TY - JOUR
T1 - Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant
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.
AB - 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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U2 - 10.1371/journal.pone.0017836
DO - 10.1371/journal.pone.0017836
M3 - Article
C2 - 21464989
AN - SCOPUS:79953037918
SN - 1932-6203
VL - 6
JO - PloS one
JF - PloS one
IS - 3
M1 - e17836
ER -