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. Hi,
    I found you and your clinic over the Internet. I have been struggling with upper buttock lower back pain for 4 1/2 months. I have had extreme allergies in the last two years so much so that I had to leave the country to get better.I now believe that it is entirely to do with my gut and the situation I find myself in today is that I cannot drink any water without pain in my back as well as food.I have an allergic response with anything that goes into my mouth. I believe I have extreme candida that is causing my sensitivities.I am on the fourth day of a fast but the only thing I can consume without pain is vegetable juice with garlic,clove,oregano and black walnut tincture. I would love to be tested at your clinic but I am six hours away and we’ve already spent thousands of dollars trying to get me well. So any info you can give me at this time would be really appreciated.
    Thanks Rebecca Donvito

  2. I’ve always been very careful with my diet because of psoriasis that started at 18. Over the years I became intolerant to whole wheat even as I was taking probiotics and eating prebiotics foods. A high cholesterol / triglyceride /pressure diagnosis prompted me to switch to a whole foods plant based diet 2 years ago. My cholesterol, triglycerides, and high blood pressure plummeted in only a few weeks and I lost 20 pounds while maintaining a nice muscle mass. I stayed away from wheat because I was afraid of my gut reacting but I reintroduced it slowly a few months ago and haven’t had any issues. It feels good to eat bread and other grains again! I believe I restored my gut bacteria, removing the ones associated with animal foods was the key. I no longer take probiotics. And, as a bonus, psoriasis is almost completely gone and psoriatic arthritis as well. I’ve always exercised but I have to say now it’s much easier.