Microbiology and Biophysics (Drescher)

Pignon, Estelle et al. (2024) ‘Engineering microbial consortia: uptake and leakage rate differentially shape community arrangement and composition’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.07.19.604250.

Ohmura, Takuya et al. (2024) ‘In vivo Microrheology Reveals Local Elastic and Plastic Responses Inside Three‐dimensional Bacterial Biofilms’, Advanced Materials [Preprint]. Available at: https://doi.org/10.1002/adma.202314059.

Alexander, Ashley M. et al. (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). Available at: https://doi.org/10.1099/mic.0.001445.

Beuzon, C. et al. (2024) ‘Cooperative colonization of the host and pathogen dissemination involves stochastic and spatially structured expression of virulence traits’. Research Square Platform LLC. Available at: https://doi.org/10.21203/rs.3.rs-4131469/v1.

Moscovitz, Sofia Zoe et al. (2023) ‘Evolution of genotypic and phenotypic diversity in multispecies biofilms’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2023.10.08.561388.

Alexander, Ashley M. et al. (2023) ‘Experimentally Evolved Staphylococcus aureus Survives in the Presence of Pseudomonas aeruginosa by Acquiring Mutations in the Amino Acid Transporter, GltT’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2023.07.24.550428.

Lubrano, Paul et al. (2023) ‘Purine nucleotide limitation undermines antibiotic action in clinical Escherichia coli’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2023.06.22.546106.

Daniels, M., van Vliet, S. and 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), pp. 406–416. Available at: https://doi.org/10.1038/s41396-022-01312-w.

van Vliet, S. and Ackermann, M. (2023) ‘Alma Dal Co (1989-2022)’, Nature ecology & evolution, 7(3), pp. 310–311. Available at: https://doi.org/10.1038/s41559-022-01978-7.

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

Hallatschek, Oskar et al. (2023) ‘Proliferating active matter’, Nature Reviews Physics, pp. 1–13. Available at: https://doi.org/10.1038/s42254-023-00593-0.

Jeckel, H. et al. (2023) ‘Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations’, Nature Microbiology [Preprint]. Available at: https://doi.org/10.1038/s41564-023-01518-4.

Jelli, Eric et al. (2023) ‘Single-cell segmentation in bacterial biofilms with an optimized deep learning method enables tracking of cell lineages and measurements of growth rates’, Molecular Microbiology, 119(6), pp. 659–676. Available at: https://doi.org/10.1111/mmi.15064.

Manner, Christina et al. (2023) ‘A genetic switch controls Pseudomonas aeruginosa surface colonization’, Nature Microbiology, 8(8), pp. 1520–1533. Available at: https://doi.org/10.1038/s41564-023-01403-0.

Skinner, Dominic J. et al. (2023) ‘Topological packing statistics of living and nonliving matter’, Science Advances, 9(36), p. eadg1261. Available at: https://doi.org/10.1126/sciadv.adg1261.

Vidakovic, Lucia et al. (2023) ‘Biofilm formation on human immune cells is a multicellular predation strategy of Vibrio cholerae’, Cell, 186(12), pp. 2690–2704.e20. Available at: https://doi.org/10.1016/j.cell.2023.05.008.

Bettenworth, V. et al. (2022) ‘Frequency modulation of a bacterial quorum sensing response’, Nature Communications, 13(1). Available at: https://doi.org/10.1038/s41467-022-30307-6.

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

Jeckel, Hannah et al. (2022) ‘Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species’, PLoS Biology, 20(10), p. e3001846. Available at: https://doi.org/10.1371/journal.pbio.3001846.

Ren, Zhi et al. (2022) ‘Interkingdom assemblages in human saliva display group-level surface mobility and disease-promoting emergent functions’, Proceedings of the National Academy of Sciences of the United States of America, 119(41), p. e2209699119. Available at: https://doi.org/10.1073/pnas.2209699119.

Skinner, D.J. et al. (2022) ‘Topological packing statistics distinguish living and non-living matter’, arXiv [Preprint]. Available at: https://doi.org/10.48550/arXiv.2209.00703.

Teschler, Jennifer K. et al. (2022) ‘VxrB Influences Antagonism within Biofilms by Controlling Competition through Extracellular Matrix Production and Type 6 Secretion’, mBio, 13(4), p. e0188522. Available at: https://doi.org/10.1128/mbio.01885-22.

