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The present study was designed to clarify the taxonomic status of two species classified as  Bacillus cereus sensu lato , namely  B. cereus sensu stricto  and  Bacillus thuringiensis . To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of  B. cereus  and  B. thuringiensis  formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as  B. cereus sensu lato . However, since average nucleotide identity and digital DNA–DNA hybridization similarities between the two types of  Bacillus  were slightly higher than the thresholds used to distinguish between closely related species we conclude that  B. cereus  and  B. thuringiensis  should continue to be recognized as validly published species. The  B. thuringiensis  strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as  B. thuringiensis  gv.  thuringiensis  and  B. thuringiensis  gv.  cytolyticus . The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as  B. thuringiensis  were assigned to several polyphyletic groups/subclades within the  B. cereus – B. thuringiensis  clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify  B. thuringiensis  strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the  B. thuringiensis  genomovars and between them and  B. cereus .

frontiers in microbiology

Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars