16S ribosomal RNA gene sequencing can only identify bacterial species that are present in high abundance within a sample, making it ineffective for studying microbial diversity in complex environments.

16S ribosomal RNA gene sequencing actually allows us to see many different bacteria, even those that are only a few percent of the community, because the method amplifies the 16S gene from every organism in the sample. The key idea is that PCR amplification and high‑throughput sequencing can generate thousands of reads from a single sample, giving enough coverage to detect rare taxa. For example, a soil sample might contain a species that makes up only 0. 5 % of the DNA; with enough sequencing depth, that species will still generate enough reads to be identified. Therefore, 16S sequencing is a powerful tool for studying microbial diversity in complex environments, not limited to only high‑abundance species.