Strain-level bacterial analysis from shotgun metagenomics: a review

Identifying bacterial strains and characterizing their population, genetic variety and functional gene sets is essential for bacterial pathogen discovery, epidemiology, and infection control. With the development of high throughput sequencing and bioinformatics tools, we can characterize the individual bacterial strains in the context of complex community. In this review, we present the current works of strain-level bacterial analysis from metagenomics in three aspects: genetic diversity, outbreak tracing and functional gene profile. The work provides related references for the applications of bacterial analysis from metagenomics in clinical and environmental microbiology, and public health.