16S phylogenetic profiling

A mainstay of microbiomics is 16S rDNA sequencing. Using this method, it is possible to get an overview of the community composition of a microbiome and identify differences between groups and variation within groups.

In 16S rDNA sequencing, the 16S rRNA gene of all bacteria in a sample is amplified in a PCR reaction. The amplified 16S rDNA is then sequenced and by comparing these sequences to annotated databases, the taxonomy of each sequence can be inferred.

The process targets the entire bacterial diversity simultaneously and gives the relative abundance of all taxa down to genus level in the sample. The technique is not always able to differentiate different species or strains within a genus why other methods may be required (e.g. whole metagenome sequencing or real-time qPCR) if a higher taxonomic resolution is required.

It is an efficient first tool for surveying the community composition of a microbiome of interest, and although it only directly provides taxonomic data, the functional potential of the microbiome community can be inferred by using databases that links taxonomy to function.

Figure: Generalized UniFrac analysis of microbiome community composition of patients receiving treatment or placebo versus healthy controls. Treatment has a normalizing effect on the microbiome.