The invention provides a method for rapidly detecting microbial species, and particularly, the method comprises the following steps: constructing a double-level
database and a corresponding
gene cluster; constructing a reference matrix X based on the
database and the
gene cluster; comparing to-be-detected third-generation
sequencing data with the
gene cluster to generate equivalence classes, and constructing a counting matrix Y based on the equivalence classes and the
gene cluster; based on the counting matrix Y and the reference matrix X, determining the gene abundance in the to-be-detected sample; and determining microbial species in the sample to be detected based on the gene abundance. The rapid
pathogen detection method provided by the invention is high in analysis speed, fully utilizes the advantages of the three-generation
sequencing data, and can more directly obtain the
microorganism composition information of the sample; the method is low in computing resource demand, easy to deploy and high in precision detection capability.