"Allergy and autoimmunity cause increasing burden to societies worldwide. We study the effect of microbiome on the skin, the forefront barrier to environment, on autoimmunity and allergy, using atopic dermatitis (AD) and psoriasis (PSO) as paradigmatic examples. We have detailed information about the genetic risk factors, as well as the molecular and cellular players in AD and PSO, but we know very little how microbe-host interaction triggers and regulate inflammatory cascade leading to allergic or autoimmune reaction. We propose that environmental and genetic factors, characteristic to particular disease, initiate a cascade of inflammatory events through the modulation of anti-microbial defence. The dysregulation of innate as well as adaptive immune responses leads to inappropriate responses to physical, microbial or allergen challenge, finally manifesting in the clinical symptoms of AD or PSO. We propose to use high-throughput whole microbiome and transcriptomics analysis with bioinformatics and systems biology to unravel the pathways during the host-pathogen interactions which may trigger an allergic or autoimmune reaction. We will identify key microbes and molecular targets to develop novel intervention strategies to decrease and prevent the burden of allergy and autoimmunity."