The 16S ribosomal RNA (rRNA) gene is a highly conserved gene found in the small subunit (SSU) of prokaryotic ribosomes. It is present in all bacteria and most archaea. The gene codes for the 16S rRNA molecule, which is a key component of the ribosomal machinery responsible for protein synthesis within the cell.

The 16S rRNA gene is particularly useful in the field of microbiology for several reasons:

Conservation and Variability: While a large portion of the 16S rRNA gene is conserved (remains relatively unchanged) across different species of bacteria, there are certain hypervariable regions within the gene that differ considerably. This combination of conserved and variable regions makes it ideal for both the identification and classification of bacteria.

Phylogenetics and Taxonomy: Sequences of the 16S rRNA gene are often used to determine evolutionary relationships among bacteria, helping scientists classify and identify organisms. By comparing the 16S rRNA gene sequences, one can deduce the evolutionary lineage and make phylogenetic trees, which show the evolutionary relationships between different bacterial species or strains.

Metagenomics and Environmental Sampling: In environmental studies, where diverse microbial communities exist, sequencing the 16S rRNA gene from a sample can provide an overview of the bacterial communities present. This technique is particularly useful for understanding the composition of microbiomes in various environments, from soil and water to the human gut.

Clinical Diagnostics: The 16S rRNA gene can also be used to identify unknown bacterial pathogens in clinical samples. If a patient has an infection caused by a rare or previously unidentified bacterium, sequencing the 16S rRNA gene can assist in its identification.

Culture-independent Analysis: Traditional microbiology often relies on culturing organisms, but many bacteria from environmental samples are not readily culturable under standard laboratory conditions. By analyzing the 16S rRNA gene directly from environmental samples, researchers can detect and study bacteria that might otherwise remain undiscovered.

To exploit these uses, various techniques like polymerase chain reaction (PCR), next-generation sequencing (NGS), and Sanger sequencing are applied to amplify and sequence the 16S rRNA gene from samples of interest.

16S is by far the target used by most of our Ripseq customers. Both in Sanger and in NGS.