Role of the Microbiome in Food Allergy

Gender Differences in the Interplay between Vitamin D and Microbiota in Allergic and Autoimmune Diseases

The synergic role of vitamin D and the intestinal microbiota in the regulation of the immune system has been thoroughly described in the literature. Vitamin D deficiency and intestinal dysbiosis have shown a pathogenetic role in the development of numerous immune-mediated and allergic diseases. The physiological processes underlying aging and sex have proven to be capable of having a negative influence both on vitamin D values and the biodiversity of the microbiome. This leads to a global increase in levels of systemic inflammatory markers, with potential implications for all immune-mediated diseases and allergic conditions. Our review aims to collect and analyze the relationship between vitamin D and the intestinal microbiome with the immune system and the diseases associated with it, emphasizing the effect mediated by sexual hormones and aging.

Targeting Food Allergy with Probiotics

The globally dramatic increase in food allergy prevalence and severity is demanding effective preventive and therapeutic strategies. Food allergy derives from a defect of immune tolerance mechanisms. Immune tolerance is modulated by gut microbiome composition and function, and gut microbiome dysbiosis has been associated with the development of food allergy. Selected probiotic strains could regulate immune tolerance mechanisms. The mechanisms are multiple and are still not completely defined. Increasing evidence is providing useful information on the choice of optimal bacterial species/strains, dosage, and timing for intervention. The increased knowledge on the crucial role played by postbiotic gut microbiome-derived metabolites, such as butyrate, is also opening the way to a post- biotic approach in the stimulation of immune tolerance.

Alteration of taste perception, food neophobia and oral microbiota composition in children with food allergy

Currently, the mechanisms underlying sensory perception and sensory performance in children with food allergies are far from being understood. As well, only recently, single research afforded the oral host-commensal milieu, addressing oral microbial communities in children with peanut allergies. To bridge the current gaps in knowledge both in the sensory and microbial fields, a psychophysiological case-control study was performed in allergic children (n = 29) and a healthy sex-age-matched control group (n = 30). Taste perception, food neophobia, and liking were compared in allergic and non-allergic children. The same subjects were characterized for their oral microbiota composition by addressing saliva to assess whether specific profiles were associated with the loss of oral tolerance in children with food allergies. Our study evidenced an impaired ability to correctly identify taste qualities in the allergic group compared to controls. These results were also consistent with anatomical data related to the fungiform papillae on the tongue, which are lower in number in the allergic group. Furthermore, distinct oral microbial profiles were associated with allergic disease, with significant down-representations of the phylum Firmicutes and of the genera Veillonella spp., Streptococcus spp., Prevotella spp., and Neisseria spp. For the first time, this study emphasizes the link between sensory perception and food allergy, which is a novel and whole-organism view of this pathology. Our data indicated that an impaired taste perception, as regards both functionality and physiologically, was associated with food allergy, which marginally influences the food neophobia attitude. It is also accompanied by compositional shifts in oral microbiota, which is, in turn, another actor of this complex interplay and is deeply interconnected with mucosal immunity. This multidisciplinary research will likely open exciting new approaches to therapeutic interventions.

Immunomodulatory role of oral microbiota in inflammatory diseases and allergic conditions

In recent years, the interplay between oral microbiota and systemic disease has gained attention as poor oral health is associated with several pathologies. The oral microbiota plays a role in the maintenance of overall health, and its dysbiosis influences chronic inflammation and the pathogenesis of gum diseases. Periodontitis has also been associated with other diseases and health complications such as cancer, neurogenerative and autoimmune disorders, chronic kidney disease, cardiovascular diseases, rheumatic arthritis, respiratory health, and adverse pregnancy outcomes. The host microbiota can influence immune cell development and immune responses, and recent evidence suggests that changes in oral microbiota composition may also contribute to sensitization and the development of allergic reactions, including asthma and peanut allergies. Conversely, there is also evidence that allergic reactions within the gut may contribute to alterations in oral microbiota composition. Here we review the current evidence of the role of the oral microbiota in inflammatory diseases and health complications, as well as its future relevance in improving health and ameliorating allergic disease.

Combined IgE neutralization and Bifidobacterium longum supplementation reduces the allergic response in models of food allergy

IgE is central to the development of allergic diseases, and its neutralization alleviates allergic symptoms. However, most of these antibodies are based on IgG1, which is associated with an increased risk of fragment crystallizable-mediated side effects. Moreover, omalizumab, an anti-IgE antibody approved for therapeutic use, has limited benefits for patients with high IgE levels. Here, we assess a fusion protein with extracellular domain of high affinity IgE receptor, FcεRIα, linked to a IgD/IgG4 hybrid Fc domain we term IgE_TRAP, to reduce the risk of IgG1 Fc-mediated side effects. IgE_TRAP shows enhanced IgE binding affinity compared to omalizumab. We also see an enhanced therapeutic effect of IgE_TRAP in food allergy models when combined with Bifidobacterium longum, which results in mast cell number and free IgE levels. The combination of IgE_TRAP and B. longum may therefore represent a potent treatment for allergic patients with high IgE levels.

IgE is a critical component of the allergic response and therapeutic targeting can alleviate symptomology. Here the authors propose the combined use of Bifidobacterium longum and a FcεRIα extracellular domain linked to a IgD/IgG4 hybrid Fc domain fusion protein called IgE_TRAP and show reduction of mast cell and IgE levels in models of food allergy.

