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Is Your Gut Microbiome Putting You At Risk For Food Allergies?

Laura Kunces, PhD, RD
Onegevity

Food allergies in children seem to be as common as skinning a knee – seems like every child has one or maybe two foods they are allergic or sensitive to. Although it is estimated that 5-10 percent of children have food allergies, only 1-3 percent continue to suffer from food allergies into adulthood, although having food allergies continue into adulthood is on the rise.


It should be noted that food allergies and food intolerances are not the same things. Whereas a food allergy causes a reaction by the immune system, a food intolerance (or sensitivity) is less serious and characterized by GI symptoms such as gas, cramping, and bloating. 


A food allergy can occur at any time in a person’s life.


Medical insurance statistics indicate that food allergies are on the rise. And although we are visiting the hospital more frequently, seeking newer treatment options, and spending more money on the diagnosis and treatment of food allergies, they don’t appear to be going away. The lists of potentially allergenic foods include more than 170 foodstuffs, although the most likely triggers continue to be tree nuts, eggs, peanuts, fish, shellfish, milk, wheat, soy, and seeds.


What is a food allergy?

Food allergies are a lack of immune tolerance to dietary antigens,1 which means the immune system is unable to tolerate what it perceives as “toxins” from foods and instead activates specific regulatory T cells, known as Tregs. And we now believe the incidence of food allergies is influenced by epigenome-genome-environment interactions, which can lead to changes in immune system functionality.


What affects your risk for food allergies?

Unfortunately, some unmodifiable risk factors can predispose you to a higher risk for food allergies. Males tend to have a higher incidence of food allergies than do females. Ethnicity plays a role, too; there is an increased risk among Asian and African-Americans children. And scientists have now identified several genetic links, including a familial risk, human leukocyte antigen (HLA), and other specific genes.2


Many environmental associations have been found to either provide protection from or increase the risk of acquiring a food allergy through modulation of gut microbiota structure and function. Coming from a large family or living in quarters with many residents, exposure to pets and other animals, eating a varied diet full of fibers, certain probiotics, fermented foods, and antioxidants are all associated with a decreased incidence of food allergies.


Sufficient vitamin D status and regular consumption of omega-3 fatty acids can positively influence the development and function of the gut.3


Effects of early-life feeding play an important role too. 

Researchers suggest that having early colonization of the gut is important.4 Children who are breastfed tend to have fewer food allergies. Studies of the gut microbiome and food allergies show that the gut goes through incredible changes in early life, and gut dysbiosis by three months of life can have a profound effect on food sensitization starting as early as age one.4


Researchers have found that an elevated Enterobacteriaceae-to-Bacteroidaceae ratio and a decreased abundance of Ruminococcaceae during early life is associated with food allergies.


On the other hand, some exposures are associated with risk of developing food allergies: being born by C-section, early-life exposure to medications like antibiotics or gastric acidity inhibitors, and picky eaters who tend to only eat saturated fats and processed foods are big contributors. 


What is the latest research on the gut microbiome and food allergies?

Current research points to early gut dysbiosis (microbial imbalance) as a primary underlying factor for developing a food allergy and modulation of the trajectory of its course.5 In animal models, Treg cells were reduced in mice treated with antibiotics or in germ-free mice, with a consequent predisposition to allergy development. Scientists introduced Clostridia, or bacteria-derived short-chain fatty acids (SCFA) to the germ-free mice and found it increased the number of Treg cells and reduced their allergic response.6


In children with an allergy to cow’s milk, soy and rice-based formulas are the usual alternatives. One study found that children with an allergy to cow’s milk had low counts of Coriobacteriaceae and Bifidobacteriaceae in their stool after consuming a soy or rice alternative. However, when children consumed a highly hydrolyzed milk formula, Coriobacteriaceae and the genus Collinsella (the major bacteria that metabolizes lactose in the gut) increased.7 


In the same study, researchers found fecal butyrate levels had a positive correlation with Coriobacteriaceae.7 Consumption of a hydrolyzed casein formula plus probiotics (L. rhamnosus GG) increased short-chain fatty acid-producing bacteria and butyrate levels, which are associated with immune tolerance.8


These findings suggest an otherwise intolerant individual might be able to tolerate a cow’s milk product in the presence of the right proportion of gut bacteria.


There now seems to be a consensus that no particular bacterial taxa is associated with food allergies; rather, a broad range of microbes can make a positive or negative effect on immune tolerance mechanisms.


Technology has advanced our understanding of food allergies.

We know vastly more now about the microbiome than we did 25 years ago, and we have made the most progress in the past 10 years. Most of the advances are due to the technology revolution that can sequence the gut’s microbiota population. 


The original sequencing method was called 16S sequencing – it measures ribosomal RNA (rRNA) genes. Typical 16S sequencing is cheap, quick, and does a marginal job measuring microbial diversity and detecting dysbiosis, although we are still unsure how stable RNA is over time and when it is exposed to temperature changes. And although 16S sequencing does identify bacteria, it is not to the same precision and accuracy as advanced newer methods.


The newer, more advanced technology is called whole metagenome shotgun sequencing. Onegevity Health uses this technology to evaluate DNA fragmentation, sequence, and reconstruct overlapping sequences, and assemble them into a continuous sequence. With this method, there is deep sequencing of all genes present and no amplification bias of genes (as there can be in other techniques). It costs more, takes longer, and requires advanced bioinformatics analysis, but it has unparalleled accuracy for the depth of bacteria identification and measurement, including down to the strain level.  


Discovering patterns and functions of gut microbiota takes advanced metagenomic shotgun sequencing precision.


Although Onegevity's Gutbio test will not diagnose a food allergy, it will give you insightful information as to the types and amounts of bacteria present in your stool that might be influencing intolerances to food and foodstuffs. Gut health is an important piece of your whole-body health puzzle and should be considered in the context of your genotype and phenotype, everyday diet, environment, and lifestyle – past and present.



1.       Sicherer S, Sampson H. Food allergy: A review and update on epidemiology, pathogenesis, diagnosis, prevention, and management. J Allergy Clin Immunol 2018;141(1):41-58.

2.       Loh W, Tang M. The epidemiology of food allergy in the global context. Int J Environ Res Public Health 2018;15(9). doi:10.3390/ijerph15092043.

3.       Berni-Canani R, Paparo L, Nocerino R, et al. Gut microbiome as target for innovative strategies against food allergy. Front Immunol 2019;10:191.

4.       Azad M, Konya T, Guttman D, et al. Infant gut microbiota and food sensitization: associations in the first year of life. Clin Exp Allergy 2015;45(3):632-643.

5.       Savage J, Lee-Sarwar K, Sordillo J, et al. A prospective microbiome-wide association study of food sensitization and food allergy in early childhood. Allergy 2018;73(1):145-152.

6.       Atarashi K, Tanoue T, Shima T, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011;331(6015):337-341.

7.       Díaz M, Guadamuro L, Espinosa-Martos I, et al. Microbiota and derived parameters in fecal samples of infants with non-IgE cow’s milk protein allergy under a restricted diet. Nutrients 2018;10(10). doi:10.3390/nu10101481

8.       Berni-Canani R, De Filippis F, Nocerino R, et al. Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow’s milk allergy. Sci Rep 2018;8(1):12500.