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A Beginner’s Guide to Microbial Sequencing – 16S/18S/ITS Amplicon Sequencing vs. Shotgun Metagenomic Sequencing


Shotgun metagenomic sequencing provides information on the total genomic DNA from all organisms in a sample, avoiding the need for isolation and cultivation of microorganisms or amplification of target regions. This is crucial because it is believed that nearly 99% of all microorganisms cannot be cultivated in the laboratory. Differently from the targeted approach used in the 16S/18S/ITS amplicon sequencing, shotgun metagenomic sequencing uses next-generation sequencing (NGS) technology to provide not only information on the taxonomic annotations of each organism but also the functional profiling, gene prediction and microbial interaction of the whole community.

Learning Objectives:

  • A general analysis of both 16S/18S/ITS amplicon metagenomic sequencing and shotgun metagenomic sequencing
  • Gain insights into a variety of research strategies


Xiaorui Han -Senior Product Manager, Novogene America