The Gut Microbiome in Food Sensitivities

Adverse reactions to food affect about 20% of the global population and stem from a range of immune and non-immune mechanisms (Turnbull et al., 2014). Food intolerances, such as lactose intolerance, are typically non-immune and involve digestion issues that often lead to gut symptoms due to microbial fermentation. In contrast, food sensitivities can be immune-mediated, including classic IgE-driven allergies that may lead to severe reactions like anaphylaxis, as well as non-IgE-mediated conditions such as protein-induced enterocolitis. Some disorders, like non-celiac wheat sensitivity (NCWS), involve both immune mechanisms but are not yet fully understood. NCWS, in particular, lacks reliable diagnostics and may be triggered by components like gluten, fructans, or α-amylase-trypsin inhibitors (ATIs), which can provoke inflammation. The rising prevalence of food sensitivities, especially celiac disease, suggests that environmental factors—like diet, microbiota shifts, and infections—play a role beyond genetics (Caminero et al., 2019).

Explored also was how gut bacteria contribute to gluten metabolism, a process often overlooked in the context of coeliac disease. Researchers cultured human fecal samples using gluten as the main nitrogen source and identified 144 bacterial strains from 35 species, with 94 of them able to break down gluten. Many strains also degraded the 33-mer peptide, a key immunogenic fragment involved in coeliac disease. Most bacteria belonged to the Firmicutes and Actinobacteria phyla, especially the Lactobacillus, Streptococcus, Staphylococcus, Clostridium, and Bifidobacterium genera. These findings suggest that gut microbes may influence gluten processing in the body and hold potential for future coeliac disease therapies (Caminero et al., 2014).

Another study explored the gut microbiota and short-chain fatty acid (SCFA) profiles in individuals with persistent IgE-mediated food allergies, including milk, sesame, peanut, and tree nut allergies. Researchers compared gut bacteria from 233 allergic patients and 58 non-allergic controls using DNA sequencing of fecal samples. They found that allergic individuals had significantly different microbiota compositions and lower bacterial diversity compared to controls. Notably, the beneficial species Prevotella copri was abundant in non-allergic individuals and strongly linked to higher SCFA levels—compounds known to support gut and immune health. These differences in microbial composition and SCFA profiles not only helped distinguish allergic from non-allergic individuals with high accuracy but also revealed unique bacterial signatures associated with different types of food allergies (Goldberg et al, 2020). The findings highlight the potential of targeting gut bacteria, especially P. copri and SCFA pathways, for diagnosing or even treating persistent food allergies.

This study from the Consortium of Food Allergy Research found that children with egg allergy have distinct early-life gut microbiota compared to healthy controls. By analyzing fecal samples from infants aged 3 to 16 months, researchers discovered that egg-allergic children had greater microbial diversity and specific bacterial families—like Lachnospiraceae, Streptococcaceae, and Leuconostocaceae—were more prevalent. While certain microbes were linked to egg sensitization, no connection was found between early microbiota and whether the allergy resolved by age 8 (Fazlollahi et al., 2018). 

Research has shown that changes in the intestinal microbiome may play a role in the development of food allergies, although this connection is less understood compared to its association with asthma. A study collected microbiome samples from children aged 3-6 months and assessed food sensitization and allergies at age 3. The findings revealed that specific gut bacteria, such as Haemophilus, Dialister, and Clostridium, were underrepresented in children with food sensitization, while other bacteria like Citrobacter, Oscillospira, and Lactococcus were less abundant in those with diagnosed food allergies (Savage et al., 2018). These results suggest that the microbiome could be involved in the development of food allergies, offering potential pathways for prevention and treatment strategies.

A recent analysis of American Gut Project data reveals a strong link between gut microbiota diversity and the presence of allergies in adults. Researchers found that individuals with food allergies (such as peanut or tree nut) and non-food allergies (such as drug, bee sting, or seasonal allergies) exhibited significantly lower gut microbiota richness compared to those without allergies. This reduction in microbial diversity, dysbiosis, was especially pronounced in participants with peanut and seasonal allergies. In addition to overall reduced diversity, these individuals had distinct microbial profiles characterized by increased levels of Bacteroidales and reduced levels of Clostridiales, two major bacterial groups in the gut (Hua et al., 2015). These shifts in microbial composition may disrupt immune regulation and contribute to allergic responses and suggests that strategies aimed at restoring microbial harmony could be promising for allergy prevention or treatment in adults.

Recent research has focused on how gut-derived metabolites (produced from nutrients by bacteria) and specific probiotic strains may restore or enhance immune tolerance. While the exact mechanisms are still being studied, growing evidence points to the potential for targeted interventions—such as using specific microbes or post-biotic compounds (non-living microbial products)—to prevent or manage food allergies. This opens the door to novel, microbiome-focused therapies based on timing, dosage, and microbial strain selection, with a special interest in how these interventions might influence immune function through epigenetic pathways (Canani et al., 2019). Environmental influences—such as industrialization and diets high in processed foods—can disrupt the gut microbiota and weaken the intestinal barrier, potentially heightening the risk of allergic sensitization. Changes in both the composition and function of the gut microbiome have also been linked to the development of food allergies (Poto et al., 2023). Additionally, microbiome testing and identifying unique microbial signatures relating to food allergies/intolerances can help incorporate more targeted prevention measures and improve quality of life.