Blogpost shared by Microbiome Insights: "16S rRNA Gene Sequencing vs. Shotgun Metagenomic Sequencing"

A form of amplicon sequencing, 16S rRNA gene sequencing targets and reads a region of the 16S rRNA gene which is found in all Bacteria and Archaea, meaning this type of sequencing can only identify these types of microorganisms. Other types of amplicon sequencing can identify other microorganisms, such as ITS sequencing for fungi or 18S sequencing for protists. The output of 16S rRNA sequencing provides sequencing ‘reads’ (strings of DNA sequence) that can be analysed using a number of basic bioinformatic steps, which when combined together are known as ‘pipelines’.

Shotgun metagenomic sequencing involves randomly breaking (‘fragmenting’) DNA into many small pieces, much like a shotgun would break something up into many pieces. These fragmented pieces of DNA are then sequenced and their DNA sequences are stitched back together using bioinformatics to identify the species and genes present in the sample. Unlike 16S rRNA sequencing, shotgun metagenomic sequencing can read all genomic DNA in a sample, rather than just one specific region of DNA.

More about this blogpost can you find here.