Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant

Henry S. Gibbons, Stacey M. Broomall, Lauren A. McNew, Hajnalka Daligault, Carol Chapman, David Bruce, Mark Karavis, Michael Krepps, Paul A. McGregor, Charles Hong, Kyong H. Park, Arya Akmal, Andrew Feldman, Jeffrey S. Lin, Wenling E. Chang, Brandon W. Higgs, Plamen Demirev, John Lindquist, Alvin Liem, Ed Fochler & 9 others Timothy D. Read, Roxanne Tapia, Shannon Johnson, Kimberly A. Bishop-Lilly, Chris Detter, Cliff Han, Shanmuga Sozhamannan, C. Nicole Rosenzweig, Evan W. Skowronski

Research output: Contribution to journalArticle

Abstract

Background: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS). Results: Archival strains and two "present day" type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86% identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the "military" isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of "military" isolates on lactate-containing media, and showed that the "military" strains exhibited a hypersporulating phenotype. Conclusions: Our analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.

Original languageEnglish (US)
Article numbere17836
JournalPLoS One
Volume6
Issue number3
DOIs
StatePublished - 2011

Fingerprint

Bacillus atrophaeus
Bacilli
Bacillus
Genome
genomics
Genes
Firearms
genome
sequence analysis
metabolomics
Biological Warfare
Biological Warfare Agents
Biological warfare
Genetic Selection
Lactic Acid
Bacillus (bacteria)
Nucleotides
History
Bacillus subtilis
lactates

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Gibbons, H. S., Broomall, S. M., McNew, L. A., Daligault, H., Chapman, C., Bruce, D., ... Skowronski, E. W. (2011). Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant. PLoS One, 6(3), [e17836]. https://doi.org/10.1371/journal.pone.0017836

Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant. / Gibbons, Henry S.; Broomall, Stacey M.; McNew, Lauren A.; Daligault, Hajnalka; Chapman, Carol; Bruce, David; Karavis, Mark; Krepps, Michael; McGregor, Paul A.; Hong, Charles; Park, Kyong H.; Akmal, Arya; Feldman, Andrew; Lin, Jeffrey S.; Chang, Wenling E.; Higgs, Brandon W.; Demirev, Plamen; Lindquist, John; Liem, Alvin; Fochler, Ed; Read, Timothy D.; Tapia, Roxanne; Johnson, Shannon; Bishop-Lilly, Kimberly A.; Detter, Chris; Han, Cliff; Sozhamannan, Shanmuga; Rosenzweig, C. Nicole; Skowronski, Evan W.

In: PLoS One, Vol. 6, No. 3, e17836, 2011.

Research output: Contribution to journalArticle

Gibbons, HS, Broomall, SM, McNew, LA, Daligault, H, Chapman, C, Bruce, D, Karavis, M, Krepps, M, McGregor, PA, Hong, C, Park, KH, Akmal, A, Feldman, A, Lin, JS, Chang, WE, Higgs, BW, Demirev, P, Lindquist, J, Liem, A, Fochler, E, Read, TD, Tapia, R, Johnson, S, Bishop-Lilly, KA, Detter, C, Han, C, Sozhamannan, S, Rosenzweig, CN & Skowronski, EW 2011, 'Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant', PLoS One, vol. 6, no. 3, e17836. https://doi.org/10.1371/journal.pone.0017836
Gibbons, Henry S. ; Broomall, Stacey M. ; McNew, Lauren A. ; Daligault, Hajnalka ; Chapman, Carol ; Bruce, David ; Karavis, Mark ; Krepps, Michael ; McGregor, Paul A. ; Hong, Charles ; Park, Kyong H. ; Akmal, Arya ; Feldman, Andrew ; Lin, Jeffrey S. ; Chang, Wenling E. ; Higgs, Brandon W. ; Demirev, Plamen ; Lindquist, John ; Liem, Alvin ; Fochler, Ed ; Read, Timothy D. ; Tapia, Roxanne ; Johnson, Shannon ; Bishop-Lilly, Kimberly A. ; Detter, Chris ; Han, Cliff ; Sozhamannan, Shanmuga ; Rosenzweig, C. Nicole ; Skowronski, Evan W. / Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant. In: PLoS One. 2011 ; Vol. 6, No. 3.
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abstract = "Background: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS). Results: Archival strains and two {"}present day{"} type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86{\%} identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the {"}military{"} isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of {"}military{"} isolates on lactate-containing media, and showed that the {"}military{"} strains exhibited a hypersporulating phenotype. Conclusions: Our analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.",
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AU - Gibbons, Henry S.

AU - Broomall, Stacey M.

AU - McNew, Lauren A.

AU - Daligault, Hajnalka

AU - Chapman, Carol

AU - Bruce, David

AU - Karavis, Mark

AU - Krepps, Michael

AU - McGregor, Paul A.

AU - Hong, Charles

AU - Park, Kyong H.

AU - Akmal, Arya

AU - Feldman, Andrew

AU - Lin, Jeffrey S.

AU - Chang, Wenling E.

AU - Higgs, Brandon W.

AU - Demirev, Plamen

AU - Lindquist, John

AU - Liem, Alvin

AU - Fochler, Ed

AU - Read, Timothy D.

AU - Tapia, Roxanne

AU - Johnson, Shannon

AU - Bishop-Lilly, Kimberly A.

AU - Detter, Chris

AU - Han, Cliff

AU - Sozhamannan, Shanmuga

AU - Rosenzweig, C. Nicole

AU - Skowronski, Evan W.

PY - 2011

Y1 - 2011

N2 - Background: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS). Results: Archival strains and two "present day" type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86% identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the "military" isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of "military" isolates on lactate-containing media, and showed that the "military" strains exhibited a hypersporulating phenotype. Conclusions: Our analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.

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