Teschler, Jennifer K. et al. (2022) ‘Mechanisms underlying Vibrio cholerae biofilm formation and dispersion’, Annual Reviews of Microbiology, 76, pp. 503–532. Available at: https://doi.org/10.1146/annurev-micro-111021-053553.

Goes, A. et al. (2021) ‘Interaction of myxobacteria-derived outer membrane vesicles with biofilms: Antiadhesive and antibacterial effects’, Nanoscale, 13(34), pp. 14287–14296. Available at: https://doi.org/10.1039/d1nr02583j.

Jeckel, Hannah et al. (2021) ‘Multispecies phase diagram of biofilm architectures reveals biophysical principles of biofilm development’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2021.08.06.455416.

Dal Co, A. et al. (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). Available at: https://doi.org/10.1038/s41559-021-01430-2.

Hartmann, R. et al. (2021) ‘Publisher Correction: Quantitative image analysis of microbial communities with BiofilmQ (Nature Microbiology, (2021), 6, 2, (151-156), 10.1038/s41564-020-00817-4)’, Nature Microbiology, 6(2). Available at: https://doi.org/10.1038/s41564-021-00863-6.

Bond, Matthew C. et al. (2021) ‘Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells’, eLife, 10, p. e65355. Available at: https://doi.org/10.7554/elife.65355.

Di­az-Pascual, Francisco et al. (2021) ‘Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies’, eLife, 10, p. e70794. Available at: https://doi.org/10.7554/elife.70794.

Hartmann, Raimo et al. (2021) ‘Quantitative image analysis of microbial communities with BiofilmQ’, Nature Microbiology, 6(2), pp. 151–156. Available at: https://doi.org/10.1038/s41564-020-00817-4.

Jeckel, Hannah and Drescher, Knut (2021) ‘Advances and opportunities in image analysis of bacterial cells and communities’, FEMS Microbiology Reviews, 45(4), p. fuaa062. Available at: https://doi.org/10.1093/femsre/fuaa062.

Maestre-Reyna, Manuel et al. (2021) ‘Vibrio cholerae biofilm scaffolding protein RbmA shows an intrinsic, phosphate-dependent autoproteolysis activity’, IUBMB Life, 73(2), pp. 418–431. Available at: https://doi.org/10.1002/iub.2439.

Singh, Praveen K. et al. (2021) ‘Vibrio cholerae biofilm dispersal regulator causes cell release from matrix through type IV pilus retraction’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2021.05.02.442311.

Skinner, Dominic J. et al. (2021) ‘Topological Metric Detects Hidden Order in Disordered Media’, Physical Review Letters, 126(4), p. 048101. Available at: https://doi.org/10.1103/physrevlett.126.048101.

Wimmi, Stephan et al. (2021) ‘Dynamic relocalization of cytosolic type III secretion system components prevents premature protein secretion at low external pH’, Nature communications, 12(1), p. 1625. Available at: https://doi.org/10.1038/s41467-021-21863-4.

Wong, Gerard C. L. et al. (2021) ‘Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation’, Physical biology, 18(5), p. 051501. Available at: https://doi.org/10.1088/1478-3975/abdc0e.

Yordanov, Stoyan et al. (2021) ‘Single-objective high-resolution confocal light sheet fluorescence microscopy for standard biological sample geometries’, Biomedical Optics Express, 12(6), pp. 3372–3391. Available at: https://doi.org/10.1364/boe.420788.

van Vliet, Simon et al. (2020) ‘Global dynamics of microbial communities emerge from local interaction rules’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2020.07.25.220822.

Brückner, Stefan et al. (2020) ‘Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family’, eLife, 9, p. e55587. Available at: https://doi.org/10.7554/elife.55587.

Gallego-Hernandez, A. L. et al. (2020) ‘Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity’, Proceedings of the National Academy of Sciences of the United States of America, 117(20), pp. 11010–11017. Available at: https://doi.org/10.1073/pnas.1916571117.

Hartmann, Raimo et al. (2020) ‘BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology’, Molecular Microbiology, 114(1), pp. 140–150. Available at: https://doi.org/10.1111/mmi.14501.

Ishikawa, Takuji et al. (2020) ‘Stability of dancing Volvox’, Journal of Fluid Mechanics, 903, p. A11. Available at: https://doi.org/10.1017/jfm.2020.613.

