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

Abstract

The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis. Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of ≈92.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at ≈92.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness. IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.

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

“…The virulence and antibiotic resistance genes were annotated using BTyper version 2.3.3 (default settings) (Carroll et al, 2017) and insecticidal toxin-encoding genes were annotated using BTyper3 version 3.0.2 (Carroll et al, 2020). CRISPR-Cas genes were detected using CRISPRCasFinder (Couvin et al, 2018) (Supplemental Table 3).…”

“…The first set (Supplemental Table 5) comprised up to five strains of B. cereus or B. thuringiensis selected from differentiated clades in BCSL_114 and B. thuringiensis phylogenetic trees from previous population structure analyses (Bazinet, 2017, Gillis et al, 2018. The second set comprised 1) the closest genomes to our strain identified using the phylogeny reconstruction of the first dataset (underlined in Figure 5), 2) 121 strains closely related to those according to phylogeny analysis of B. cereus group strains from Carroll et al (2020), and 3) B. thuringiensis YBT-1518 type strain as outgroup (Supplemental Table 6). To ensure the assembly quality of both datasets, only genomes with an N50 size over 20 kbp were selected.…”

“…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).…”

“…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).…”

The fully resolved genome ofBacillus thuringiensisHER1410 reveals acry-containing chromosome, two megaplasmids & an integrative plasmidial prophage

“…483 Furthermore, to find the closest genomes to our strain, we performed a focused 484 analysis using the obtained similar strains to HER1410. These strains belong to 485 the same cluster within the phylogeny analysis of B. cereus group from a recent 486 work on its population structure (Carroll et al, 2020). Thus, we selected the 126 487 strains included in this cluster, with the addition of HER1410, and B. thuringiensis Interestingly, as reported here for HER1410, entomocidus has been suggested 512 to harbor cry genes within the chromosome (Carlson and Kolsto, 1993).…”