Dr. Simon van Vliet

Manfredi, P., Santi, I., Maffei, E., Hernandez Gonzalez, H. A., Conroy, S., Lezan, E., Ahrnè, E., Thürkauf, N., van Vliet, S., Zamboni, N., Schmidt, A., & Jenal, U. (2025). Coenzyme A depletion causes antibiotic tolerance in Pseudomonas aeruginosa [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.10.24.684135

Pignon, Estelle, Holló, Gábor, Steiner, Théodora, van Vliet, Simon, & Schaerli, Yolanda. (2025). Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia [Journal-article]. The ISME Journal, 19(1). https://doi.org/10.1093/ismejo/wraf122

Ramesh, Divvya, Fara, Emanuele, Oschmann, Franziska, Ugolini, Giovanni Stefano, Stocker, Roman, van Vliet, Simon, Ackermann, Martin, & Schubert, Olga T. (2025). When less is not more: Limits to the evolution of metabolic dependence in spatially structured microbial communities [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.05.09.651753

López-Pagán, Nieves, Rufián, José S., Luneau, Julien, Sánchez-Romero, María-Antonia, Aussel, Laurent, van Vliet, Simon, Ruiz-Albert, Javier, & Beuzón, Carmen R. (2025). Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection [Journal-article]. Nature Microbiology, 10(4), 958–972. https://doi.org/10.1038/s41564-025-01966-0

Henderson, Alyssa, Del Panta, Alessia, Schubert, Olga T., Mitri, Sara, & van Vliet, Simon. (2025). Disentangling the feedback loops driving spatial patterning in microbial communities [Journal-article]. Npj Biofilms and Microbiomes, 11(1). https://doi.org/10.1038/s41522-025-00666-1

Kaczmarczyk, Andreas, van Vliet, Simon, Jakob, Roman Peter, Dias Teixeira, Raphael, Scheidat, Inga, Reinders, Alberto, Klotz, Alexander, Maier, Timm, & Jenal, Urs. (2024). A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-48295-0

Pignon, Estelle, Holló, Gábor, Steiner, Théodora, van Vliet, Simon, & Schaerli, Yolanda. (2024). Engineering microbial consortia: uptake and leakage rate differentially shape community arrangement and composition [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.07.19.604250

Alexander, Ashley M., Luu, Justin M., Raghuram, Vishnu, Bottacin, Giulia, van Vliet, Simon, Read, Timothy D., & Goldberg, Joanna B. (2024). Experimentally evolved Staphylococcus aureus shows increased survival in the presence of Pseudomonas aeruginosa by acquiring mutations in the amino acid transporter, GltT. Microbiology (United Kingdom), 170(3). https://doi.org/10.1099/mic.0.001445

Beuzon, C., Lopez-Pagan, N., Rufian, J., Luneau, J., Sanchez-Romero, M.-A., Aussel, L., Vliet, S. v., & Ruiz-Albert, J. (2024). Cooperative colonization of the host and pathogen dissemination involves stochastic and spatially structured expression of virulence traits [Posted-content]. Research Square Platform LLC. https://doi.org/10.21203/rs.3.rs-4131469/v1

Alexander, Ashley M., Luu, Justin M., Raghuram, Vishnu, Bottacin, Giulia, van Vliet, Simon, Read, Timothy D., & Goldberg, Joanna B. (2023). Experimentally Evolved Staphylococcus aureus Survives in the Presence of Pseudomonas aeruginosa by Acquiring Mutations in the Amino Acid Transporter, GltT [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.07.24.550428

Daniels, M., van Vliet, S., & Ackermann, M. (2023). Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community. ISME Journal, 17(3), 406–416. https://doi.org/10.1038/s41396-022-01312-w

van Vliet, S., & Ackermann, M. (2023). Alma Dal Co (1989-2022). Nature Ecology & Evolution, 7(3), 310–311. https://doi.org/10.1038/s41559-022-01978-7

Dal Co, A., Ackermann, M., & van Vliet, S. (2023). Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals. Cell Systems, 14(2), 98–108. https://doi.org/10.1016/j.cels.2022.12.009

Bettenworth, V., van Vliet, S., Turkowyd, B., Bamberger, A., Wendt, H., McIntosh, M., Steinchen, W., Endesfelder, U., & Becker, A. (2022). Frequency modulation of a bacterial quorum sensing response. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-30307-6

Daniels, Michael, van Vliet, Simon, & Ackermann, Martin. (2022). Changes in interactions over ecological time scales influence single cell growth dynamics in a metabolically coupled marine microbial community [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.02.08.479118

van Vliet, Simon, Hauert, Christoph, Fridberg, Kyle, Ackermann, Martin, & Dal Co, Alma. (2022). Global dynamics of microbial communities emerge from local interaction rules. PLoS Computational Biology, 18(3), e1009877. https://doi.org/10.1371/journal.pcbi.1009877

Moreno-Gámez, Stefany, Dal Co, Alma, van Vliet, Simon, & Ackermann, Martin. (2021). Microfluidics for Single-Cell Study of Antibiotic Tolerance and Persistence Induced by Nutrient Limitation. In Verstraeten, Natalie; Michiels, Jan (Ed.), Bacterial Persistence: Methods and Protocols (pp. 107–124). Springer US. https://doi.org/10.1007/978-1-0716-1621-5_8

