The 16S ribosomal ribonucleic acid, often shortened to 16S rRNA, is an important constituent of the small subunit (SSU) of prokaryotic ribosomes as well as mitochondria and chloroplasts.

How the 16S rRNA is involved in a prokaryotic ribosome

DNAsegment coding for rRNA is called either rRNA gene or rDNA. For the purposes of sequencing, sequence information is obtained from the 16S gene because DNA is much easier to process and sequence vs RNA.

To use as a barcode, a gene should have the following characteristics.

• It should be ubiquitously present. Otherwise, we cannot include all organisms. All members of Bacteria and Archaea are known to have 16S gene.
• It should contain sufficient phylogenetic information. 16S is about 1,500 bp long, which is not too short or long.
• It should have enough genetic variation. The genetic variation within 16S gene found among prokaryotes is adequate to be used in the phylogenetic analysis for the broad taxonomic ranges. It is successfully used to infer phylogenetic relationship among phyla while also used in the comparison among species in the same genus.
• It should be easily amplified by PCR. 16S gene has multiple conserved regions that can be used as the priming sites. This becomes a significant advantage for NGS-based short read sequencing.
• There should be a repository of sequence identifications. After many years of international collaboration, we have 16S sequence database holding almost all known species of Bacteria and Archaea. By searching 16S sequence against these databases, anyone, even without knowledge of serious taxonomy, can identify newly isolated strains.