Multiscale study of the oral and gut environments in children with high- and low-threshold peanut allergy

BACKGROUND

The oral and gut microbiomes have each been associated with food allergy status. Within food allergy, they may also influence reaction thresholds.

OBJECTIVE

Our aim was to identify oral and gut microbiota associated with reaction thresholds in peanut allergy.

METHODS

A total of 59 children aged 4 to 14 years with suspected peanut allergy underwent double-blind, placebo-controlled food challenge to peanut. Those children who reacted at the 300-mg or higher dose of peanut were classified as high-threshold (HT), those who reacted to lower doses were classified as low-threshold (LT), and those children who did not react were classified as not peanut allergic (NPA). Saliva and stool samples collected before challenge underwent DNA isolation followed by 16S rRNA sequencing and short-chain fatty acid measurement.

RESULTS

The 59 participants included 38 HT children and 13 LT children. Saliva microbiome α-diversity (Shannon index) was higher in LT children (P = .017). We identified saliva and stool microbiota that distinguished HT children from LT children, including oral Veillonella nakazawae (amplicon sequence variant 1979), which was more abundant in the HT group than in the LT group (false discovery rate [FDR] = 0.025), and gut Bacteroides thetaiotaomicron (amplicon sequence variant 6829), which was less abundant in HT children than in LT children (FDR = 0.039). Comparison with NPA children revealed consistent ordinal trends between these discriminating species and reaction thresholds. Importantly, many of these threshold-associated species were also correlated with short-chain fatty acid levels at the respective body sites, including between oral V nakazawae and oral butyrate (r = 0.57; FDR = 0.049).

CONCLUSION

Findings from this multiscale study raise the possibility of microbial therapeutics to increase reaction thresholds in children with food allergy.

The Environmental Microbiome, Allergic Disease, and Asthma

The environmental microbiome represents the entirety of the microbes and their metabolites that we encounter in our environments. A growing body of evidence supports the role of the environmental microbiome in risk for and severity of allergic diseases and asthma. The environmental microbiome represents a ubiquitous, lifelong exposure to non-self antigens. During the critical window between birth and 1 year of life, interactions between our early immune system and the environmental microbiome have 2 consequences: our individual microbiome is populated by environmental microbes, and our immune system is trained regarding which antigens to tolerate. During this time, a diversity of exposures appears largely protective, dramatically decreasing the risk of developing allergic diseases and asthma. As we grow older, our interactions with the environmental microbiome change. While it continues to exert influence over the composition of the human microbiome, the environmental microbiome becomes increasingly a source for antigenic stimulation and infection. The same microbial exposure protective against disease development may exacerbate disease severity. Although much has been learned about the importance of the environmental microbiome in allergic disease, much more remains to be understood about these complicated interactions between our environment, our microbiome, our immune system, and disease.

Mode of Birth Is Not Associated With Food Allergy Risk in Infants

BACKGROUND

The association between mode of delivery and the risk of food allergy remains unclear due to the absence of studies with both challenge-proven food allergy outcomes and detailed information on the type of caesarean delivery.

OBJECTIVE

We assessed whether emergency or elective caesarean, or caesarean delivery in the presence or absence of labor initiation, is associated with the risk of food allergy.

METHODS

The HealthNuts study recruited 5276 12-month-old infants who underwent skin prick testing and oral food challenge to ascertain food allergy status, and linked the child's study data to additional birth data from the Victorian Perinatal Data Collection.

RESULTS

Parents of 3006 children consented to data linkage, and birth data were obtained on 2045. In this subgroup, 30% were born by caesarean and 13% had food allergy. Caesarean delivery, compared with vaginal birth, was not associated with the risk of food allergy (adjusted odds ratio [aOR]: 0.95, 95% confidence interval [CI]: 0.70, 1.30). Neither caesarean delivery before the onset of labor, nor after the onset of labor, was associated with the risk of food allergy (aOR: 0.83, 95% CI: 0.55-1.23 and aOR: 1.13, 95% CI: 0.75-1.72, respectively). Delivery by elective or emergency caesarean, compared with vaginal delivery, was not associated with risk of food allergy (aOR: 1.05, 95% CI: 0.71-1.55 and aOR: 0.86, 95% CI: 0.56-1.31). There was no evidence of effect modification by breastfeeding, older siblings, pet dog ownership, or maternal allergy.

CONCLUSION

Caesarean delivery, either with or without labor, or elective or emergency, was not associated with the risk of food allergy in a population-based cohort of 12-month-old infants.

Diet Diversity Through the Life-Course as an Opportunity Toward Food Allergy Prevention

The prevalence of food allergies (FA) is increasing worldwide. Generally, the onset of allergies, including FA, begins in early childhood and may persist and/or develop through the life-course. Even though epidemiological studies have focused mainly on children, allergies can also occur for the first-time during adulthood. Within the prolongation of life, it is expected that allergies will be encountered more often even in older people. Recent findings suggest that an early exposure to diverse food antigens may promote the development of immune tolerance. Accordingly, diet diversity during the first year of life or even earlier may have a positive impact on the prevention of allergies. The anti-inflammatory properties of some dietary nutrients may positively contribute to a tolerogenic immune environment too. Diet diversity is associated with a more favorable microbiome, and increasing evidence suggests a promising role of gut microbiota manipulation in inducing immune tolerance. Unjustified avoidance of allergenic foods may expose to intakes of some nutrients below recommended levels through the life-course, even more in cases of self-diagnosis and treatment of presumed forms of food intolerance. Nutritional strategies including the early exposure to a variety of food antigens are a promising area of research for preventive purposes through the life-course possibly extending positive outcomes to older stages. The aim of this paper is to highlight the role of diet diversity in preventing the development of FA starting in early life, as well as to provide an overview of the main strategies to prevent related nutritional issues throughout the life-course.

