Allergies are diseases involving many cell subsets. The specific reactivities and contributions to the clinical picture are closely interdependent and not fully deciphered yet. The interplay between the different actors of the cellular immune system is further complexified by the existence of the commensal intestinal flora, also called the microbiota. Gut microbiota is partially under supervision of the immune system, and dysregulations or changes in the composition of the microbiota, for example due to antibiotics uptake during childhood and /or different eating habits, may impact adaptative and innate immune functions. Characterization of the gut microbiota of human hosts undergoing immunotherapy might be of high interest to delineate interactions between microbiota and adaptive immune system.