Choosing the Right Approach for Microbiome Profiling

Microbiome profiling is a powerful tool in diagnostic testing, enabling the identification and analysis of microorganisms which influence health. Two main sequencing methods are commonly used for this purpose: 16S rRNA gene sequencing and Whole Genome Sequencing (WGS).

• 16S rRNA sequencing targets a specific gene found in all bacteria and archaea, allowing for a cost-effective and efficient way to identify taxonomic composition, typically at the genus level. When using long-read technologies to sequence the full-length 16S gene, classification accuracy can be improved to the species level. It is widely used in clinical and consumer microbiome tests for its speed, affordability, and reliable insights into bacterial diversity.
• WGS, captures the entire genetic material of an organism. Unlike targeted approaches like 16S rRNA sequencing—which only focuses on a single gene—WGS analyzes all the DNA present in a sample. This includes not only bacteria but also viruses, archaea, fungi, and even eukaryotic organisms if present

Each method offers distinct advantages depending on the test’s purpose. In the following sections, we outline the specific strengths and limitations of both methods to help guide the selection of the most appropriate approach for microbiome testing.