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

Abstract

The present study was designed to clarify the taxonomic status of two species classified as <i>Bacillus cereus sensu lato</i>, namely <i>B. cereus sensu stricto</i> and <i>Bacillus thuringiensis</i>. 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 <i>B. cereus</i> and <i>B. thuringiensis</i> formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as <i>B. cereus sensu lato</i>. However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of <i>Bacillus</i> were slightly higher than the thresholds used to distinguish between closely related species we conclude that <i>B. cereus</i> and <i>B. thuringiensis</i> should continue to be recognized as validly published species. The <i>B. thuringiensis</i> strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as <i>B. thuringiensis</i> gv. <i>thuringiensis</i> and <i>B. thuringiensis</i> gv. <i>cytolyticus</i>. The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as <i>B. thuringiensis</i> were assigned to several polyphyletic groups/subclades within the <i>B. cereus</i>-<i>B. thuringiensis</i> clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify <i>B. thuringiensis</i> 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 <i>B. thuringiensis</i> genomovars and between them and <i>B. cereus</i>.