What is 16s rRNA Sequencing?

16s rRNA sequencing has become one of the leading methods for phylogenetic studies. The popularization of 16s sequencing methods has been due in large part to the wide availability of PCR and Next-generation sequencing facilities, such as MRDNA. But what is 16s rRNA sequencing? And why should you choose 16s sequencing methods over other DNA sequencing methods?


16s rRNA sequencing refers to sequencing the 16s rRNA gene that codes for the small subunit (SSU) of the ribosome found in prokaryotes such as Bacteria and Archaea. There are several factors that make the 16s rRNA gene the perfect target to complete your taxonomy or phylogeny studies.


  • Because the 16s gene codes for the SSU of the prokaryotic ribosome, researchers can rely on the fact that the their target gene will be present in every cell.
  • The 16s gene contains both highly conserved regions as well as hypervariable regions.
    • The presence of the highly conserved regions allow researchers to design primer pairs that will accurately and reliably amplify the 16s hypervariable region of their choice.
    • The presence of the hypervariable regions affords researchers the ability to differentiate between closely related genera or species detected in their samples.
  • The overall size of the 16s rRNA gene is relatively short. ~1500bp. While sequencing the entire 16s gene is difficult due to read length restrictions of many NGS platforms, sequencing one or more hypervariable regions is relatively quick and affordable.
    • Two of our most requested assays for 16s rRNA sequencing are 27F-519R (V1-V3 region) and 515F-806R (V4 region).
    • For questions regarding pricing feel free to contact us or visit our 16 ribosomal sequencing page.

MRDNA 16s Sequencing Primers


Often times, researchers will have some confusion regarding the differences between 16s metagenomic sequencing methods and shotgun metagenomic sequencing methods. See our article regarding shotgun metagenome sequencing to answer all of your questions. In short, shotgun metagenome sequencing is aptly named due to the fact that the goal of this DNA sequencing method is to sequence all genes from all organisms in a given sample. Whereas in the case of 16s metagenome sequencing, the goal is to sequence the 16s rRNA gene specifically.


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