Third-generation metagenomic sequencing refers to the process of assembling the genome of the core bacterial community by using the third-generation single-molecule real-time sequencing technology of PacBio to study the genome of the microbial community in a specific environment, which, based on the analysis of microbial diversity, population structure, and evolutionary relationship, can further explore the relationship between microbial community functional activity, mutual cooperation and the environment, and explore the potential biological significance. Compared with the second-generation sequencing method, the long-read length of the third-generation metagenome using PacBio SMRT sequencing can reduce partial assembly errors and effectively improve the resolution of microbial community identification.