Dal Co, A., van Vliet, S., Kiviet, D. J., Schlegel, S., & Ackermann, M. (2021). Author Correction: Short-range interactions govern the dynamics and functions of microbial communities (Nature Ecology & Evolution, (2020), 4, 3, (366-375), 10.1038/s41559-019-1080-2). Nature Ecology and Evolution, 5(5). https://doi.org/10.1038/s41559-021-01430-2

Henriques, Gil J. B., van Vliet, Simon, & Doebeli, Michael. (2021). Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities. PLoS Computational Biology, 17(9), e1008896. https://doi.org/10.1371/journal.pcbi.1008896

van Vliet, Simon, Hauert, Christoph, Ackermann, Martin, & Dal Co, Alma. (2020). Global dynamics of microbial communities emerge from local interaction rules [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.07.25.220822

Dal Co, Alma, van Vliet, Simon, Kiviet, Daniel Johannes, Schlegel, Susan, & Ackermann, Martin. (2020). Short-range interactions govern the dynamics and functions of microbial communities. Nature ecology & evolution, 4(3), 366–375. https://doi.org/10.1038/s41559-019-1080-2

van Vliet, Simon, & Doebeli, Michael. (2020). Reply to Daybog and Kolodny: Necessary requirements for holobiont-level selection are robust to model assumptions. Proceedings of the National Academy of Sciences of the United States of America, 117(22), 11864. https://doi.org/10.1073/pnas.2005559117

Dal Co, Alma, Ackermann, Martin, & van Vliet, Simon. (2019). Metabolic activity affects the response of single cells to a nutrient switch in structured populations. Journal of the Royal Society, Interface, 16(156), 20190182. https://doi.org/10.1098/rsif.2019.0182

Dal Co, Alma, van Vliet, Simon, & Ackermann, Martin. (2019). Emergent microscale gradients give rise to metabolic cross-feeding and antibiotic tolerance in clonal bacterial populations. Philosophical Transactions B: Biological Sciences, 374(1786), 20190080. https://doi.org/10.1098/rstb.2019.0080

van Vliet, Simon, & Doebeli, Michael. (2019). The role of multilevel selection in host microbiome evolution. Proceedings of the National Academy of Sciences of the United States of America, 116(41), 20591–20597. https://doi.org/10.1073/pnas.1909790116

Patsch, Deborah, van Vliet, Simon, Marcantini, Lorenzo Garbani, & Johnson, David R. (2018). Generality of associations between biological richness and the rates of metabolic processes across microbial communities. Environmental Microbiology, 20(12), 4356–4368. https://doi.org/10.1111/1462-2920.14352

van Vliet, Simon, Dal Co, Alma, Winkler, Annina R., Spriewald, Stefanie, Stecher, Bärbel, & Ackermann, Martin. (2018). Spatially Correlated Gene Expression in Bacterial Groups: The Role of Lineage History, Spatial Gradients, and Cell-Cell Interactions. Cell Systems, 6(4), 496–507. https://doi.org/10.1016/j.cels.2018.03.009

Vliet, S. v., Co, A. D., R. Winkler, A., Spriewald, S., Stecher, B., & Ackermann, M. (2017). Local interactions lead to spatially correlated gene expression levels in bacterial groups [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/109991

Bayramoglu, Bihter, Toubiana, David, van Vliet, Simon, Inglis, R. Fredrik, Shnerb, Nadav, & Gillor, Osnat. (2017). Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective. Scientific Reports, 7, 42068. https://doi.org/10.1038/srep42068

van Vliet, Simon, & Ackermann, Martin. (2017). Stochastic gene expression: bacterial elites in chemotaxis. Molecular Systems Biology, 13(1), 909. https://doi.org/10.15252/msb.20167458

van Vliet, Simon. (2015). Bacterial Dormancy: How to Decide When to Wake Up. Current Biology, 25(17), R753–5. https://doi.org/10.1016/j.cub.2015.07.039

van Vliet, Simon, & Ackermann, Martin. (2015). Bacterial Ventures into Multicellularity: Collectivism through Individuality. PLoS Biology, 13(6), e1002162. https://doi.org/10.1371/journal.pbio.1002162

van Vliet, Simon, Hol, Felix J. H., Weenink, Tim, Galajda, Peter, & Keymer, Juan E. (2014). The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations. BMC Microbiology, 14, 116. https://doi.org/10.1186/1471-2180-14-116

Barends, R., Van Vliet, S., Baselmans, J.J.A., Yates, S.J.C., Gao, J.R., & Klapwijk, T.M. (2009). Enhancement of quasiparticle recombination in Ta and Al superconductors by implantation of magnetic and nonmagnetic atoms. Physical Review B - Condensed Matter and Materials Physics, 79(2). https://doi.org/10.1103/physrevb.79.020509

Barends, R., Van Vliet, S., Baselmans, J.J.A., Yates, S.J.C., Gao, J.R., & Klapwijk, T.M. (2009). Quasiparticle relaxation in high Q superconducting resonators. Journal of Physics: Conference Series, 150. https://doi.org/10.1088/1742-6596/150/5/052016