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The Phylogeny of

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  • Authors: Richard T. Okinaka1, Paul Keim2
  • Editors: Patrick Eichenberger3, Adam Driks4
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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; 3: New York University, New York, NY; 4: Loyola University Medical Center, Maywood, IL
    • Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
  • Received 17 October 2012 Accepted 15 December 2015 Published 12 February 2016
  • Richard Okinaka, [email protected]
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  • Abstract:

    The three main species of the , , , and , were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits. isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen. , the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease, and , a common soil organism, is also an occasional opportunistic pathogen of humans. In addition to these three historical species designations, are three less-recognized and -understood species: , , and . All of these “species” combined comprise the 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. These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species. But the pathogenic properties of and the biopesticide applications of appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained. represents a classic example of a now common bacterial species taxonomic quandary.

  • Citation: Okinaka R, Keim P. 2016. The Phylogeny of . Microbiol Spectrum 4(1):TBS-0012-2012. doi:10.1128/microbiolspec.TBS-0012-2012.

References

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2016-02-12
2019-10-19

Abstract:

The three main species of the , , , and , were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits. isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen. , the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease, and , a common soil organism, is also an occasional opportunistic pathogen of humans. In addition to these three historical species designations, are three less-recognized and -understood species: , , and . All of these “species” combined comprise the 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. These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species. But the pathogenic properties of and the biopesticide applications of appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained. represents a classic example of a now common bacterial species taxonomic quandary.

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The Phylogeny of
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Citation: Okinaka R, Keim P. 2016. The phylogeny of . microbiolspec 4(1): doi:10.1128/microbiolspec.TBS-0012-2012
/content/microbiolspec/10.1128/microbiolspec.TBS-0012-2012.fig1
FIGURE 1
AFLP-based phylogenetic tree of . 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.
microbiolspec/4/1/TBS-0012-2012-fig1_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig1.gif
Image of FIGURE 1

Click to view

FIGURE 1

AFLP-based phylogenetic tree of . 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.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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/content/microbiolspec/10.1128/microbiolspec.TBS-0012-2012.fig2
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 () (C) to show that the fragment has two sequence types, 55 and 49, that had experienced recombination events with two other distinct clades.
microbiolspec/4/1/TBS-0012-2012-fig2_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig2.gif
Image of FIGURE 2

Click to view

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 () (C) to show that the fragment has two sequence types, 55 and 49, that had experienced recombination events with two other distinct clades.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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/content/microbiolspec/10.1128/microbiolspec.TBS-0012-2012.fig3
FIGURE 3
A graph of the distribution of gene families across 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.
microbiolspec/4/1/TBS-0012-2012-fig3_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig3.gif
Image of FIGURE 3

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FIGURE 3

A graph of the distribution of gene families across 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.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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FIGURE 4
Whole-genome phylogeny of . 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.
microbiolspec/4/1/TBS-0012-2012-fig4_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig4.gif
Image of FIGURE 4

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FIGURE 4

Whole-genome phylogeny of . 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.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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