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House dust mites (HDMs) are a major source of allergens and the dominant trigger of allergic diseases.Knowledge about the HDM genome and its endosymbiotic microbiota has been very limited up to now.Here we combined the results from the genome, transcriptome, proteome and microbiome of Dermatophagoides farinae to elucidate a broad spectrum of mite allergens.We identified eight non-canonical allergen homologs and a ubiquinol-cytochrome c reductase binding protein (UQCRB) homolog as a novel major allergen candidate.We identified Enterobacter as a predominant bacterial genus inhabiting the mite.This work provides a tool for future identification and characterization of HDM allergens and can be used by developers of diagnostics and immunotherapeutic vaccines.One sentence summary Genomic/proteomic experiments were combined to produce a dust mite genome draft, which revealed biologically and clinically important allergen genes and can be used as a future investigative tool.