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Within <jats:italic>B. cereus<\/jats:italic> 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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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 <jats:italic>B. cereus<\/jats:italic> sensu lato into seven phylogenetic groups. While group I, V and VII represent <jats:italic>B. pseudomycoides<\/jats:italic>, <jats:italic>B. toyonensis<\/jats:italic> and <jats:italic>B. cytotoxicus<\/jats:italic>, which are distinguishable at species level (ANI border \u2265 96 %), strains ascribed to the other five species do not match phylogenic groups. The chromosomal enterotoxin operons <jats:italic>nheABC<\/jats:italic> and <jats:italic>hblCDAB<\/jats:italic> are abundant within <jats:italic>B. cereus<\/jats:italic> both isolated from infections and from the environment. While the duplicated <jats:italic>hbl<\/jats:italic> variant <jats:italic>hbl<\/jats:italic><jats:sub>\n                    <jats:italic>a<\/jats:italic>\n                  <\/jats:sub> is present in 22 % of all strains investigated, duplication of <jats:italic>nheABC<\/jats:italic> 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 <jats:italic>B. cereus<\/jats:italic> sensu lato as accurately as whole-genome comparisons. Comparison to the phylogeny of enterotoxin genes uncovered ample evidence for horizontal transfer of <jats:italic>hbl, cytK<\/jats:italic> and <jats:italic>plcR,<\/jats:italic> as well as frequent deletion of both toxins and duplication of <jats:italic>hbl<\/jats:italic>. No evidence for <jats:italic>nhe<\/jats:italic> deletion was found and stable horizontal transfer of <jats:italic>nhe<\/jats:italic> is rare. Therefore, evolution of <jats:italic>B. cereus<\/jats:italic> enterotoxin operons is shaped unexpectedly different for yet unknown reasons.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Frequent exchange of the pathogenicity factors <jats:italic>hbl, cytK<\/jats:italic> and <jats:italic>plcR<\/jats:italic> in <jats:italic>B. cereus<\/jats:italic> sensu lato appears to be an important mechanism of <jats:italic>B. cereus<\/jats:italic> virulence evolution, including so-called probiotic or non-pathogenic species, which might have consequences for risk assessment procedures. In contrast, exclusively vertical inheritance of <jats:italic>nhe<\/jats:italic> was observed, and since <jats:italic>nhe<\/jats:italic>-negative strains appear to be extremely rare, we suggest that fitness loss may be associated with deletion or horizontal transfer of the <jats:italic>nhe<\/jats:italic> operon.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12862-015-0529-4","type":"journal-article","created":{"date-parts":[[2015,11,10]],"date-time":"2015-11-10T11:54:39Z","timestamp":1447156479000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":112,"title":["Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe"],"prefix":"10.1186","volume":"15","author":[{"given":"Maria-Elisabeth","family":"B\u00f6hm","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Huptas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktoria Magdalena","family":"Krey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0394-9890","authenticated-orcid":false,"given":"Siegfried","family":"Scherer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,11,10]]},"reference":[{"key":"529_CR1","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1098\/rstb.1887.0011","volume":"178","author":"GC Frankland","year":"1887","unstructured":"Frankland GC, Frankland PF. 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