Global Phylogenomic Analysis and Genome Homology Reveals New rare Phylogenetic groups, “Synonymous” Species, and the Need to Simplify Nomenclature and Pathogens Identification in the <i>Bacillus cereus</i> Group

Abstract Bacteria in the Bacillus cereus Group sensu lato (Bc Group sl) may have serious detrimental effects on the health and safety of numerous foods. Over the past decade, phylogenetic studies have shifted toward the delineation of an increasing number of closely related species. For an improved understanding, this study attempts to fill existing gaps in the data to build a complete, robust and useful phylogenetic structure that contains all 29 currently described species. The obtained phylogenetic structure features all of the known major phylogenetic groups (designated I to VII) and their subgroups, but also highlights the existence of seven new rare groups or sub-groups. The positioning of the 29 species revealed that some are synonymous, which casts doubt on the accuracy of their genomic delimitation. Four species matched with the previously described sub-groups III-5, III-9 and III-12, which are specifically known for their virulence potential. B. thuringiensis strains were dispersed throughout the majors groups II to VI, demonstrating that this species is not a genomic species restricted to group IV but should be instead considered a variety largely spread into the Bc Group sl. A similar pattern was observed for B. mycoides in 10 phylogenetic groups/species. These results highlight the need for a simplified nomenclature of the Bc Group sl, which should be developed through a collaboration between relevant stakeholders. In the meantime, an updated version of the panC database is proposed, named CereusID, that integrates data from the present work and enables the identification of all phylogenetic entities within Bc Group sl: https://toolcereusid.shinyapps.io/cereusid/ .