Otto, Simon B. et al. (2020) ‘Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms’, mSystems, 5(4), pp. e00425–20. Available at: https://doi.org/10.1128/msystems.00425-20.

Peschek, Nikolai et al. (2020) ‘RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae’, Nature Communications, 11(1), p. 6067. Available at: https://doi.org/10.1038/s41467-020-19890-8.

Rode, Daniel K. H., Singh, Praveen K. and Drescher, Knut (2020) ‘Multicellular and unicellular responses of microbial biofilms to stress’, Biological Chemistry, 401(12), pp. 1365–1374. Available at: https://doi.org/10.1515/hsz-2020-0213.

Schwechheimer, Carmen et al. (2020) ‘A tyrosine phosphoregulatory system controls exopolysaccharide biosynthesis and biofilm formation in Vibrio cholerae’, PLoS Pathogens, 16(8), p. e1008745. Available at: https://doi.org/10.1371/journal.ppat.1008745.

Simmons, Emilia L. et al. (2020) ‘Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria’, mSystems, 5(3), pp. e00877–19. Available at: https://doi.org/10.1128/msystems.00877-19.

Colin, Remy, Drescher, Knut and Sourjik, Victor (2019) ‘Chemotactic behaviour of Escherichia coli at high cell density’, Nature Communications, 10(1), p. 5329. Available at: https://doi.org/10.1038/s41467-019-13179-1.

Díaz-Pascual, Francisco et al. (2019) ‘Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function’, Nature Microbiology, 4(12), pp. 2136–2145. Available at: https://doi.org/10.1038/s41564-019-0579-2.

Drescher, Knut (2019) ‘Bakterielle Multizellularität in Biofilmen’, BIOspektrum, 25(3), pp. 258–260. Available at: https://doi.org/10.1007/s12268-019-1038-6.

Hartmann, Raimo et al. (2019) ‘Emergence of three-dimensional order and structure in growing biofilms’, Nature Physics, 15(3), pp. 251–256. Available at: https://doi.org/10.1038/s41567-018-0356-9.

Jeckel, Hannah et al. (2019) ‘Learning the space-time phase diagram of bacterial swarm expansion’, Proceedings of the National Academy of Sciences of the United States of America, 116(5), pp. 1489–1494. Available at: https://doi.org/10.1073/pnas.1811722116.

Jeckel, Hannah, Matthey, Noémie and Drescher, Knut (2019) ‘Common concepts for bacterial collectives’, eLife, 8, p. e47019. Available at: https://doi.org/10.7554/elife.47019.

Nisbett, Lisa-Marie et al. (2019) ‘NosP Signaling Modulates the NO/H-NOX-Mediated Multicomponent c-Di-GMP Network and Biofilm Formation in Shewanella oneidensis’, Biochemistry, 58(48), pp. 4827–4841. Available at: https://doi.org/10.1021/acs.biochem.9b00706.

Pearce, Philip et al. (2019) ‘Flow-Induced Symmetry Breaking in Growing Bacterial Biofilms’, Physical Review Letters, 123(25), p. 258101. Available at: https://doi.org/10.1103/physrevlett.123.258101.

Beuter, Dominik et al. (2018) ‘Selective Enrichment of Slow-Growing Bacteria in a Metabolism-Wide CRISPRi Library with a TIMER Protein’, ACS Synthetic Biology, 7(12), pp. 2775–2782. Available at: https://doi.org/10.1021/acssynbio.8b00379.

Dragoš, Anna et al. (2018) ‘Division of Labor during Biofilm Matrix Production’, Current Biology, 28(12), pp. 1903–1913.e5. Available at: https://doi.org/10.1016/j.cub.2018.04.046.

Martínez-García, Ricardo et al. (2018) ‘Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms’, PLoS Computational Biology, 14(4), p. e1006094. Available at: https://doi.org/10.1371/journal.pcbi.1006094.

Simmons, Matthew et al. (2018) ‘Phage mobility is a core determinant of phage-bacteria coexistence in biofilms’, ISME Journal, 12(2), pp. 531–543. Available at: https://doi.org/10.1038/ismej.2017.190.

