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Allergies, Asthma, or Eczema? How Improving Your Gut Health May Help

Updated: May 22, 2022

By Stephanie Deppe, M.D.

A loved one of mine was recently hospitalized for an asthma attack. It was her first severe episode and frightening for everyone involved. I am fortunate to have never had allergies, and so I was reminded of how devastating they can be. Allergies are unfortunately common, and they are only increasing in prevalence. They already affect up to 30% of people worldwide and are the 6th leading cause of chronic disease in the U.S. (1).

Why are allergies becoming so common, and what can we possibly due to prevent or even treat them (outside of antihistamines and prescriptions)? Like with nearly any disease, it seems to come back–at least in part–to the gut. I recently came across a fascinating article that reviews the strong association between gut health and allergies–eczema, asthma, allergic rhinitis, and food allergies (1). Here, I have summarized the article and included some additional thought-provoking studies.

Did you know that the GI tract contains more than one hundred trillion bacteria? The gut microbiome should be rich in a diverse bacterial flora and without overgrowth of opportunistic bacteria. Dysbiosis, or overgrowth of undesirable bacteria, can lead to a myriad of outcomes that have deleterious effects on the body. Bacteria play key roles in regulating immunity and preventing intestinal wall permeability or “leaky gut.” Dysbiosis can lead to an increased production of unhealthy bacterial byproducts, intestinal barrier breakdown, and eventually disease.

Gut Health and Food Allergens

Unfortunately, food allergens are common in children and increasing in prevalence. Common allergens include peanuts, nuts, soy, cow’s milk, eggs, shellfish and wheat. Allergens may be outgrown, but allergies to peanuts and tree nuts, and seafood often persist (1). Several studies have found that whether or not a food allergy will last beyond infancy is associated with the diversity of the gut microbiome. Infants with reduced microbial richness and dysbiosis were more likely to develop a food allergy by one year of life as compared to those infants with a more diverse gut microbiome (2). In fact, every quartile increase in bacteria diversity was associated with a 55% reduction in the risk of developing a food allergy!

Studies that have looked into the gastrointestinal bacterial diversity and abundance of children have found strong correlations between over or underabundance of certain bacterial species and the presence of food allergies. For example, in infants with milk allergy, those that had Clostridia and Firmicutes at 3 and 6 months of life were more likely to outgrow their milk allergy by age 8 (3). It seems that the newborn period is a critical period in the development of food allergies.

Respiratory Allergens

Allergic rhinitis (AR) is the most common manifestation of respiratory allergy and affects up to 30% of people during adulthood and 40% of children (1). Research has also demonstrated an association between gut health and the presence of AR in both children and adults. A 2021 study of 57 adults with AR found that allergy-sufferers had reduced gut microbial diversity and dysbiosis as compared to healthy adults (4). Another study in infants found that those with lower levels of gut diversity within the first month of life were more likely to develop asthma by age 7 (5). Lower levels of gut bacterial diversity have been associated with an increased prevalence of atopic diseases (6).

This data makes sense when considering the “hygiene hypothesis,” wherein it is thought that our overly hygienic world limits the exposure we have to bacteria in our environment–thus contributing to the development of allergies. This would reduce the bacterial diversity in our guts, which is only compounded by a fiber-poor (equaling prebiotic-poor) Western diet. In fact, children raised in rural areas or on farms have a lower incidence of allergic diseases and asthma (1). This is likely because they are exposed to the microbes present in the soil, animals, and surroundings of their homes.

It also makes sense then that antibiotic use is associated with atopic disease. In a study published in 2019, researchers looked at Epic electronic health records between 2007 and 2016 of infants and children who had a diagnosis of asthma or AR. They found that antibiotic use in the first 12 months of life was associated with an increased risk for developing asthma, and that antibiotic use at any point in life was associated both with an increased risk for developing asthma or allergic rhinitis (7).

Eczema and Gut Health

Atopic dermatitis affects more than 20% of children in affluent countries. As with allergic rhinitis, asthma and food allergies, research has also shown that dysbiosis and poor bacterial diversity are associated with the presence of eczema in children and adults (1). In mouse studies, antibiotic administration exacerbated symptoms of eczema and resulted in higher levels of serum IgE antibodies (8). Conversely, giving probiotics to adults with eczema for at least 8 weeks actually resulted in reduced severity of eczema-related symptoms, which was demonstrated in multiple studies (9).

What Can You Do?

First of all, if you are planning on children or have an infant at home, there are steps you can take to help reduce the chance of future allergies or asthma. Taking a probiotic during pregnancy and eating a plant-rich diet has actually been shown to influence the gastrointestinal health of the newborn (1). If there are no medical contraindications, having a vaginal delivery is also preferred due to the exposure to the vaginal flora during descent. Infants born by vaginal delivery have a microbiota that differs from those infants born by c-section, wherein the latter tend to have higher levels of strains associated with skin flora and opportunistic bacteria.

