What is a primary advantage of whole-genome shotgun metagenomic sequencing over traditional sequencing methods?

Whole‑genome shotgun metagenomic sequencing reads every DNA fragment from a mixed sample, so it captures all organisms present, even those that cannot be grown in a lab. Traditional methods, like 16S rRNA sequencing, only look at a single marker gene, missing many species and their genes. By sequencing everything, researchers can see the full range of microbes and their functional genes, giving a complete picture of the community’s potential. For example, in a soil sample, shotgun sequencing will detect both bacteria and fungi and reveal the enzymes they carry, while 16S would only show bacterial species. This breadth of information is the main advantage.