Microbial diversity is vast and most of it still remains to be explored thanks to a pronounced cultivation bottleneck. To help in this exploration, we need a consistent phylogenetic road map to guide us. Much of my career has been focused on providing just such a road map, first through the 16S rRNA gene (Greengenes) and more recently through the Genome Taxonomy Database (GTDB). The GTDB provides a complete (domain to species) phylogenetically consistent genome-based taxonomy for bacterial and archaeal genomes sourced from the NCBI Assembly database. It is currently in its ninth release (09-RS220) and incorporates almost 600,000 genomes. The GTDB has been mostly well received by the scientific community but is not suitable for classification of many pathogens because pathogenic traits often occur at the subspecies level or are horizontally transferred between species. This is not captured in the strictly vertical classification scheme used by GTDB. I will present a proposed solution to this quandary using the Bacillus cereus group as a case study, which should hopefully make GTDB more useful to clinical microbiologists.