A small study of 18 infants found that swabbing the mouth, face and body of infants born by c-section with the vaginal fluids from their mothers actually resulted in a bacterial makeup that was similar to infants born by vaginal delivery when testing at one month of age (10). Personally, if I were to ever require a c-section in the future and there were no medical issues, such as group B strep infection or chorioamnionitis, I would likely do this for my newborn.

Breastfeeding also has a hugely beneficial effect on the infant microbiome. Breast milk is rich in beneficial bacteria such as Bifidobacterium, Streptococci, and Lactobacillus. It also contains oligosaccharides and secretory IgA, which feed beneficial bacteria and help protect against infections. In infants born by c-section, breastfeeding has been found to partially re-establish the gut microbiota to what it otherwise would have been with a vaginal delivery (11).

For adults and children who already have allergies, improving gut health can be accomplished through diet and prebiotics and probiotics. A change in dietary intake can rapidly influence the gut microbiome. Switching from a meat-based diet to primarily plant-based diet resulted in changes in bacterial flora in as little as two days (12)! There are distinct differences between the gut microbiota of individuals eating a high fiber, plant-based diet as compared to those eating animal-rich diets. Consuming a plant-based diet supports beneficial microbiota and the production of short chain fatty acids. These compounds have several beneficial effects, including reducing inflammation, preventing intestinal permeability, and supporting brain health (13).

You can also supplement with probiotics and prebiotics. If you choose to take a probiotic, I recommend rotating formulations every few months. You may also consider comprehensive gut testing, which yield information on whether or not dysbiosis is present and can guide targeted decisions for supporting gut health. These tests can be ordered through a Functional Medicine physician. Additionally, you may want to consider allergy treatment with sublingual immunotherapy to reduce symptoms long-term.

I am fascinated by the ever-growing body of research linking the importance of gut health with a huge variety of diseases. I hope this information was enlightening, and that you may find relief for yourself or your loved ones who are suffering from allergies.

To your health,

Dr. Deppe


  1. Han P, Gu J-Q, Li L-S, Wang X-Y, Wang H-T, Wang Y, et al. The Association Between Intestinal Bacteria and Allergic Diseases—Cause or Consequence? Frontiers in Cellular and Infection Microbiology. 2021 Apr 15;11.

  2. ‌Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, et al. Infant gut microbiota and food sensitization: associations in the first year of life. Clinical & Experimental Allergy. 2015 Feb 25;45(3):632–43.

  3. Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, et al. Early-life gut microbiome composition and milk allergy resolution. Journal of Allergy and Clinical Immunology [Internet]. 2016 Oct [cited 2020 Nov 18];138(4):1122–30. Available from:

  4. Watts AM, West NP, Zhang P, Smith PK, Cripps AW, Cox AJ. The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls. International Archives of Allergy and Immunology. 2020 Sep 24;182(2):94–105.

  5. 1. Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L, Jenmalm MC. Low gut microbiota diversity in early infancy precedes asthma at school age. Clinical & Experimental Allergy. 2014 May 24;44(6):842–50.

  6. 1. Valkonen M, Wouters IM, Täubel M, Rintala H, Lenters V, Vasara R, et al. Bacterial Exposures and Associations with Atopy and Asthma in Children. PloS One [Internet]. 2015 [cited 2022 Apr 4];10(6):e0131594. Available from:

  7. ‌1. Ni J, Friedman H, Boyd BC, McGurn A, Babinski P, Markossian T, et al. Early antibiotic exposure and development of asthma and allergic rhinitis in childhood. BMC Pediatrics. 2019 Jul 5;19(1).

  8. ‌1. Kim H-J, Lee S-H, Hong S-J. Antibiotics-Induced Dysbiosis of Intestinal Microbiota Aggravates Atopic Dermatitis in Mice by Altered Short-Chain Fatty Acids. Allergy, Asthma & Immunology Research. 2020;12(1):137.

  9. ‌Rusu E, Enache G, Cursaru R, Alexescu A, Radu R, Onila O, et al. Prebiotics and probiotics in atopic dermatitis. Experimental and Therapeutic Medicine [Internet]. 2019 Aug 1;18(2):926–31. Available from:

  10. ‌Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. 2016 Feb 1;22(3):250–3.

  11. Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, et al. The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding. Frontiers in Microbiology. 2019 Mar 26;10.

  12. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2013 Dec 11;505(7484):559–63.

  13. Silva YP, Bernardi A, Frozza RL. The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication. Frontiers in Endocrinology [Internet]. 2020 Jan 31;11(25). Available from:

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