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 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 .

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes

“…Note that a recently proposed "genomovar" framework for B. cereus sensu stricto/B. thuringiensis (56) is not adopted here, due to the lack of genomospecies boundaries between their type strains (shown here and elsewhere [33][34][35], including the paper proposing the framework [56]), as well as the lack of a standardized species definition for B. thuringiensis (B. thuringiensis has been used to refer to any B. cereus group species capable of producing Bt toxins [29] or to the genomospecies formed by the B. thuringiensis type strain genome [56]).…”

Completed Genomic Sequence ofBacillus thuringiensisHER1410 Reveals aCry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage

“…Phylogenetic positioning of HER1410 HER1410 strain has been classified either as serovar israelensis (Daugelavicius et al 2007, Gaidelyte et al 2005, Gaidelyte et al 2006, or thuringiensis (Gillis, A., Mahillon, J., 2014b andVerheust et al, 2005), being the latter fundamented on plasmidic profile, type of crystal and insecticidal activity. Several studies have proposed to resolve the conflict between genomics and phenotypical classification (Bazinet, 2017, Baek et al, 2019, Carroll et al, 2020. While B. thuringiensis has always been characterized by their ability to produce entomopathogenic crystals, some crystal producing strains are more genetically similar to B. cereus s. s. (Carroll et al, 2020).…”

“…Here we aimed to characterize HER1410, not only by its capacity of producing entomotoxins, but also by its genomic features. Multiple different approaches have been used to stablish the population structure of B. cereus s. l. such as multi-locus sequence typing, ANI or core genes-based phylogenies (Bolotin et al, 2017, Baek et al, 2019, Carroll et al, 2020. Here, in order to provide a high resolution on the population structure, we performed a phylogenomics analysis based on a MSA of the core genes present in the pangenome (Page et al, 2015).…”

Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses

“…This method provides a higher phylogenetic resolution compared to the 16S rRNA gene analysis method, especially for the order Enterobacterales where limited 16S rRNA phylogenetic resolution is insufficient for identification of members in the family Enterobacteriaceae and Erwiniaceae. Therefore, genome-based phylogenetic tree analysis is now used frequently for taxonomic identification [15][16][17][18].…”