Witold Piotr Kot
Witold Piotr Kot

Postdoc

 Research-at-a-glance

- Nucleic acids sequencing
- Bacteriophages
- Bacteriophage resistance mechanisms
- Phage therapy / biocontrol
- Bacteriophage genome modifications

Research

Our research group, Environmental Microbial Genomics, is focusing on genomic and metagenomic studies in a highly customized manner using in-house, high-throughput and full genome sequencing (Illumina and Nanopore sequencers) of pro- and eukaryotic organisms. The group uses sequence-analysis based information to describe genomic traits of keystone species and their prevalence in natural and artificial microbial communities and metagenomes, including information on bacteriophages and how other mobile genetic elements shape microbial evolution and traits.
My research is focused on viruses of microorganisms, their hosts, microbial ecology and phage-host interactions and alternative bases. I am studying bacteriophages using a cross-disciplinary approach with both classical and molecular methods.

Projects

- Bacteriophages as biocontrol agents in agriculture
- The use of alterative bases in bacteriophage genomes
- Manipulating gut microbiomes via FMT or bacteriophage therapy
- Mobility of genetic parasites and their role in shaping bacterial evolution
- Microbiomics, mobilomics and viromics

Collaborating partners

- Prof. Sylvain Moineau, University Laval, Canada - phage biology, CRISPR-Cas systems
- Prof. Valery Crécy-Lagard, University of Florida - DNA modifications
- Prof. Dennis Sandris Nielsen, University of Copenhagen, FOOD – Metagenomics and amplicon sequencing
- Dr. Horst Neve, Max Rubner-Institut, Germany- Electron Microscopy
- Prof. Peter Dedon, MIT, USA- Mass Spectrometry of nucleic acids

Funding

- 2015-2017: The Danish Council for Independent Research- Science and Production- Individual PostDoc Grant 
- 2016-2018: AUFF Individual Starting Grant 
- 2018-2020: VILLUM Foundation Experiment Grant

Selected publications

Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Carstens AB, Fa Lui C, Tremblay D, Jacob-Sera D, Sassanfar M, Lee Y-J, Weigele P, Moineau S, Hatfull GF, Dedon P, Hansen LH, Crecy-Lagard V. “7-Deazaguanine modifications protect phage DNA from host restriction systems”. 2019. Nature Communications. Doi: 10.1038/s41467-019-13384-y

Kot W, Vogensen FK, Sørensen SJ, Hansen LH. “DPS–a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque”. 2014. J Virol Methods, 196; 152-156.

D.R. Alves, A Gaudion, J.E. Bean, P Perez-Esteban, T. C. Arnot, D.R. Harper, W. Kot, L.H. Hansen, M.C. Enright, A Tobias A Jenkins. “Combined use of bacteriophage K and a novel bacteriophage to reduce Staphylococcus aureus biofilm formation.” 2014. Applied and Environmental Microbiology, 80(21):6694-6703.

Kot W, Mahony J, Murphy J, Ainsworth S, Neve H, Hansen LH, et al. “Investigation of the relationship between lactococcal host cell wall polysaccharide genotype and 936 phage receptor binding protein phylogeny”. 2013. Applied and Environmental Microbiology, 79.

 

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