Gut microbiome in the first 1000 days and risk for childhood food allergy

Impact of antimicrobial exposure at delivery and siblings on early Bifidobacterium succession and allergy development up to 24 months of age

BACKGROUND

Allergic diseases such as asthma, eczema, and food allergies are rising globally. The infant gut microbiota, particularly the dominance of Bifidobacterium, shapes immune development and allergy risk. In Japan-where Bifidobacterium prevalence is notably high-longitudinal investigations focusing on the pre-weaning period, when external influences are relatively limited, remain scarce. Therefore, based on consistent hypotheses and findings from previous studies, we investigated how two important early factors-antibiotic exposure at birth and the presence of older siblings-influence the gut environment in early infancy and subsequent allergy development.

RESULTS

In a prospective cohort of 121 Japanese infants, stool samples were collected at seven time points from birth through 24 months. We quantified the relative abundances of Bifidobacterium, Bacteroides, Clostridium, and Faecalibacterium and recorded allergic outcomes at 2 years. Both antimicrobial exposure at delivery and sibling presence significantly altered gut microbiota composition and overall diversity in early infancy. Although the full cohort showed no consistent diversity or Bifidobacterium differences by allergic status, in several subgroups where these two factors were excluded, infants who had an allergy by 24 months exhibited marked shifts in early gut microbiota community structure-particularly in beta diversity-and reduced Bifidobacterium occupancy during the pre-weaning period (1-6 months) versus non-allergic peers. Moreover, infants whose gut microbiota was initially affected by these factors showed a recovery in diversity after weaning, a rebound more pronounced in non-allergic individuals.

CONCLUSIONS

These findings indicate that both the initial community configuration and its capacity to rebound after perturbation are critical determinants of allergy risk. By focusing on dynamic changes through weaning and adjusting for decisive confounders, this study refines insight beyond prior cross-sectional work. Early interventions that preserve or restore microbial diversity and Bifidobacterium dominance may therefore offer a promising strategy to mitigate allergic disease development.

Early-life antibiotic dysbiosis impairs microbial tryptophan- nicotinic acid metabolism exacerbating food allergy in adulthood

Food allergy (FA) pathogenesis links to intestinal dysbiosis, with antibiotic exposure a suspected risk factor, yet mechanisms are unclear. Our study shows early life (EL) antibiotic exposure in mice heightens susceptibility to OVA - induced allergic intestinal inflammation. EL - antibiotics cause intestinal dysbiosis, like Clostridia and Muribaculaceae depletion and Sutterellaceae enrichment, disrupting tryptophan metabolism and reducing nicotinic acid (NA). NA deficiency impairs gut barrier and Th2/Treg balance. However, NA supplementation restores these via GPR109A. In human pediatric cohorts, food - allergic children with EL - antibiotic exposure have lower gut NA levels. We integrated mouse and human data with multi - omics, revealing EL - Abx regulates FA through the "microbiota - metabolism - immunity" axis, and suggest targeting NA pathway to counter antibiotic - related FA risk.

The Impact of Probiotic Supplementation on the Development of the Infant Gut Microbiota: An Exploratory Follow-Up of a Randomised Controlled Trial

Early-life establishment of the gut microbiota plays a role in lifelong health, with disruptions linked to heightened risks of metabolic and immune disorders. Probiotic supplementation may be used to modulate the infant gut microbiome to promote favourable development. Here, we evaluate how Lab4B probiotic supplementation shapes the development of the infant gut microbiome over the first 6 months. Faecal samples collected from infants enrolled in PROBAT (ISRCTN26287422), a randomised, double-blind, placebo-controlled trial, were analysed using culture-dependent and -independent (16S rDNA and metagenomic shotgun sequencing) techniques to examine the composition, diversity, and metabolic capabilities of the microbiome, as well as the abundance of antimicrobial resistance genes (ARGs). Probiotic supplementation encouraged the development of a microbiome with a distinct composition characterised by elevated abundances of Bifidobacteriaceae in the first 6 weeks (p = 0.006) and Lactobacillaceae throughout the first 6 months (p < 0.05 at every 6-week time point), accelerated microbial diversification, reduced abundance of beta-lactam- and cephalosporin-resistance genes, and differences in predicted metabolic capabilities at the start and end points. Supplementation of this neonatal population, which is at high risk of atopy, with the Lab4B probiotic significantly influenced the development of the infant gut microbiota during the first 6 months.

