The Gut Flora-Food Allergies Connection

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The prevalence of food allergies and intolerances has risen exponentially within the past decade. Emerging research indicates that alterations in the intestinal flora may play an important role in the development of these disorders. Read on to learn how a disrupted gut microbiome predisposes to food allergies and intolerances and how restoration of the microbiome may be beneficial in the treatment of these conditions.

What Are Food Allergies and Intolerances?

Food allergy is defined as an immune response to a food that occurs reproducibly on exposure and generates adverse health effects. (1) Food allergies may be IgE-, non-IgE-, or IgG-mediated. IgE-mediated food allergies occur when the immune system produces IgE antibodies to foods; the antibodies bind to mast cells and basophils, stimulating the release of proinflammatory cytokines that induce an acute, and sometimes life-threatening, allergic response. Non-IgE-mediated food allergies involve components of the immune system other than IgE and can take up to several days to manifest; the symptoms are usually isolated to the GI tract. (2) While still controversial, there is evidence to suggest that food allergies can also be IgG-mediated; this type of allergy causes a delayed hypersensitivity to foods. (3, 4)

Probiotics for Food Allergies and Intolerances

Food intolerances, on the other hand, are non-immunological reactions to food. These reactions are typically associated with enzymatic deficiencies, malabsorption, or sensitivity to certain food components such as gluten or histamine. (5) They can cause a wide variety of gastrointestinal and inflammatory symptoms. Both food allergies and food intolerances significantly decrease quality of life. They take a toll on physical health, diminish the pleasure of eating, and provoke a state of hypervigilance about potential allergens lurking in food.

Food Allergies and Intolerances Are on the Rise

Nowadays, allergy-friendly aisles have become commonplace in grocery stores, and many schools and restaurants offer dietary accommodations for individuals with food allergies and intolerances. However, food allergies and intolerances have not always been such a big concern. In fact, it is only within the past decade that the prevalence of these conditions has skyrocketed. (6) Between 1997 and 2011, IgE-mediated food allergies increased by 50 percent in American children. (7) In addition, research has found that more than 20 percent of the population of industrialized countries, including the United States, United Kingdom, Australia, and China, suffer from food allergies or intolerances. (8, 9, 10)

Despite the dramatic rise in food allergies and intolerances, few treatment options are available. Conventional medicine advises patients to strictly avoid their trigger foods and to have epinephrine on hand for accidental exposures. However, neither of these strategies addresses the underlying cause of food allergy and intolerance. Novel treatment approaches are desperately needed. An emerging body of research indicates that alterations in the normal human gut flora play a role in the development of food allergies and intolerances. Modulation of the gut microbiota may alleviate food allergies and intolerances and potentially restore tolerance to triggering foods. (11, 12)

The Hygiene Hypothesis

The average human body contains an astonishing quantity of bacteria—nearly 40 trillion bacterial cells, to be exact! Humans evolved alongside these bacteria, and their presence within our bodies is crucial for our health. This concept has been elucidated in the “hygiene hypothesis.” The hygiene hypothesis states that a lack of early childhood exposure to microbes increases susceptibility to allergic disease by altering the intestinal microbiota and suppressing the normal development of the immune system. (13) Lifestyle factors that reduce microbial exposure early in life deprive the immune system of the stimulation it needs to prevent allergic disease. Factors that reduce microbial exposure include:

Antibiotic Use

In industrialized countries, infants and children often receive multiple courses of antibiotics early in life; this has a significant effect on immunity and may increase their risk of developing food allergies. (14) Maternal use of antibiotics before and during pregnancy also results in microbiome disruption and increases childhood risk of food allergies. (15) In addition, the widespread use of pharmaceuticals in agriculture has led to the presence of antibiotic residues in meat, dairy, and eggs. The consumption of residues in these foods may lead to chronic microbiome disruption. (16)

Chemical Exposure

Exposure to certain synthetic chemicals disrupts the human microbiome. Triclosan, a synthetic antibacterial substance, and parabens, a common preservative used in body products, have been linked to sensitization to food allergens. (17, 18)

