The historical domestication of a Clostridium botulinum strain used for the industrial production of botulinum neurotoxin.
4 affiliations
- 1The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011.
- 2Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011.
- 3Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706.
- 4Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI 48824.
Abstract
Laboratory production of botulinum neurotoxin (BoNT) began more than 90 y ago for medical, military, and later pharmaceutical applications, creating one of the longest-running examples of microbial cultivation under sustained human control. A single Clostridium botulinum Group I lineage, Army Hall A (AHA), was established by the US military in 1942 and later gave rise to Hall A-hyper (HAH), the strain widely used for pharmaceutical BoNT production. We analyzed more than 1,000 C. botulinum genomes to identify AHA's closest relatives and to infer the most recent common ancestor (MRCA) shared with its nearest lineage. Relative to this MRCA, AHA accumulated nearly 100 genetic changes, including 46 single-nucleotide substitutions, 44 small insertions or deletions, and several large deletions and structural variants that led to the loss of more than 80 genes. A nonsense mutation in mutS generated a hypermutator phenotype that accelerated mutation rates and increased genetic diversity. This event is inferred to have occurred early in the lineage's domestication and appears to have facilitated laboratory-adaptive traits, including the lack of sporulation and increased BoNT yield. Competition experiments under standard growth conditions confirmed substantial laboratory adaptation, with AHA exhibiting a strong fitness advantage over a close relative. Together, these results reconstruct the genomic trajectory of a bacterium evolving under prolonged human-mediated selection and provide a genome-resolved example of microbial domestication. The findings show how laboratory conditions, industrial selection, and changing mutation rates can shape bacterial evolution, and they offer a general framework for understanding domestication and laboratory adaptation across microbial systems.
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BibTeX
@article{keim2026historical,
title = {{The historical domestication of a Clostridium botulinum strain used for the industrial production of botulinum neurotoxin.}},
author = {Paul Keim and Roxanne Nottingham and Miriam A Guevara and Ely F Miller and Amy J Vogler and Charles H D Williamson and Theresa Smith and Richard G Posner and Sabine Pellett and Richard E Lenski and Jason W Sahl},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = oct,
doi = {10.1073/pnas.2605155123},
url = {https://europepmc.org/article/MED/42879488},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - The historical domestication of a Clostridium botulinum strain used for the industrial production of botulinum neurotoxin.
AU - Paul Keim
AU - Roxanne Nottingham
AU - Miriam A Guevara
AU - Ely F Miller
AU - Amy J Vogler
AU - Charles H D Williamson
AU - Theresa Smith
AU - Richard G Posner
AU - Sabine Pellett
AU - Richard E Lenski
AU - Jason W Sahl
PY - 2026
DA - 2026/10/15
JO - Proceedings of the National Academy of Sciences of the United States of America
DO - 10.1073/pnas.2605155123
UR - https://europepmc.org/article/MED/42879488
AB - Laboratory production of botulinum neurotoxin (BoNT) began more than 90 y ago for medical, military, and later pharmaceutical applications, creating one of the longest-running examples of microbial cultivation under sustained human control. A single Clostridium botulinum Group I lineage, Army Hall A (AHA), was established by the US military in 1942 and later gave rise to Hall A-hyper (HAH), the strain widely used for pharmaceutical BoNT production. We analyzed more than 1,000 C. botulinum genomes to identify AHA's closest relatives and to infer the most recent common ancestor (MRCA) shared with its nearest lineage. Relative to this MRCA, AHA accumulated nearly 100 genetic changes, including 46 single-nucleotide substitutions, 44 small insertions or deletions, and several large deletions and structural variants that led to the loss of more than 80 genes. A nonsense mutation in mutS generated a hypermutator phenotype that accelerated mutation rates and increased genetic diversity. This event is inferred to have occurred early in the lineage's domestication and appears to have facilitated laboratory-adaptive traits, including the lack of sporulation and increased BoNT yield. Competition experiments under standard growth conditions confirmed substantial laboratory adaptation, with AHA exhibiting a strong fitness advantage over a close relative. Together, these results reconstruct the genomic trajectory of a bacterium evolving under prolonged human-mediated selection and provide a genome-resolved example of microbial domestication. The findings show how laboratory conditions, industrial selection, and changing mutation rates can shape bacterial evolution, and they offer a general framework for understanding domestication and laboratory adaptation across microbial systems.
SN - 0027-8424
SN - 1091-6490
ER -