Allergic diseases, such as respiratory, cutaneous, and food allergy, have dramatically increased in prevalence over the last few decades. Increasing use of antibiotics has been linked with dysbiosis and enhanced prevalence of allergies and asthma. Despite the clear involvement of the microbiome in atopic disease, it remains to be determined whether microbial alterations are a cause or a consequence of the disease.

Human microbiota is defined as the multitude of microorganisms that live in or are associated with a variety of human tissues: the gut, respiratory tract, skin and genital tract. Recent advances in metagenomic sequencing and bioinformatics have enabled detailed characterization of these vital microbial communities and their role in different diseases. In particular, the relationship of microbiota with immune responses and immunological or allergic diseases is well known. The composition of gut, respiratory and skin microbiota can influence systemic inflammatory responses that mediate food allergy, rhinitis, asthma, immunodeficiency diseases, atopic dermatitis and chronic urticaria. This review discusses the role of microbiota in the major allergic Type 2 diseases evaluating the composition of the main commensal bacteria species and their relation with these pathologies.