New perspective on fecal microbiota transplantation in liver diseases

Chronic liver disease including non-alcoholic fatty liver disease and alcohol-related liver disease is one of the most common diseases worldwide. The gut-liver axis plays an important role in the pathogenesis of liver disease. Small intestinal bacterial overgrowth, dysbiosis, leaky bowel, bacterial translocation, and imbalanced metabolites are related to the progression of chronic liver disease. Recently, novel therapeutic approaches for microbiota modulation such as personalized diet, probiotics, prebiotics, antibiotics, engineered microbiotas, phage therapy, stomach operation, and fecal microbiota transplantation (FMT) have been proposed with numerous promising results in the effectiveness and clinical application. Although the evidence is still lacking, FMT, a type of fecal bacteriotherapy, has been known as a candidate for the treatment of liver disease. This review article focuses on the most recent advances in our understanding of FMT in chronic liver disease such as non-alcoholic and alcohol-related liver disease.

Role of Microbiota-Derived Metabolites in Alcoholic and Non-Alcoholic Fatty Liver Diseases

Chronic liver disease encompasses diseases that have various causes, such as alcoholic liver disease (ALD) and non-alcoholic fatty liver disease (NAFLD). Gut microbiota dysregulation plays a key role in the pathogenesis of ALD and NAFLD through the gut-liver axis. The gut microbiota consists of various microorganisms that play a role in maintaining the homeostasis of the host and release a wide number of metabolites, including short-chain fatty acids (SCFAs), peptides, and hormones, continually shaping the host's immunity and metabolism. The integrity of the intestinal mucosal and vascular barriers is crucial to protect liver cells from exposure to harmful metabolites and pathogen-associated molecular pattern molecules. Dysbiosis and increased intestinal permeability may allow the liver to be exposed to abundant harmful metabolites that promote liver inflammation and fibrosis. In this review, we introduce the metabolites and components derived from the gut microbiota and discuss their pathologic effect in the liver alongside recent advances in molecular-based therapeutics and novel mechanistic findings associated with the gut-liver axis in ALD and NAFLD.

Primary prevention of food allergy in 2021: Update and proposals of French-speaking pediatric allergists

During the past years, there has been an alarming increase in cases of food allergy and anaphylaxis in ever-younger children. Often, these children have multiple food allergies and food sensitizations, involving allergens with high anaphylactic potential, such as peanuts and nuts, which have a major influence on their quality of life and future. After reviewing the current epidemiological data, we discuss the main causes of the increase in food allergies. We analyze data from studies on the skin barrier and its fundamental role in the development of sensitization and food allergies, data on the tolerogenic digestive tract applied in particular to hen eggs and peanuts, as well as data on the prevention of allergy to cow milk proteins. In light of these studies, we propose a practical guide of recommendations focused on infants and the introduction of cow milk, the management of eczema, and early and broad dietary diversification including high-risk food allergens, such as peanut and nuts while taking into account the food consumption habits of the family.

Water Kefir and Derived Pasteurized Beverages Modulate Gut Microbiota, Intestinal Permeability and Cytokine Production In Vitro

Fermentation is an ancient food preservation process, and fermented products have been traditionally consumed in different cultures worldwide over the years. The interplay between human gut microbiota, diet and host health is widely recognized. Diet is one of the main factors modulating gut microbiota potentially with beneficial effects on human health. Fermented dairy products have received much attention, but other sources of probiotic delivery through food received far less attention. In this research, a combination of in vitro tools mimicking colonic fermentation and the intestinal epithelium have been applied to study the effect of different pasteurized and non-pasteurized water kefir products on gut microbiota, epithelial barrier function and immunomodulation. Water kefir increased beneficial short-chain fatty acid production at the microbial level, reduced detrimental proteolytic fermentation compounds and increased Bifidobacterium genus abundance. The observed benefits are enhanced by pasteurization. Pasteurized products also had a significant effect at the host level, improving inflammation-induced intestinal epithelial barrier disruption and increasing IL-10 and IL-1β compared to the control condition. Our data support the potential health benefits of water kefir and demonstrate that pasteurization, performed to prolong shelf life and stability of the product, also enhanced these benefits.

Multidimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy

BACKGROUND

The oral mucosa is the initial interface between food antigens, microbiota, and mucosal immunity, yet, little is known about oral host-environment dynamics in food allergy.

OBJECTIVE

Our aim was to determine oral microbial, metabolic, and immunologic profiles associated with peanut allergy.

METHODS

We recruited 105 subjects (56 with peanut allergy and 49 healthy subjects) for salivary microbiome profiling using 16S ribosomal RNA sequencing, short-chain fatty acid (SCFA) metabolite assays using liquid chromatography/mass spectrometry, and measurement of oral secreted cytokines using multiplex assays. Analyses within and across data types were performed.

