Shallow shotgun sequencing will enable deeper resolution in taxonomic identification, relative to 16S sequencing. It is expected that shallow shotgun sequencing will typically yield much more consistent species level ID’s and, with the CosmosID bioinformatics tool, strain level calls as well. For human samples, it is not uncommon to see most of the alpha diversity captured of the sample and so depending on your research question, shallow shotgun sequencing can be a very useful tool for general surveillance and profiling of the microbiome. It is also possible to retrieve the most abundant functional genes within a sample.
The other main advantage is that shallow shotgun data is significantly less error-prone and doesn’t suffer the amplification bias that 16S amplicon sequencing will yield. Prices for shallow shotgun start from just $99 USD per sample, including bioinformatic analysis, making the two methods equally accessible to researchers..