Immune therapies in coeliac disease and food allergies: Advances, challenges, and opportunities

Coeliac disease and food allergy management primarily relies on the strict avoidance of dietary antigens. This approach is challenging to maintain in real-world settings and in food allergy carries the risk of life-threatening anaphylaxis. Despite their distinct pathogenesis, both disorders are driven by maladaptive responses to dietary proteins, creating opportunities for shared treatment strategies. In food allergy, desensitisation therapies such as oral, sublingual, and epicutaneous immunotherapy are well-established, complemented by biologics like omalizumab and dupilumab. However, the induction of sustained tolerance remains challenging. In contrast, therapeutic advancements for coeliac disease are still in their early stages. Current efforts focus on gluten detoxification or modification, immune blockade or modulation, tolerogenic approaches, and barrier restoration. Emerging therapies, including JAK and BTK inhibitors and microbiome-targeted interventions, support further targeted treatment options for both conditions. Biomarkers tracking gluten-specific T cells have emerged as valuable tools for immunomonitoring and symptom assessment in coeliac disease, although standardisation of patient-reported outcome measures and gluten challenge protocols is still needed. Food allergy trials are reliant on double-blind placebo-controlled food challenges to measure allergen reactivity, but these are time-consuming, carry risks, and underscore the need for surrogate biomarkers. The successful development of immune-targeted therapies will require building an immune toolset to optimally assess systemic responses to antigens in both conditions. Clinically, this could lead to better outcomes for patients who might otherwise remain undiagnosed or untreated due to the absence of significant enteropathy or allergen-specific symptoms.

[Causal association between gut microbiota and food allergy: a Mendelian randomization analysis]

OBJECTIVES

To analyze the potential causal relationship between gut microbiota and food allergy (FA) using two-sample Mendelian randomization (MR) methods.

METHODS

Data from genome-wide association studies on gut microbiota and FA were utilized. MR analysis was conducted employing inverse variance weighting, MR-Egger regression, and weighted median methods to assess the causal relationship between gut microbiota and FA. Cochrane's Q test was used to evaluate heterogeneity of instrumental variables, MR-PRESSO analysis was conducted to test for outliers and pleiotropy, and MR-Egger regression was employed to assess horizontal pleiotropy. The "leave-one-out" method was used to evaluate the impact of removing individual single nucleotide polymorphisms on the causal relationship.

RESULTS

Inverse variance weighting analysis revealed that the phylum Verrucomicrobia, family Verrucomicrobiaceae, order Verrucomicrobiales, genus Ruminococcaceae UCG013, and genus Akkermansia were negatively associated with FA (P<0.05). Sensitivity analyses confirmed the reliability of the findings, indicating no heterogeneity or pleiotropy present.

CONCLUSIONS

There is a causal relationship between gut microbiota and FA, with Verrucomicrobia, Verrucomicrobiaceae, Verrucomicrobiales, Ruminococcaceae UCG013, and Akkermansia potentially reducing the risk of developing FA. These findings provide potential targets for the treatment and prevention of FA; however, further research is needed to explore the specific mechanisms by which the microbiota influence FA.

Gut-lung Axis mediates asthma pathogenesis: Roles of dietary patterns and their impact on the gut microbiota

The gut-lung axis, a vital signaling network linking the gastrointestinal and pulmonary systems, regulates immune responses and the progression of respiratory diseases. Nutritional components can modulate the gut microbiome and regulate the synthesis of critical intestinal microbial metabolites, which are essential for maintaining immune homeostasis and supporting respiratory health. Conversely, poor dietary habits exacerbate asthma and other respiratory conditions through the modulation of systemic inflammation and immune responses. Dietary interventions, such as the Mediterranean diet, are reported to restore microbial balance and improve respiratory health by increasing the production of anti-inflammatory metabolites, potentiating immune responses, and preserving epithelial barrier integrity. In contrast, Western dietary patterns, which are characterized by high fat and low fiber intake, disrupt microbial diversity, resulting in increased levels of pro-inflammatory metabolites that aggravate airway inflammation and asthma severity. This review aimed to elucidate the mechanisms underlying the regulatory effects of gut microbes and their metabolites on asthma. Additionally, previous findings related to the gut-lung axis have been summarized, providing insights into potential therapeutic strategies for asthma management.

Food Allergy, Nutrition, Psychology, and Health

This article explores food allergy and the nascent field of nutritional psychiatry. Individuals with food allergy experience lower levels of "food freedom" than their nonallergic counterparts, which can create cognitive, emotional, social, nutritional, and financial burdens. Patterns of food avoidance may influence neuroinflammatory states and the gut microbiome; these changes may be associated with neuropsychiatric symptoms. Food restriction may promote disruption of the microbiome neuroimmune axis, which has been linked to various allergic diseases. Targeted psychological counseling strategies can provide benefit. Food allergy and restricted diets may impact dietary health benefits.