RESULTS

The oral microbiome of individuals with peanut allergy was characterized by reduced species in the orders Lactobacillales, Bacteroidales (Prevotella spp), and Bacillales, and increased Neisseriales spp. The distinct oral microbiome of subjects with peanut allergy was accompanied by significant reductions in oral SCFA levels, including acetate, butyrate, and propionate, and significant elevation of IL-4 secretion. Decreased abundances of oral Prevotella spp and Veillonella spp in subjects with peanut allergy were significantly correlated with reduced oral SCFA levels (false discovery rate < 0.05), and increased oral Neisseria spp was correlated with lower oral SCFA levels (false discovery rate < 0.05). Additionally, oral Prevotella spp abundances were correlated with decreased local secretion of TH2-stimulating epithelial factors (IL-33 and thymic stromal lymphopoietin) and TH2 cytokines (IL-4, IL-5, and IL-13), whereas oral Neisseria spp abundance was positively associated with a TH2-skewed oral immune milieu.

CONCLUSION

Our novel multidimensional analysis of the oral environment revealed distinct microbial and metabolic profiles associated with mucosal immune disturbances in peanut allergy. Our findings highlight the oral environment as an anatomic site of interest to examine host-microbiome dynamics in food allergy.

Microbial Model Construction Activity for Introducing Students to Microbiome and Metagenomic Fields

Educational activities in biology teaching focused on model construction allow students to make the invisible evident. The development and integration of these pedagogical strategies in emerging sciences is essential and necessary in the classroom of noncollege academia. A two-component pedagogical activity was developed to expose high school students to the emerging disciplines of microbiomes and metagenomics. An introductory talk about microbiomes and host-microbe interactions was designed and presented to high school students at an educational center in the western region of Puerto Rico. After the talk, the students were organized into teams and required to choose one of the microbiome cases discussed to generate an oral presentation and a model describing the microbe's relationship with the host (microbiome interactions). A total of five models were generated by the students, which represented bacterial and yeast interaction with animals and plants. The teaching-learning process was assessed using pre/posttests and model evaluation instruments. The combination of the talk, model construction, and oral presentation increased the general knowledge of the participants by 43% from pre- to posttest. The students' knowledge of the concepts of metagenomics and microbiomes increased 30% and 49%, respectively. The data support that students were able to define and integrate the concepts successfully after the implementation of the educational strategies. This team-based educational model of exposing students to emerging disciplines is necessary to promote the active learning process in current topics in science in a nontraditional way.

Potential beneficial effects of kefir and its postbiotic, kefiran, on child food allergy

Food allergies are known as the public health problem, affecting people of all age groups, but more commonly in babies and children, with consequences for nutritional status and quality of life. The increase in the consumption of healthy foods has consequently led to an increased demand for functional foods with specific health benefits. Thus, the pharmaceutical industry's interest in natural products has grown every time and is therefore considered as an alternative to synthetic drugs. Kefir has been outstanding for several years as promising in the manufacture of various pharmaceutical products, due to its nutritional and therapeutic properties for the treatment of many diseases. Currently, a wide variety of new functional foods are appearing on the market, representing an important segment. Postbiotics, for example, has stood out for being a product with action similar to probiotics, without offering side effects. The kefiran is the postbiotic from kefir that promotes potential beneficial effects on food allergy from the intestinal microbiome to the immune system. In this context, it is necessary to know the main promoting component of this functional effect. This review compiles the benefits that kefir, and especially its postbiotic, kefiran, can bring to food allergy. In addition, it serve as a subsidy for studies on the development of innovative nutraceutical products, including the use of kefiran as an alternative therapy in food allergy.

Butyrate as a bioactive human milk protective component against food allergy

BACKGROUND

Food allergy (FA) is a growing health problem worldwide. Effective strategies are advocated to limit the disease burden. Human milk (HM) could be considered as a protective factor against FA, but its mechanisms remain unclear. Butyrate is a gut microbiota-derived metabolite able to exert several immunomodulatory functions. We aimed to define the butyrate concentration in HM, and to see whether the butyrate concentration detected in HM is able to modulate the mechanisms of immune tolerance.

METHODS

HM butyrate concentration from 109 healthy women was assessed by GS-MS. The effect of HM butyrate on tolerogenic mechanisms was assessed in in vivo and in vitro models.

RESULTS

The median butyrate concentration in mature HM was 0.75 mM. This butyrate concentration was responsible for the maximum modulatory effects observed in all experimental models evaluated in this study. Data from mouse model show that in basal condition, butyrate up-regulated the expression of several biomarkers of gut barrier integrity, and of tolerogenic cytokines. Pretreatment with butyrate significantly reduced allergic response in three animal models of FA, with a stimulation of tolerogenic cytokines, inhibition of Th2 cytokines production and a modulation of oxidative stress. Data from human cell models show that butyrate stimulated human beta defensin-3, mucus components and tight junctions expression in human enterocytes, and IL-10, IFN-γ and FoxP3 expression through epigenetic mechanisms in PBMCs from FA children. Furthermore, it promoted the precursors of M2 macrophages, DCs and regulatory T cells.

CONCLUSION

The study's findings suggest the importance of butyrate as a pivotal HM compound able to protect against FA.

Genetics of Food Allergy

The risk factors for food allergy (FA) include both genetic variants and environmental factors. Advances using both candidate-gene association studies and genome-wide approaches have led to the identification of FA-associated genes involved in immune responses and skin barrier functions. Epigenetic changes have also been associated with the risk of FA. In this chapter, we outline current understanding of the genetics, epigenetics and the interplay with environmental risk factors associated with FA. Future studies of gene-environment interactions, gene-gene interactions, and multi-omics integration may help shed light on the mechanisms of FA, and lead to improved diagnostic and treatment strategies.

