To explore the functional role of gut microbiota in diet-modulated illnesses, using systems biology-driven methods to evaluate probiotic treatment effects was the purpose of the study. Understanding the function of host–gut microbial and gut microbe-microbe interactions in allergic and non-allergic children may aid in the selection of effective and targeted probiotics for customized treatments. Food allergy is on the rise, particularly in Western countries where growing epidemiological data show a prevalence of small family groups, a lower rate of infections in childhood compared to low-income countries, and high consumption of sterile foods, all of which stimulate a poor trigger of the gut immune system. As a result, emerging treatment methods for a food allergy include probiotic delivery beginning in infancy, modifying gut microbiota through immune system activation at the mucosal level.

At the moment, new insights for probiotic selection should take into account both phenotyping and genotyping bacterial features, as well as host-microbial cross-talk at the gut level, by employing multi-component systems biology approaches to reveal gut ecosystem dynamics in terms of bacteria phylotypes and their metabolic activities. Furthermore, new food procedures must be explored in order to evaluate the real performance of probiotic strains given to allergic patients.