A web-based questionnaire to evaluate risk factors to develop cow milk allergy

Many environmental, genetic, and epigenetic variables are considered to influence the evolution of cow's milk allergy (CMA). The gastro-intestinal microbiota may play a direct role in or inhibit tolerance development. In this study, we planned to evaluate the presence of previously identified risk factors for microbiota composition. This study used a cross-sectional electronic survey in Turkiye, utilizing a national convenience sample of 270 children with CMA, as reported by their caregivers, and 2154 healthy controls. We developed a web-based questionnaire to gather information on pregnancy and maternal-related factors, delivery mode, feeding patterns, antibiotic use, and the presence of pets in the home. The risk factors affecting CMA were maternal age (OR 0.897; 0.862-0.934, p < 0.01), presence of maternal allergic disorders (OR 3.070; 1.891-4.983, p < 0.001) and in both parents (OR 3.831; 1.202-12.210, p < 0.001), maternal weight at conception (OR 1.016; 1.003-1.030, p < 0.05), maternal weight gain during pregnancy (OR 1.033; 1.012-1.056, p < 0.01), (absence of a) pet at home (OR 1.394; 1.003-1.938, p < 0.05), intrapartum antibiotic use (OR 1.469; 1.092-1.975, p < 0.05), antibiotic use during the first 6 months of life (OR 1.933; 1.306-2.863, p < 0.001), and number of householders (OR 0.794; 0.650-0.969, p < 0.05).

CONCLUSION

In addition to allergic disorders in parents, maternal weight and weight gain during pregnancy, intrapartum and first 6 months of life antibiotic use, and the presence of pets at home were found to be microbiota-related risk factors in children with CMA. Potential strategies related to microbiota composition may contribute positively to the disease's development and progression.

WHAT IS KNOWN

• The gut microbiome contributes to the development of cow milk allergy, and disrupted microbiota maturation during the first year of life appears to be common in pediatric food allergies. • Factors that influence an infant's microbiota within the first 1000 days and the relationship between these factors and microbiota may enhance allergy diagnosis, prevention, and treatment.

WHAT IS NEW

• Besides parental allergy disorders, maternal weight and weight gain during pregnancy, antibiotic use during intrapartum and first six months of life, and the presence of pets at home were identified as microbiota-related risk factors in children with CMA.

Atopic dermatitis and IgE-mediated food allergy: Common biologic targets for therapy and prevention

OBJECTIVE

To highlight common mechanistic targets for the treatment of atopic dermatitis (AD) and IgE-mediated food allergy (IgE-FA) with potential to be effective for both diseases and prevent atopic progression.

DATA SOURCES

Data sources were PubMed searches or National Clinical Trials (NCT)-registered clinical trials related to AD, IgE-FA, and other atopic conditions, especially focused on the pediatric population.

STUDY SELECTIONS

Human seminal studies and/or articles published in the past decade were emphasized with reference to preclinical models when relevant. NCT-registered clinical trials were filtered by inclusion of pediatric subjects younger than 18 years with special focus on children younger than 12 years as a critical period when AD and IgE-FA diseases may often be concurrent.

RESULTS

AD and IgE-FA share several pathophysiologic features, including epithelial barrier dysfunction, innate and adaptive immune abnormalities, and microbial dysbiosis, which may be critical for the clinical progression between these diseases. Revolutionary advances in targeted biologic therapies have shown the benefit of inhibiting type 2 immune responses, using dupilumab (anti-interleukin-4Rα) or omalizumab (anti-IgE), to potentially reduce symptom burden for both diseases in pediatric populations. Although the potential for biologics to promote disease remission (AD) or sustained unresponsiveness (IgE-FA) remains unclear, the refinement of biomarkers to predict infants at risk for atopic disorders provides promise for prevention through timely intervention.

CONCLUSION

AD and IgE-FA exhibit common features that may be leveraged to develop biologic therapeutic strategies to treat both conditions and even prevent atopic progression. Future studies should be designed with consistent age stratification in the pediatric population and standardized regimens of adjuvant oral immunotherapy or dose escalation (IgE-FA) to improve cross-study interpretation.

Pathogenic mechanisms in the evolution of food allergy

The early development of the neonatal immune system is profoundly influenced by exposure to dietary and microbial antigens, which shapes mucosal tolerance. Successful oral tolerance induction is crucially dependent on microbially imprinted immune cells, most notably the RORγt+ regulatory T (Treg) and antigen presenting cells and is essential for preventing food allergy (FA). The development of FA can be envisioned to result from disruptions at key checkpoints (CKPTs) that govern oral tolerance induction. These include gut epithelial sensory and effector circuits that when dysregulated promote pro-allergic gut dysbiosis. They also include microbially imprinted immune regulatory circuits that are disrupted by dysbiosis and pro-allergic immune responses unleashed by the dysregulation of the aforementioned cascades. Understanding these checkpoints is essential for developing therapeutic strategies to restore immune homeostasis in FA.