What is right for you? 16S/ITS sequencing Vs Whole genome metagenomics

Deep dive into 16S/ITS sequencing and whole genome metagenomics

June 23, 2022

It can be difficult to decide which detection method is suitable for your project and lab when planning a microbial NGS experiment. You first need to consider what question you are trying to answer. What information will you need from the sequencing run? Here are three questions to ask yourself as you prepare your microbial experiment:

Are you interested in species or strain identification?

Defining your aim for species identification or strain-level identification will help determine which method would work best for your desired outcome. If you are looking at bacterial profiling at the species level, 16S rRNA sequencing should work well to identify bacteria down to the genus and species level. However, 16S sequencing typically does not provide the resolution needed to see inter-species variation caused by mutations or gene flow. If you are looking at species sub-types, or at down to the strain level of identification, whole genome sequencing would provide deeper information to see inter-species diversity.

Are you looking for bacteria/fungi/archaea detection or detection of all microbial species?

Another question to ask yourself is, what are you looking to detect? 16S/ITS sequencing will work best in identifying bacteria, fungi, and archaea. But for all microbial species, WGS will provide an in-depth analysis of the microbial communities in your sample.

Read cost – is it important to you?

Read cost is another factor to consider when choosing your microbial detection method. 16S sequencing is less read-intensive as it consumes fewer sequencing resources and allows you to run more samples per sequencing run. Although it allows for less multiplexing of samples due to a higher read budget, WGS provides more valuable metagenomic data from your samples.

To find our the pros and cons of 16S/ITS sequencing and whole genome metagenomics, watch this webinar from our experts. Learn how to decide which ideal method will help answer your microbiome questions.