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Background   Bacillus cereus  sensu lato comprises eight closely related species including the human pathogens  Bacillus anthracis  and  Bacillus cereus . Within  B. cereus  sensu lato, chromosomally and plasmid-encoded toxins exist. While plasmid-mediated horizontal gene transfer of the emetic toxin, anthrax and insecticidal toxins is known, evolution of enterotoxin genes within the group has not been studied.    Results  We report draft genome assemblies of 25 strains, a phylogenetic network of 142 strains based on ANI derived from genome sequences and a phylogeny based on whole-genome SNP analysis. The data clearly support subdivision of  B. cereus  sensu lato into seven phylogenetic groups. While group I, V and VII represent  B. pseudomycoides ,  B. toyonensis  and  B. cytotoxicus , which are distinguishable at species level (ANI border ≥ 96 %), strains ascribed to the other five species do not match phylogenic groups. The chromosomal enterotoxin operons  nheABC  and  hblCDAB  are abundant within  B. cereus  both isolated from infections and from the environment. While the duplicated  hbl  variant  hbl   a   is present in 22 % of all strains investigated, duplication of  nheABC  is extremely rare (0.02 %) and appears to be phylogenetically unstable. Distribution of toxin genes was matched to a master tree based on seven concatenated housekeeping genes, which depicts species relationships in  B. cereus  sensu lato as accurately as whole-genome comparisons. Comparison to the phylogeny of enterotoxin genes uncovered ample evidence for horizontal transfer of  hbl, cytK  and  plcR,  as well as frequent deletion of both toxins and duplication of  hbl . No evidence for  nhe  deletion was found and stable horizontal transfer of  nhe  is rare. Therefore, evolution of  B. cereus  enterotoxin operons is shaped unexpectedly different for yet unknown reasons.    Conclusions  Frequent exchange of the pathogenicity factors  hbl, cytK  and  plcR  in  B. cereus  sensu lato appears to be an important mechanism of  B. cereus  virulence evolution, including so-called probiotic or non-pathogenic species, which might have consequences for risk assessment procedures. In contrast, exclusively vertical inheritance of  nhe  was observed, and since  nhe -negative strains appear to be extremely rare, we suggest that fitness loss may be associated with deletion or horizontal transfer of the  nhe  operon.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-015-0529-4) contains supplementary material, which is available to authorized users.

bmc evolutionary biology

Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe