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Shotgun metagenomics is now widely applied in microbiome studies. This is because it provides valuable functional information down to the strain level and for all types of microorganisms (including archaea, fungi, and viruses)
Lewis et al. 2015 Cell Host Microbe. 18: 489-500
A beneficial spin-off from metagenomic sequencing projects has been their deposition into easily accessible databases. This has allowed researchers to leverage these datasets to create reference databases for future studies. Examples include a database with > 150,000 microbial reference genomes (Pasolli et al. 2019 Cell 176: 649-62 e620) and a human gut micro…