All bacteria and archaea contain a ribosomal subunit known as 16S that is around 1,500 nucleotides long and contains nine hypervariable regions (V1-V9) spread out among highly conserved regions that are genus- or species specific. Sequencing of the 16S ribosomal RNA (rRNA) gene, an established genetic marker, is the gold standard for the analysis of bacterial samples for identification and classification of both pure cultures and mixed sample analysis in complex microbial communities, such as soil samples, oral cavity samples, or human gut microbiomes.
The main reason for using the V3 and V4 regions in majority of the cases is that these regions contain the maximum nucleotide heterogeneity and displays the maximum discriminatory power needed for complex samples, to evaluate bacterial diversity and detect the abundance of microbes in various environments.