Construction of clone libraries with phylogenetic marker genes is a widely used method for assessing microbial community composition and diversity. Based on the long-read lengths generated by Sanger sequencing, sequence analysis of cloned libraries provides phylogenetic resolution far beyond that of other methods. Since this method does not require the acquisition of pure cultures of microorganisms from the environment, it breaks the limitation of using traditional microbial isolation and purification methods to investigate the diversity of microorganisms in the environment. Sequence analysis of cloned libraries has been widely applied to investigate microbial diversity in various ecosystems such as soil, water, sediment, gut, fermented food, contaminated samples, etc., and to analyze the composition of bacterial, archaeal and fungal communities in environmental samples.