A SAD Diet

Consumption of a Standard American Diet (SAD), high in refined carbohydrates and depleted of important nutrients, has been linked to an increased risk of food allergies and intolerances. (19) The relationship between diet and allergic disease risk appears to begin early in life; research has discovered that infants who eat a diet high in vegetables, fruits, and home-prepared foods during their first year of life have a reduced incidence of allergic disease compared to infants who consume fewer of these foods. (20)

C-section Birth

Infants born via C-section do not pick up commensal microbes such as Lactobacilli and Bifidobacteria in the birth canal, and are thus at an increased risk of developing allergic disease during childhood. (21)

Formula Feeding

Breastfeeding plays a significant role in the establishment of gut flora and immunity in infants; formula feeding, rather than breastfeeding, alters this process and has been associated with an increased risk of allergic disease. (22, 23)

Time Spent Indoors

Most people in industrialized societies spend a significant portion of their lives indoors. Research suggests that our disconnect with nature reduces the bacterial diversity of the human microbiome and is associated with an increased prevalence of allergic disease. (24)

For more information on the hygiene hypothesis and its impacts on our health, check out my previous podcast on the topic.

Alterations in Gut Flora, Food Allergies, and Food Intolerance

Notable differences have been observed in the gut flora between food-allergic and nonallergic individuals, suggesting that alterations in the normal human gut flora play an important role in the pathogenesis of food allergies and intolerances. (25) The normal human microbiome is composed of a diverse array of bacteria, including Bacteroides, Enterobacteria, Bifidobacteria, and Lactobacilli. These commensal bacteria interact with the mucosal immune system of the gut to promote immune tolerance of foods. (26) Lifestyle factors that decrease numbers of beneficial gut microbes can impair immune tolerance, resulting in allergic sensitization or intolerance to foods.

Alterations in specific types of gut bacteria have been linked to the development of food allergies. Most of the studies examining this phenomenon have been conducted in infants and children. In children, decreased Lactobacilli and increased Staphylococcus aureus are associated with egg and milk allergies. (27) Children with decreased levels of L. rhamnosus, L. casei, L. paracasei, and Bifidobacterium adolescentis during their first two months of life were found to be at a higher risk of developing allergic sensitization to cow’s milk, egg white, and inhalant allergens. (28) Reduced Bacteroides, Proteobacteria, and Actinobacteria are also associated with food allergen sensitization in infants. (29)

In addition to increasing the risk of food allergies, a lack of microbiome diversity may predispose to non-immunologic food intolerances such as gluten, FODMAP, and histamine intolerance. Certain species of bacteria assist in the breakdown of gluten proteins, and a lack of these may predispose to gluten intolerance. (30) Bacterial overgrowth of the small intestine is a common cause of FODMAP intolerance. (31) Histamine intolerance may occur when there is an overgrowth of bacteria that produce histamine or that make enzymes that interfere with the metabolism of histamine. (32, 33)

Gut bacteria and food allergies: what do they have in common?

Probiotics for Food Allergies and Intolerances

The therapeutic use of probiotics could truly be a breakthrough in the prevention and treatment of food allergies and intolerances. Prenatal supplementation with Bifidobacterium bifidum, B. lactis, Lactobacillus acidophilus, and Lactobacillus rhamnosus has been found to prevent food allergy-induced atopic sensitization in infants with a familial predisposition to food allergies. (34, 35, 36) Administration of L.salivarius, L. paracasei, Bifidobacterium animalis, and Bifidobacterium bifidum to pregnant women and to their infants significantly reduced the incidence of atopic sensitization to common food allergens in the infants. (37)

Probiotic supplementation may also decrease atopic sensitization, and potentially reverse sensitization, postnatally. In infants with an allergy to cow’s milk, supplementation with Lactobacillus rhamnosus promoted the acquisition of tolerance to milk proteins, thus reversing sensitization. (38) In older children with cow’s milk allergy, L. rhamnosus enhanced the production of IL-10, an anti-inflammatory cytokine, and alleviated allergic symptoms. (39) A meta-analysis of studies found that early-life supplementation with Lactobacillus and Bifidobacterium strains reduced the risk of atopic sensitization in children; however, it found that L. acidophilus increased the risk of sensitization. (40) Inconsistent findings such as this could be related to variations in probiotic dosing or duration of treatment. It is important to note that most of the studies assessing the efficacy of probiotics for the treatment of food allergies have been conducted prenatally, in infants, and in children. The gut microbiome in early life differs from that in adulthood, so the probiotic interventions discussed here may be more beneficial for the prevention and reversal of food allergies in young children, rather than in adults. More research is needed to determine whether probiotic supplementation can alleviate food allergies in adults.

