Advances in culture-independent sequencing technologies have led to a rapid expansion in the number of bacterial genomes, necessitating a robust genome-based taxonomy for describing microbial diversity and for constructing accurate genome-based phylogenies that normalize taxonomic ranks according to evolutionary divergence, and overcome inconsistencies in historical classification schemes. Parks et al. present a standardized bacterial taxonomy inferred from the concatenation of ubiquitous single-copy proteins that covers 94,759 bacterial genomes. In this new taxonomy — referred to as the genome taxonomy database (GTDB) taxonomy — ~58% of these genomes had changes to their existing taxonomy and 99 new phyla are described, including six major monophyletic units of the Proteobacteria and the merger of the Candidate Phyla Radiation into a single phylum. The authors anticipate that the GTDB will improve the classification of uncultured bacteria.