear the full interview with Dr. Song on the connection between food allergies and the gut microbiome on our podcast, Raising Healthy Families with Moms Meet and KIWI. Listen now.


Dr. Elisa Song is an integrative pediatrician, pediatric functional medicine expert, and mom to two thriving children. In her integrative pediatric practice, Whole Family Wellness, she’s helped thousands of kids get to the root causes of their health concerns and helped their parents understand how to help their children thrive—body, mind, and spirit—by integrating conventional pediatrics with functional medicine, homeopathy, acupuncture, herbal medicine, and essential oils. Dr. Song created Healthy Kids Happy Kids as an online holistic pediatric resource to help practitioners and parents bridge the gap between conventional and integrative pediatrics with an evidence-based, pediatrician-backed approach.