What is the primary reason why whole-genome shotgun metagenomic sequencing is preferred over targeted sequencing methods in analyzing microbial communities?

Whole‑genome shotgun metagenomics sequences all DNA in a sample, not just a few marker genes, so it can detect every organism present and reveal their functional genes. This unbiased approach lets researchers see both known and novel microbes and understand what they can do, which targeted methods miss because they rely on specific primers. By analyzing all the reads, scientists can build a comprehensive picture of community composition, diversity, and metabolic potential. For example, in a soil sample, shotgun sequencing might uncover a previously unknown bacterium that produces a unique antibiotic, something a 16S rRNA survey would never detect.