Phylogenomic Comparison of Bacillus cereus Group Strains to Recently Identified Type Strains Supports the Species Reclassification of Many Strains

Background. The Bacillus cereus Group (BcG) is a group of closely related species that are important in health (eg, B. anthracis and B. cereus) and biotechnology (eg, B. thuringiensis). Recently, many new species were added to the BcG, bringing the current total to 18 species. With this recent expansion of the BcG, it is useful to revisit the species classification of existing BcG strains to determine whether their species assignments require realignment with the most current taxonomy of the group. This is particularly relevant for older strains that may have been assigned to a species at a time when taxonomic differentiation was primarily based upon phenotypic observations.

Methods. The whole genome sequences of 21 ATCC and 14 BEI Resources strains from BcG species were obtained via Illumina sequencing. The genome-to-genome distances (GGDs) between the genomes of these strains and that of the 18 BcG type strains present in GenBank were determined by using the Genome-to-Genome Distance Calculator (GGDC); genomes were compared in a pairwise manner. These GGDs were used as the basis for inferring phylogeny via FastME 2.0.

Results. The pairwise analysis of the 18 type strain genomes shows that 16 of these are correctly identified as independent species. Two of the type strains fall within the circumscription of other type strains. B. weihenstephanensis NBRC 101238^T falls within the circumscription of B. mycoides ATCC 6462^T with a GGD of 78.7%, which indicates that it represents a subspecies of B. mycoides. Additionally, B. thuringiensis ATCC 10792^T falls within the circumscription of B. cereus ATCC 14579^T with a GGD of 71.1%, which indicates that it may represent a subspecies of B. cereus. Of the 35 ATCC/BEI Resources genomes examined, 17 were confirmed as correctly belonging to the assigned species. Of the remaining strains, 13 fell within the circumscription of species other than their assigned species. Five strains did not fall within the circumscription of any existing species (but are closely related to each other at GGDs ≥91.1%), suggesting that they may represent a novel species within the BcG.

Conclusions. The phylogenomic analysis described here illustrates the importance of reexamining the identity of existing strains via the most recent tools and taxonomic information. Particularly with items deposited decades before our modern understanding of genotypic characterization, such phylogenomic reexaminations enable the taxonomic reassessment of strains to ensure their accurate alignment with the most current taxonomy.