Association between physical activity and changes in intestinal microbiota composition: A systematic review

INTRODUCTION

The intestinal microbiota comprises bacteria, fungi, archaea, protists, helminths and viruses that symbiotically inhabit the digestive system. To date, research has provided limited data on the possible association between an active lifestyle and a healthy composition of human microbiota. This review was aimed to summarize the results of human studies comparing the microbiome of healthy individuals with different physical activity amounts.

METHODS

We searched Medline/Ovid, NIH/PubMed, and Academic Search Complete between August-October 2020. Inclusion criteria comprised: (a) cross-sectional studies focused on comparing gut microbiome among subjects with different physical activity levels; (b) studies describing human gut microbiome responses to any type of exercise stimulus; (c) studies containing healthy adult women and men. We excluded studies containing diet modifications, probiotic or prebiotic consumption, as well as studies focused on diabetes, hypertension, cancer, hormonal dysfunction. Methodological quality and risk of bias for each study were assessed using the Risk Of Bias In Non-randomized Studies-of Interventions tool. The results from cross-sectional and longitudinal studies are shown independently.

RESULTS

A total of 17 articles were eligible for inclusion: ten cross-sectional and seven longitudinal studies. Main outcomes vary significantly according to physical activity amounts in longitudinal studies. We identified discrete changes in diversity indexes and relative abundance of certain bacteria in active people.

CONCLUSION

As literature in this field is rapidly growing, it is important that studies incorporate diverse methods to evaluate other aspects related to active lifestyles such as sleep and dietary patterns. Exploration of other groups such as viruses, archaea and parasites may lead to a better understanding of gut microbiota adaptation to physical activity and sports and its potentially beneficial effects on host metabolism and endurance.

Microscopic Communities: Interdisciplinary Exploration of Microbes in the Classroom

Children are aware of microbes from a young age and are rightly encouraged to wash their hands to prevent illness. However, myriad microbes live in, on, and around us, most of which are benign or beneficial. Our goal was to teach elementary students about microbiota by leveraging familiar literacy practices, social studies themes, and the arts to advance students' knowledge and reasoning skills in science. With this perspective in mind, we developed and implemented an interdisciplinary unit targeted at second grade, in which students learned about microbes and microbial communities. Our goal was to further students' conceptual knowledge of the microbes that surround them by purposefully integrating microbial communities within the second grade curriculum. Throughout the unit, students engaged in hands-on, inquiry-based science experiences and used multimodal communication (through a combination of linguistic, visual, audio, gestural, and spatial modes): they sampled microbes from their own bodies and/or environments and applied their knowledge and imagination to create their own microbes through art and story-telling, generating a class microbial community-both literal and artistic. At the end of the unit, students demonstrated knowledge of microbes and of the diversity and ubiquity of microbial communities and habitats.

Advancing Food Allergy Through Omics Sciences

Since the publication of the first draft of the human genome, there has been an explosion of new technologies with increasing power to interrogate the totality of biological molecules (eg, DNA, RNA, proteins, metabolites) and their modifications (eg, DNA methylation, histone modifications). These technologies, collectively called omics, have been widely applied in the last 2 decades to study biological systems to gain deeper insight into mechanisms driving the physiology and pathophysiology of human health and disease. Because of its complex, multifactorial nature, food allergy is especially well suited to be investigated using omics approaches. In this rostrum, we review how omic technologies have been applied to explore diverse aspects of food allergy, including adaptive and innate immune processes in food-allergic responses, the role of the microbiome in food allergy risk, metabolic changes in the gut and blood associated with food allergy, and the identification of biomarkers and potential therapeutic targets for the condition. We discuss the strengths and limitations of the studies performed thus far and the need to adopt systems biology approaches that integrate data from multiple omics to fully leverage the potential of these technologies to advance food allergy research and care.

Human microbiome and allergy

Human microbiome contributes to critical functions that impact health and disease. It influences the development of the immune system, and the pathogenesis of immunological disorders included allergy. While it is easy to understand how airway microbiome, influencing local inflammation and immune activity, could contribute to shaping asthma phenotype, it is not so obvious to understand the influence by the gut microbiome, but there is growing evidence about it. The increase of allergic disorders in western countries led to investigate the role environment is playing and how it may change our microbiome and immune system, with the hope of finding new preventive approaches for allergy.

Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention

The gut microbiota is a new frontier in health and disease. Not only many diseases are associated with perturbed microbiota, but an increasing number of studies point to a cause-effect relationship. Defining a healthy microbiota is not possible at the current state of our knowledge mostly because of high interindividual variability. A resilient microbiota could be used as surrogate for healthy microbiota. In addition, the gut microbiota is an “organ” with frontline exposure to environmental changes and insults. During the lifetime of an individual, it is exposed to challenges such as unhealthy diet, medications and infections. Impaired ability to bounce back to the pre-challenge baseline may lead to dysbiosis. It is therefore legitimate to postulate that maintaining a resilient microbiota may be important for health. Here we review the concept of resilience, what is known about the characteristics of a resilient microbiota, and how to assess microbiota resilience experimentally using a model of high fat diet challenge in humans. Interventions to maintain microbiota resilience can be guided by the knowledge of what microbial species or functions are perturbed by challenges, and designed to replace diminished species with probiotics, when available, or boost them with prebiotics. Fibers with multiple structures and composition can also be used to increase microbiota diversity, a characteristic of the microbiota that may be associated with resilience. We finally discuss some open questions and knowledge gaps.

