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The genes encoding the RNA component of the small subunit of ribosomes, commonly known as the 16S rRNA in bacteria and archaea, are among the most conserved across all kingdoms of life. Nevertheless, they contain regions that are less evolutionarily constrained and whose sequences are indicative of their phylogeny. Amplification of these genomic regions by PCR from an environmental sample and subsequent sequencing of a sufficiently large number of individual amplicons enables the analysis of the diversity of clades in the sample and a rough estimate of their relative abundance. The analytical process is known as “16S rDNA diversity analysis”, and is the focus of the present SOP.

The SOP describes the essential steps for processing 16S rRNA gene sequences. The procedure and tools are only recommendations and it is up to the user to evaluate what works best for their needs.