A plethora of researches over the past decades has revealed that micro-organisms play critical roles in a variety of diseases by dynamically interacting with hosts and their immune systems.1 Particularly, clinical associations between microbial dysbiosis and allergic diseases such as atopic dermatitis (AD), allergic rhinitis, and asthma have been repeatedly reported.2,3 The underlying mechanisms of dysbiosis found in patients with allergic diseases are yet largely unknown, and the precise role of dysbiosis in their pathophysiology is just beginning to be defined; nevertheless, it is quite clear that different patterns of microbiota exist in the patients with allergic diseases and are closely associated with disease development. This rapidly developing research area is believed to be promising, and defining the host-microbial interactions is an exciting task. At the same time, in order to achieve valuable advances in this field, it is pivotal for researchers to pay special attention to the currently available tools for microbiome investigation and acknowledge their limitations.
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