Emerging Food Allergy Biomarkers

The management of food allergy is complicated by the lack of highly predictive biomarkers for diagnosis and prediction of disease course. The measurement of food-specific IgE is a useful tool together with clinical history but is an imprecise predictor of clinical reactivity. The gold standard for diagnosis and clinical research is a double-blind placebo-controlled food challenge. Improvement in our understanding of immune mechanisms of disease, development of high-throughput technologies, and advances in bioinformatics have yielded a number of promising new biomarkers of food allergy. In this review, we will discuss advances in immunoglobulin measurements, the utility of the basophil activation test, T-cell profiling, and the use of -omic technologies (transcriptome, epigenome, microbiome, and metabolome) as biomarker tools in food allergy.

Microbiome definition re-visited: old concepts and new challenges

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

Prospective Assessment of Pediatrician-Diagnosed Food Protein-Induced Allergic Proctocolitis by Gross or Occult Blood

BACKGROUND

Food protein-induced allergic proctocolitis (FPIAP) is an early and common manifestation of food allergy, yet its epidemiology and relationship to other allergic diseases remain unclear.

OBJECTIVE

To prospectively define the incidence of FPIAP as it is being diagnosed clinically in the community and to identify factors associated with its development.

METHODS

A total of 1003 of 1162 eligible serial healthy newborn infants recruited from a single suburban pediatrics practice were followed prospectively for the diagnosis of FPIAP. Investigators reviewed each case to confirm prespecified inclusion criteria, including documented gross or occult blood in the stool.

RESULTS

A total of 903 infants were analyzed (46% females, 89% term, 32% caesarian-section, 9% neonatal antibiotics); 153 cases met inclusion criteria, a cumulative incidence of 17%, while 63 (7%) had gross blood. Infants initially fed both breast milk and formula were 61% less likely to develop FPIAP compared with those exclusively formula-fed (hazard ratio, 0.39; P = .005). Breast milk and formula at any point during the first 4 months were also associated with lower risk compared with exclusive formula or exclusive breast milk (hazard ratio, 0.44; P = .005; hazard ratio, 0.62; P = .0497). Eczema (odds ratio, 1.5; 95% confidence interval, 1.1- 2.2; P = .02) or a first-degree relative with food allergies (odds ratio, 1.9; 95% confidence interval, 1.2-2.8; P = .005) were among risk factors for FPIAP development.

CONCLUSIONS

The prospectively defined incidence of FPIAP when diagnosed clinically by community pediatricians without challenge is markedly higher than published estimates. Combination feeding of formula and breast milk is associated with the lowest rate of FPIAP in this population.

Postbiotics: A novel strategy in food allergy treatment

During the last two decades, the prevalence and severity of clinical appearances of food allergy (FA) have a significant rise. FA derives from a breakdown of immune tolerance. In recent year's clinical evidence have shown that the probiotics have significant influences on FA by improving the immune tolerance. Besides, postbiotics due to their unique characteristics (safe profile, more shelf life, resistance to mammalian enzymes and stable to digestive system conditions), may have safety superiority against their parent live cells and as a novel strategy can be applied for improvement immune tolerance and treatment of FA without any undesirable side-effects or human opportunistic infections, particularly in infants and pediatrics.

New Perspectives in Food Allergy

The improvement of the knowledge of the pathophysiological mechanisms underlying the tolerance and sensitization to food antigens has recently led to a radical change in the clinical approach to food allergies. Epidemiological studies show a global increase in the prevalence of food allergy all over the world and manifestations of food allergy appear increasingly frequent also in elderly subjects. Environmental and nutritional changes have partly changed the epidemiology of allergic reactions to foods and new food allergic syndromes have emerged in recent years. The deepening of the study of the intestinal microbiota has highlighted important mechanisms of immunological adaptation of the mucosal immune system to food antigens, leading to a revolution in the concept of immunological tolerance. As a consequence, new prevention models and innovative therapeutic strategies aimed at a personalized approach to the patient affected by food allergy are emerging. This review focuses on these new perspectives and their practical implications in the management of food allergy, providing an updated view of this complex pathology.

Food allergy and the microbiome: Current understandings and future directions

Growing evidence points to an important role for the commensal microbiota in susceptibility to food allergy. Epidemiologic studies demonstrate associations between exposures known to modify the microbiome and risk of food allergy. Direct profiling of the gut microbiome in human cohort studies has demonstrated that individuals with food allergy have distinct gut microbiomes compared to healthy control subjects, and dysbiosis precedes the development of food allergy. Mechanistic studies in mouse models of food allergy have confirmed that the composition of the intestinal microbiota can imprint susceptibility or resistance to food allergy on the host and have identified a unique population of microbially responsive RORγt-positive FOXp3-positive regulatory T cells as critical for the maintenance of tolerance to foods. Armed with this new understanding of the role of the microbiota in food allergy and tolerance, therapeutics aimed at modifying the gastrointestinal microbiota are in development. In this article we review key milestones in the development of our current understanding of how the gastrointestinal microbiota contributes to food allergy and discuss our vision for the future of the field.

