The Phylogeny of Bacillus cereus sensu lato

Richard T. Okinaka; Paul Keim

doi:10.1128/microbiolspec.TBS-0012-2012

Chapter 12 : The Phylogeny of Bacillus cereus sensu lato

Authors: Richard T. Okinaka¹, Paul Keim²

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Affiliations: 1: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073; 2: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073

Content Type: Monograph

Publication Year: 2016

Category: Bacterial Pathogenesis

Book DOI: 10.1128/9781555819323

Chapter DOI: 10.1128/microbiolspec.TBS-0012-2012

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Abstract:

The three main species of the Bacillus cereus sensu lato, B. cereus, B. thuringiensis, and B. anthracis, were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits. B. thuringiensis isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen ( 1 ). B. anthracis, the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease ( 2 ), and B. cereus, a common soil organism, is also an occasional opportunistic pathogen of humans ( 3 – 5 ). In addition to these three historical species designations, are three less-recognized and -understood species: B. mycoides, B. weihenstephanensis, and B. pseudomycoides. All of these “species” combined comprise the B. cereus sensu lato group. Despite these apparently clear phenotypic definitions, early molecular approaches to separate the first three by various DNA hybridization and 16S/23S ribosomal sequence analyses led to some “confusion” because there were limited differences to differentiate between these species ( 6 ). These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species ( 7 , 8 ). But the pathogenic properties of B. anthracis and the biopesticide applications of B. thuringiensis appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained ( 9 ). B. cereus sensu lato represents a classic example of a now common bacterial species taxonomic quandary where relatively new molecular data must somehow be incorporated into a traditional hierarchical classification system ( 10 ).

Citation: Okinaka R, Keim P. 2016. The Phylogeny of Bacillus cereus sensu lato, p 239-251. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0012-2012

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The Phylogeny of Bacillus cereus sensu lato

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Figure 1

AFLP-based phylogenetic tree of B. cereus sensu lato. This is a schematic representation redrawn from Hill et al. ( 12 ) of 332 isolates. While 10 distinct branches were identified, they formed three main clusters labeled as 1, 2, and 3 to correspond to subgroups identified by Priest et al. ( 15 ) to maintain consistency between AFLP and MLST trees based on the positions of known matching isolates in both trees.

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Figure 1

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Figure 2

An example of homologous recombination identified in MLST profiles. (A) The diversity of an original MLST subclade (Sotto) based on seven MLST fragments ( 15 ). The same branch is shown, but is now dissected by ClonalFrame ( 33 ) and separated into six consistent fragments (B) and a second inconsistent fragment (ilv) (C) to show that the ilv fragment has two sequence types, 55 and 49, that had experienced recombination events with two other distinct clades.

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Figure 2

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Figure 3

A graph of the distribution of gene families across B. cereus sensu lato genomes redrawn from Zwick et al. ( 41 ). This figure is based on the definition of the extended core as genes encoding proteins present in 49 or more genomes and accessory genes as those present in <6 genomes. The class between these extremes defined the character gene set.

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Figure 3

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Figure 4

Whole-genome phylogeny of B. cereus sensu lato. This tree was redrawn based on data sets of concatenated, conserved protein sequences by using a neighbor-joining algorithm ( 41 ). Note that the relative distribution of the isolates based on a conserved whole-genome phylogeny is essentially the same as those observed in numerous MLST and AFLP studies and separated into three major clades.

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Figure 4

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