Livestock and aquaculture face severe challenges from extreme climate and environmental changes and require a comprehensive detection platform to identify and monitor multiple pathogens. The whole microbiome microarray is made using the identifiable SNP sites of the microbial nucleic acid database, which can simultaneously detect multiple microorganisms without interference from host genomic DNA. It can detect low-level microorganisms, analyze the microbiome, and clarify the pathogen of infectious disease, effectively implementing disease prevention and treatment.