In addition to preventing and reversing food allergies in children, probiotics may also be beneficial for treating food intolerance. Supplementation with a multi-strain probiotic that included Lactobacilli, Bacillus coagulans, and Saccharomyces boulardii significantly reduced symptoms in patients with non-celiac gluten sensitivity. (41) Probiotics such as Bacillus coagulans and L. acidophilus may ameliorate SIBO, a condition associated with FODMAP intolerance. (42) Finally, while research is not yet conclusive, it has been suggested that an overgrowth of histamine-producing bacteria in the gut may contribute to histamine intolerance. The avoidance of probiotic strains that produce histamine and consumption of strains that degrade histamine may therefore be helpful for relieving or alleviating histamine intolerance. Histamine-producing strains include L. reuteri, L. casei, and L. bulgaricus. (43, 44) Histamine-degrading strains include L. rhamnosus, L. plantarum, and Bifidobacteria. (45, 46, 47) Whereas probiotic treatment for food allergies appears to be beneficial primarily for infants and children, the benefits of probiotics for food intolerances can be extended to adults.

Mechanisms of Action of Probiotics

There are several mechanisms by which probiotics ameliorate food allergies and intolerances. Probiotics upregulate commensal gut microbes, the bacteria normally present in the gut that are responsible for interacting with the immune system to promote tolerance of foods. (48) Probiotics also reduce intestinal permeability, thus decreasing antigen uptake from the intestinal lumen; this phenomenon is the first step in food allergen sensitization. (49) Allergic disorders are associated with increased activity of the Th2 branch of the immune system. Probiotics modulate the immune system in such a way that it instead favors the Th1 response, an immune response associated with resolution of allergic symptoms. (50) In addition, probiotics increase intestinal IgA, an immunoglobulin associated with immune tolerance and a reduced risk of IgE-mediated allergic diseases. (51) Finally, probiotics may ameliorate food intolerances by crowding out pathogenic bacteria and reducing intestinal inflammation.

Add Prebiotics

Prebiotics potentiate the action of probiotics by promoting their proliferation in the intestine. Several studies have found an association between supplementation with prebiotic oligosaccharides and a reduced incidence of allergic disease. (52, 53)

Eat a Whole-Foods Diet

A whole-foods, nutrient-dense diet may proffer additional protection against food allergies and intolerances. Consumption of omega-3 fatty acids; vitamins C, E, and A; beta-carotene; and zinc are associated with a decreased incidence of food allergies. (54) Conversely, a diet high in refined carbohydrates, artificial sweeteners, gluten, omega-6 fatty acids, and food additives may predispose to food allergies and intolerances. While the evidence is not conclusive, the consumption of genetically modified foods may also contribute to food allergies and intolerances, due to the potential allergenicity of the technologically altered proteins in these foods. (55)


  • Encourage your pregnant patients to consume fermented foods and probiotics, since these may help prevent the occurrence of food allergies in their infants. They should consume strains such as bifidum, B. lactis, B. animalis, L. salivarius, L. paracasei, and L. rhamnosus. Consumption of prebiotic foods as supplements should also be recommended.
  • For food-intolerant patients, suggest probiotics such as Lactobacilli, Bacillus coagulans, and Saccharomyces boulardii. For patients with histamine intolerance, histamine-degrading strains may provide the most relief.
  • Practice caution when prescribing antibiotics, as they are a primary cause of intestinal flora disruption.
  • Encourage your food-allergic and intolerant patients to eat a nutrient-dense diet low in processed foods.
  • Encourage your patients to read the labels of body care products, and avoid ones that contain triclosan and parabens.
  • Emphasize the importance of spending time in contact with nature, where beneficial microbes are abundant.