Managing Younger Siblings of Food Allergic Children

Current guidelines state that there is insufficient evidence to recommend testing siblings of food allergic children before introduction of potential allergic foods, but the topic continues to remain controversial. Although the proportion of siblings who are sensitized to a food without clinical reactivity is high in comparison to those with a true food allergy, there is still a known increased risk amongst siblings of children with food allergies that has led to much apprehension about management. The appropriateness of testing and further steps for management of sensitization in the absence of history of clinical reactivity should be discussed with parents.

Prevention of Food Allergy: The Significance of Early Introduction

Over the last two decades, the prevalence of food allergies has registered a significant increase in Westernized societies, potentially due to changes in environmental exposure and lifestyle. The pathogenesis of food allergies is complex and includes genetic, epigenetic and environmental factors. New evidence has highlighted the role of the intestinal microbiome in the maintenance of the immune tolerance to foods and the potential pathogenic role of early percutaneous exposure to allergens. The recent increase in food allergy rates has led to a reconsideration of prevention strategies for atopic diseases, mainly targeting the timing of the introduction of solid foods into infants' diet. Early recommendation for high atopy risk infants to delay the introduction of potential food allergens, such as cow's milk, egg, and peanut, until after the first year of life, has been rescinded, as emerging evidence has shown that these approaches are not effective in preventing food allergies. More recently, high-quality clinical trials have suggested an opposite approach, which promotes early introduction of potential food allergens into infants' diet as a means to prevent food allergies. This evidence has led to the production of new guidelines recommending early introduction of peanut as a preventive strategy for peanut allergy. However, clinical trials investigating whether this preventive dietary approach could also apply to other types of food allergens have reported ambiguous results. This review focuses on the latest high-quality evidence from randomized controlled clinical trials examining the timing of solid food introduction as a strategy to prevent food allergies and also discusses the possible implications of early complementary feeding on both the benefits and the total duration of breastfeeding.

Newly identified T cell subsets in mechanistic studies of food immunotherapy

Allergen-specific immunotherapy has shown promise for the treatment of food allergy and is currently being evaluated in clinical trials. Although immunotherapy can induce desensitization, the mechanisms underlying this process are not completely understood. Recent advances in high-throughput technologies along with concomitant advances in data analytics have enabled monitoring of cells at the single-cell level and increased the research focus on upstream cellular factors involved in the efficacy of immunotherapy, particularly the role of T cells. As our appreciation of different T cell subsets and their plasticity increases, the initial simplistic view that restoring Th1/Th2 balance by decreasing Th2 or increasing Th1 responses can ameliorate food allergy is being enhanced by a more complex model involving other T cell subsets, particularly Tregs. In this Review, we focus on the current understanding of T cell functions in food allergy, tolerance, and immunotherapy.

Microbial Adjuncts for Food Allergen Immunotherapy

PURPOSE OF REVIEW

Food allergen immunotherapy may benefit from adjunct therapies to enhance safety and efficacy. We review preclinical studies investigating the effects of probiotics and other microbial-based interventions on oral tolerance, describe the human clinical trial evidence thus far for microbial adjuncts, and discuss steps for translating research findings in this area to clinical therapy.

RECENT FINDINGS

Murine studies support that microbial-based interventions confer protection against sensitization and may augment treatment efficacy for food allergy. Microbial adjunct therapies can promote regulatory T cells and modulate Th1 vs. Th2 responses. There is a wide array of novel modalities utilizing microbial components. Ongoing efforts are focused on translating preclinical data into potential treatments. Probiotics, prebiotics, and microbial components have all been examined as microbial adjunct therapies in murine models of food allergy. The effects of probiotics appear to be strain-specific. Prebiotics and bacterial components are innovative modalities to modulate oral tolerance. Better characterization of dysbiosis in human cohorts with food allergy, deeper mechanistic understanding of microbial adjunct therapies, safety evaluation, and careful clinical trial design will be crucial for the development of microbial adjuncts for food allergen immunotherapy. Microbial adjunct therapies have the potential to enhance the efficacy, safety, and durability of food allergen immunotherapy.

Different immune response of dendritic cells of newborns of allergic and healthy mothers to bacterial stimuli

Continuous increasing incidence of allergic diseases is calling for identifying early prognostic markers pointing to increased risk of allergy development and establishing protocols for preventive strategies limiting allergy development in predisposed individuals. It is important to better understand the critical events occurring in early postnatal life, especially the interaction of a newborn with microbial compounds important for the maturation of the neonatal immune system and setting immunoregulatory responses as well. Dendritic cells (DC) together with the cytokine microenvironment play an important role in priming of immune responses. The capacity of monocyte-derived DC (moDC) from cord blood of children of healthy and allergic mothers to respond to microbial antigens (Escherichia coli O86 (EcO86) and delipidated Bacillus firmus (DBF)) was tested by flow cytometry and quantitative real-time PCR. Both EcO86 and DBF were able to promote maturation of moDC, but moDC of children of allergic mothers expressed higher levels of activation markers CD80 and CD83. Increased gene expression of IL-6 and lower expression of indol-amine 2,3 dioxygenase were observed in moDC of neonates of allergic mothers, in comparison to healthy ones. A higher gene expression and an increased presence of activation markers on moDC of newborns of allergic mothers indicate a generally higher reactivity of these cells, possibly enabling easier development of inappropriate immune response after an allergen encounter.

The gut microbiome in food allergy

OBJECTIVE

To review observational human, murine, and interventional trial studies that have examined the gut microbiome in food allergy, and to provide perspective on future investigations in this field.

DATA SOURCES

A review of the published literature was performed with PubMed, and clinical studies catalogued at ClinicalTrials.gov were also reviewed.

