16S18S

16S18S is not a single gene but a shorthand sometimes used to refer to the parallel analysis of two ribosomal RNA gene families: the 16S rRNA gene in bacteria and archaea, and the 18S rRNA gene in eukaryotes. Both genes encode components of the small subunit of ribosomes and are among the most widely used phylogenetic markers in their respective domains. The 16S rRNA gene is typically about 1,500 base pairs long and contains conserved regions suitable for universal primer binding, interspersed with nine hypervariable regions that provide taxonomic discrimination. The 18S rRNA gene is generally longer and more variable across major eukaryotic lineages, with a structure of conserved and variable regions that supports discrimination among many eukaryotes, but primer universality is more challenging than for 16S.

Applications: In microbial ecology and systematics, 16S rRNA gene sequencing is standard for identifying bacteria and archaea and for profiling microbial communities via amplicon sequencing. In eukaryotic studies, 18S rRNA sequencing is used to characterize protists, fungi, and other microeukaryotes, often in environmental DNA surveys or targeted barcoding efforts. Databases such as SILVA, RDP, and Greengenes (for 16S) and PR2 or SILVA (for 18S) support taxonomic assignments.

Limitations include copy number variation and potential intragenomic heterogeneity for 16S in some taxa, primer biases, and varying resolution, especially at deeper taxonomic levels or across diverse eukaryotes for 18S. In practice, researchers may use both markers to obtain complementary views of microbial diversity and ecology.