  1. I préfère now prebiotics and not probiotics . The action of Prebiotics are realy . Pr Cani (He Found the Gasseri) Said : 10 20 30 years are necessary to understand probiotics action .
    I work with 3 Prebiotics and ISAAS hais change the définition of the Prebiotics a lot of Prebiotics are knowed now

  2. I’m 25, 3 years ago it seems like over night I became (more) intolerant after I went Paleo from a fast-food diet my whole life, to milk with a chin full of eczema. 6 months later I developed several allergies to fruits and raw vegetables where my throats and mouth would tingle and close or hives on my lips, both Ig-g: carrots, celery, green beans, apples, pears, nectarine, bean sprouts, cherries. I will definitely be trying out adding more pre and probiotics to my daily routine! Thank you for this article. My allergen Dr just said that our bodies change every 7 years and that I was unlucky to change for the worst! HA! Anyway, I’ll be testing out this adult allergy recovery with the pre/probiotic intake. Thanks for this article!

    • Has this pre/probiotic intake been beneficial to you? I’m going through something similar and would like some information

      • Hi Ashley,
        I’m going through something similar as well. I took a z-pack for a sinus infection and totally messed up my gut. Fast-forward a year and now I have an IgE reaction to pretty much all fruits and vegetables… Not sure if you ever heard back from Alyssa, but I’m happy to talk if you’d like. Maybe we can help each other out.

  3. Thank you so much for educating us on the importance of our gut health and required probiotics. Would you recommend taking a soil based probiotic along with the ones you recommended in your article to alleviate food intolerances? I have heard good things about MegaSpore probiotics and would appreciate your advice on how one like that would help with overcoming my many food sensitivities.
    Thank you for all that you do to educate and inform people who are needing and wanting to learn how to take care of themselves with awareness and intention.

  4. Great article! Small error throughout the article, those mentioned are species, not strains.

  5. In many of the articles cited here, the strains were mentioned but they’ve been omitted in this article. What’s the reasoning behind that? Confusing strains with species further confuses the public in purchasing non-strain-specific probiotics (many of which have zero research behind them), which defeats the purpose of citing all this research. Strain specific probiotics are a therapeutic tool, important in the healing process of a condition. It would be even better to edit this article showing specific strains as many of them are available in the USA market for everyone to purchase without a prescription and without the help of a practitioner.

  6. I love your work and find it very useful. In this article, you refer to strains of probiotics, yet you only list species. The effects of probiotics are strain-specific and it would have been helpful to not have to click through the references to find the specific strains.

  7. I am looking for research on using 23 and me as a way to determine correct probiotic to take. I cannot do all probiotics as I have reactions so I am looking for a more specific way to determine the correct ones.
    Thank you!

  8. We recently did spectra cell for my 8 year old son and he was deficit in several vitamins and minerals. He was delivered c-section and I was given antibiotics while in labor. He was recently diagnosed with a gluten allergy (not celiac) and egg yolk allergy (been paleo/organic since 2012). I’m researching now looking for the best probiotic for him. According to this article a multi-strain probiotic (lactobacilli, bacillus coagulan and saccharomyces boulardil) supplementation or the probiotic for gut health (Bacteriodes, Enterobacteria, Bifidobacteria and Lactobacilla) might be appropriate for him. I was looking on your supplement page, and you recommend the prescript-assist soil based probiotic with many strains I’m unfamiliar with. Is this good for him or can you recommend one that is available and more appropriate for food allergies. I’m on research overload at this point. Thank you so much!

  9. My GI recommended a probiotic, Align.It is sold over the counter.The Align gave me bad diarrhea, I stopped taking the Align.He also gave me something called Ibgard,that worked great.My abdominal pain ceased. I started back on align about 2 weeks later and the diarrhea came back but not as bad as when I first started on it,
    Also Ibgard is sold over the counter also.

  10. Extensive searching on my part has turned up no strain or species of a commercially available/produced L. plantarum product that claims to reduce histamine in vivo. Nor could I find any such research (that has been conducted) associated with a commercially available, or yet to be made available, product that makes, substantiates or explores such a claim.

    The citation in this article (48) references five out of 26 unidentified proprietary winery species of L. plantarum that were discovered to reduce histamine in a WINE medium. That’s a far stretch from the claim made in your article Chris. The bottom line is…it’s inaccurate.