How does whole-genome shotgun metagenomic sequencing enhance our understanding of microbial communities in the human microbiome?

Whole‑genome shotgun metagenomic sequencing reads every piece of DNA from all microbes in a sample, so we see not only which species are present but also their genes and functions. By assembling these fragments, scientists can identify rare organisms that would be missed by targeted tests, and they can detect antibiotic‑resistance genes or metabolic pathways. The method lets us compare the genetic “toolkits” of different microbes, revealing how they interact and adapt to the host. For example, sequencing a stool sample can uncover a previously unknown bacterium that produces a vitamin the host needs. Thus, shotgun sequencing gives a comprehensive, functional map of the microbiome’s composition and activity.