Whole Genome Shotgun (WGS) metagenomic sequencing allows to sample all the genes of all the organisms present in a given complex sample. This method allows microbiologists to assess bacterial diversity and detect the abundance of microbes in various environments. WGS metagenomics also provides a means of studying non-cultivatable microorganisms that are otherwise difficult or impossible to analyse. 
This type of sequencing data can be used in a so-called (1) mapping analysis against a database of reference genes or (2) metagenomic assemblies followed by annotation of the assembled sequences and identification of the taxa present.