Abstract
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.
Highlights
Bacillus cereus sensu lato, known as the B. cereus group, is a phylogenetically defined taxon within the genus Bacillus (Cohn, 1872) which encompasses an array of Gram-stain-positive, rodshaped, facultatively anaerobic, endospore-forming bacteria that are common in natural habitats (Guinebretiere et al, 2013; Liu et al, 2017b; Patino-Navarrete and Sanchis, 2017)
It is evident from the phylogenomic tree that the B. cereus and B. thuringiensis strains are closely related and separated from the type strains of other species belonging to B. cereus sensu lato (Figure 1)
Within the clade encompassing the B. cereus and B. thuringiensis strains, three subclades were recognized at the 96% ANI cutoff; these were considered to correspond to B. cereus, B. thuringiensis genomovar cytolyticus, and B. thuringiensis genomovar thuringiensis (Figure 2A)
Summary
Known as the B. cereus group, is a phylogenetically defined taxon within the genus Bacillus (Cohn, 1872) which encompasses an array of Gram-stain-positive, rodshaped, facultatively anaerobic, endospore-forming bacteria that are common in natural habitats (Guinebretiere et al, 2013; Liu et al, 2017b; Patino-Navarrete and Sanchis, 2017). The group currently contains 21 validly published species (Liu et al, 2017a) which include Bacillus anthracis (Cohn, 1872), the causal agent of anthrax (Ezzell and Welkos, 1999; Moayeri et al, 2015); B. cereus (Frankland and Frankland, 1887), an opportunistic pathogen that causes food poisoning (Kotiranta et al, 2000; Bottone, 2010); Bacillus thuringiensis (Berliner, 1915), which produces insecticidal toxins widely used as biological control agents (Bravo et al, 2013; Raymond and Federici, 2017); and Bacillus toyonensis (Jimenez et al, 2013), which is used as a probiotic in animal nutrition. Many Bt toxins have been reported and classified based on amino acid sequences (Table 1; Crickmore et al, 1998; Berry and Crickmore, 2017)
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