Gerald B. Koudelka


Gerald B. Koudelka.

Gerald B. Koudelka


Gerald B. Koudelka


Professor, SUNY Chancellor's Award for Excellence in Teaching
Fellow, American Academy of Microbiology

Research Interests

DNA-protein interaction; DNA structure, bacterial pathogenesis


  • PhD, University at Buffalo
  • Postdoctoral Research, Harvard University

Office Hours

  • Monday, Thursday: 2:00 - 3:00pm or by appointment

Research Summary

The research in the Koudelka lab is focused around two central themes: Mechanisms of DNA Sequence Recognition; and, Evolution of Bacteriophage-encoded Exotoxins.

Mechanisms of DNA Sequence Recognition: Understanding the mechanisms used by regulatory proteins in recognizing specific DNA sequences remains one of the most important areas of study in biology. This process requires that the protein be able to seek out and recognize its particular binding sequence amidst the presence of an overwhelming number of potential non-specific binding sites. We seek to uncover the intimate biochemical and thermodynamic underpinnings of DNA sequence recognition.

Evolution of Bacteriophage-encoded Exotoxins: Phages encoding exotoxin genes are ubiquitously found within bacteria isolated from the environment. In the context of humans, these exotoxins cause diseases ranging from cholera to diphtheria to enterohemorrhagic diarrhea. However, the frequency of occurrence of the genes encoding any particular exotoxin gene in bacteriophage and/or lysogens far exceeds the number of potential animal hosts. These observations suggest that humans and other susceptible mammals are not the primary “targets” of these toxins. We are exploring the hypothesis that exotoxins arose in bacteria as part of an antipredator defense mechanism.

Selected Publications

  • Liu, Y., Koudelka, G.B. (2023) O-polysaccharides of LPS modulate E. coli uptake by Acanthamoeba. castellanii Microorganisms11, 1377 (Full text). 
  • Liu, Y., Koudelka, G.B. (2022) The oligosaccharide region of LPS governs predation of E. coli by the bacterivorous protist, Acanthamoeba castellanii Microbiology Spectrum11  e02930-22 (Full text).
  • Peng, L.; Dumevi, R.M.; Chitto, M.; Haarmann, N.; Berger, P.; Koudelka, G.; Schmidt, H.; Mellmann, A.; Dobrindt, U.; Berger, M. A Robust One-Step Recombineering System for Enterohemorrhagic Escherichia coli. Microorganisms 2022, 10, 1689. (Full text).
  • Berger, M., Aijaz, I., Berger, P., Dobrindt, U., Koudelka, G.B. (2019). Transcriptional and Translational Inhibitors Block SOS Response and Shiga Toxin Expression in Enterohemorrhagic Escherichia coliSci Rep 918777 (Full text).
  • Berger, P., Kouzel, I.U., Berger, M., Haarmann, N., Dobrindt, U., Koudelka, G.B., Mellmann, A. (2019) Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization, BMC Genomics 20:504 doi:10.1186/s12864-019-5892-x (Full text). 
  • Koudelka G.B., Arnold J.W., Chakraborty, D. (2018) Evolution of STEC virulence: Insights from the antipredator activities of Shiga toxin producing E. coli. Int J Med Microbiol. 308; 956-961. doi: 10.1016/j.ijmm.2018.07.001 (Full text).
  • Chakraborty, D., Clark, E., Mauro, S.A., Koudelka, G.B. (2018) Molecular Mechanisms Governing "Hair-Trigger" Induction of Shiga Toxin-Encoding Prophages. Viruses 10 pii: E228. doi: 10.3390/v10050228 (Full text).
  • Aijaz, I., Koudelka, G.B. (2018). Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules Microbiologyopene00636. doi: 10.1002/mbo3.636 (Full text).
  • Aijaz I, Koudelka GB. (2017) Tetrahymena phagocytic vesicles as ecological micro-niches of phage transfer. FEMS Microbiol Ecol. 93, doi: 10.1093/femsec/fix030 (Full text).
  • Colon, M.P., Chakraborty D., Pevzner, Y., Koudelka. G.B. (2016) Mechanisms determining the differential stability of of Stx+ and Stx- lysogens, Toxins 8, 96 doi:10.3390/toxins8040096 (Full text).
  • Arnold, J.W., Spacht, D., Koudelka, G.B., (2016) Molecular determinants governing the recognition and uptake of E. coli O157:H7 by Acanthamoeba castellanii, Cellular Microbiology, 18(10), 1459–1470 (Full text).
  • Arnold, J.W, Koudelka, G.B. (2014) The Trojan horse of the microbiological arms race: Phage encoded bacterial toxins as a weapon against eukaryotic predators, Env. Micro. 16, 454-466 (Full text).
  • Mauro, S.A., Opalka, H., Lindsay, K., Colon, M.P., Koudelka, G.B. (2013) The microcosm mediates the persistence of Shiga toxin producing E. coli (STEC) in freshwater ecosystems. Applied and Env. Microbiology, 79, 4821-4842 (Full text).
  • Stolfa, G., and Koudelka, G.B., (2013) Entry and Killing of Tetrahymena by Bacterially Produced Shigatoxin, mBio, 4 e00416-12; doi:10.1128/mBio.00416-12. (Full text)