STUDY SELECTIONS

The most recent relevant studies, seminal works, and topical clinical trials were selected.

RESULTS

Gut dysbiosis likely precedes the development of food allergy, and the timing of such dysbiosis is critical. Gut microbiota associated with individual food allergies may be distinct. Murine models support the importance of gut microbiota in shaping immune maturation and tolerance. Gut microbiota may affect food allergy susceptibility by modulating type 2 immunity, influencing immune development and tolerance, regulating basophil populations, and promoting intestinal barrier function. Ongoing and future interventional trials of probiotics, prebiotics, synbiotics, and fecal microbiota transfer will help translate our understanding of the gut microbiome in food allergy to clinical practice. Future work in this area will include deepening of current research foci, as well as expansion of efforts to include the virome, mycobiome, and interactions between the microbiome, host, and environment. Robust and consistent study designs, multidimensional profiling, and systems biology approaches will enable this future work.

CONCLUSION

By advancing research on the microbiome in food allergy, we can further our understanding of food allergy and derive new approaches for its prevention and therapy.

Recent developments and highlights in mechanisms of allergic diseases: Microbiome

All body surfaces are exposed to a wide variety of microbes, which significantly influence immune reactivity within the host. This review provides an update on some of the critical novel findings that have been published on the influence of the microbiome on atopic dermatitis, food allergy and asthma. Microbial dysbiosis has consistently been observed in the skin, gut and lungs of patients with atopic dermatitis, food allergy and asthma, respectively, and the role of specific microbes in allergic disorders is being intensively investigated. However, many of these discoveries have yet to be translated into routine clinical practice.

Epigenetic Regulation via Altered Histone Acetylation Results in Suppression of Mast Cell Function and Mast Cell-Mediated Food Allergic Responses

Mast cells are highly versatile cells that perform a variety of functions depending on the immune trigger, context of activation, and cytokine stimulus. Antigen-mediated mast cell responses are regulated by transcriptional processes that result in the induction of numerous genes contributing to mast cell function. Recently, we also showed that exposure to dietary agents with known epigenetic actions such as curcumin can suppress mast cell-mediated food allergy, suggesting that mast cell responses in vivo may be epigenetically regulated. To further assess the effects of epigenetic modifications on mast cell function, we examined the behavior of bone marrow-derived mast cells (BMMCs) in response to trichostatin A (TSA) treatment, a well-studied histone deacetylase inhibitor. IgE-mediated BMMC activation resulted in enhanced expression and secretion of IL-4, IL-6, TNF-α, and IL-13. In contrast, pretreatment with TSA resulted in altered cytokine secretion. This was accompanied by decreased expression of FcεRI and mast cell degranulation. Interestingly, exposure to non-IgE stimuli such as IL-33, was also affected by TSA treatment. Furthermore, continuous TSA exposure contributed to mast cell apoptosis and a decrease in survival. Further examination revealed an increase in I-κBα and a decrease in phospho-relA levels in TSA-treated BMMCs, suggesting that TSA alters transcriptional processes, resulting in enhancement of I-κBα transcription and decreased NF-κB activation. Lastly, treatment of wild-type mice with TSA in a model of ovalbumin-induced food allergy resulted in a significant attenuation in the development of food allergy symptoms including decreases in allergic diarrhea and mast cell activation. These data therefore suggest that the epigenetic regulation of mast cell activation during immune responses may occur via altered histone acetylation, and that exposure to dietary substances may induce epigenetic modifications that modulate mast cell function.

The Effect of Digestion and Digestibility on Allergenicity of Food

Food allergy prevalence numbers are still on the rise. Apart from environmental influences, dietary habits, food availability and life-style factors, medication could also play a role. For immune tolerance of food, several contributing factors ensure that dietary compounds are immunologically ignored and serve only as source for energy and nutrient supply. Functional digestion along the gastrointestinal tract is essential for the molecular breakdown and a prerequisite for appropriate uptake in the intestine. Digestion and digestibility of carbohydrates and proteins thus critically affect the risk of food allergy development. In this review, we highlight the influence of amylases, gastric acid- and trypsin-inhibitors, as well as of food processing in the context of food allergenicity.

Regulatory Immune Mechanisms in Tolerance to Food Allergy

Oral tolerance can develop after frequent exposure to food allergens. Upon ingestion, food is digested into small protein fragments in the gastrointestinal tract. Small food particles are later absorbed into the human body. Interestingly, some of these ingested food proteins can cause allergic immune responses, which can lead to food allergy. So far it has not been completely elucidated how these proteins become immunogenic and cause food allergies. In contrast, oral tolerance helps to prevent the pathologic reactions against different types of food antigens from animal or plant origin. Tolerance to food is mainly acquired by dendritic cells, epithelial cells in the gut, and the gut microbiome. A subset of CD103⁺ DCs is capable of inducing T regulatory cells (Treg cells) that express anti-inflammatory cytokines. Anergic T cells also contribute to oral tolerance, by reducing the number of effector cells. Similar to Treg cells, B regulatory cells (Breg cells) suppress effector T cells and contribute to the immune tolerance to food allergens. Furthermore, the human microbiome is an essential mediator in the induction of oral tolerance or food allergy. In this review, we outline the current understanding of regulatory immune mechanisms in oral tolerance. The biological changes reflecting early consequences of immune stimulation with food allergens should provide useful information for the development of novel therapeutic treatments.