Vidakovic, Lucia et al. (2018) ‘Dynamic biofilm architecture confers individual and collective mechanisms of viral protection’, Nature Microbiology, 3(1), pp. 26–31. Available at: https://doi.org/10.1038/s41564-017-0050-1.

Fong, Jiunn C. N. et al. (2017) ‘Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms’, eLife, 6, p. e26163. Available at: https://doi.org/10.7554/elife.26163.

Nadell, Carey D. et al. (2017) ‘Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms’, eLife, 6, p. e21855. Available at: https://doi.org/10.7554/elife.21855.

Singh, Praveen K. et al. (2017) ‘Vibrio cholerae Combines Individual and Collective Sensing to Trigger Biofilm Dispersal’, Current Biology, 27(21), pp. 3359–3366.e7. Available at: https://doi.org/10.1016/j.cub.2017.09.041.

Besharova, Olga et al. (2016) ‘Diversification of Gene Expression during Formation of Static Submerged Biofilms by Escherichia coli’, Frontiers in Microbiology, 7, p. 1568. Available at: https://doi.org/10.3389/fmicb.2016.01568.

Drescher, Knut et al. (2016) ‘Architectural transitions in Vibrio cholerae biofilms at single-cell resolution’, Proceedings of the National Academy of Sciences of the United States of America, 113(14), pp. E2066–72. Available at: https://doi.org/10.1073/pnas.1601702113.

Nadell, Carey D., Drescher, Knut and Foster, Kevin R. (2016) ‘Spatial structure, cooperation and competition in biofilms’, Nature Reviews Microbiology, 14(9), pp. 589–600. Available at: https://doi.org/10.1038/nrmicro.2016.84.

Nadell, Carey D., Hartmann, Raimo and Drescher, Knut (2016) ‘An Emerging Grip on the Growth of Grounded Bacteria’, ACS Nano, 10(10), pp. 9109–9110. Available at: https://doi.org/10.1021/acsnano.6b06461.

Nadell, Carey D. et al. (2015) ‘Extracellular matrix structure governs invasion resistance in bacterial biofilms’, ISME Journal, 9(8), pp. 1700–9. Available at: https://doi.org/10.1038/ismej.2014.246.

Persat, Alexandre et al. (2015) ‘The mechanical world of bacteria’, Cell, 161(5), pp. 988–997. Available at: https://doi.org/10.1016/j.cell.2015.05.005.

Drescher, Knut et al. (2014) ‘Solutions to the public goods dilemma in bacterial biofilms’, Current Biology, 24(1), pp. 50–55. Available at: https://doi.org/10.1016/j.cub.2013.10.030.

Kim, Minyoung Kevin et al. (2014) ‘Filaments in curved streamlines: Rapid formation of; Staphylococcus aureus; biofilm streamers’, New Journal of Physics, 16(6), p. 065024. Available at: https://doi.org/10.1088/1367-2630/16/6/065024.

Drescher, Knut et al. (2013) ‘Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems’, Proceedings of the National Academy of Sciences of the United States of America, 110(11), pp. 4345–50. Available at: https://doi.org/10.1073/pnas.1300321110.

Dunkel, Jörn et al. (2013) ‘Fluid dynamics of bacterial turbulence’, Physical Review Letters, 110(22), p. 228102. Available at: https://doi.org/10.1103/physrevlett.110.228102.

Nadell, Carey D. et al. (2013) ‘Cutting through the complexity of cell collectives’, Proceedings of the Royal Society B: Biological Sciences, 280(1755), p. 20122770. Available at: https://doi.org/10.1098/rspb.2012.2770.

O’Loughlin, Colleen T. et al. (2013) ‘A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation’, Proceedings of the National Academy of Sciences of the United States of America, 110(44), pp. 17981–17986. Available at: https://doi.org/10.1073/pnas.1316981110.

Sareh, Sina et al. (2013) ‘Swimming like algae: biomimetic soft artificial cilia’, Journal of the Royal Society, Interface, 10(78), p. 20120666. Available at: https://doi.org/10.1098/rsif.2012.0666.

Wensink, Henricus H. et al. (2012) ‘Meso-scale turbulence in living fluids’, Proceedings of the National Academy of Sciences of the United States of America, 109(36), pp. 14308–13. Available at: https://doi.org/10.1073/pnas.1202032109.

Drescher, Knut et al. (2011) ‘Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering’, Proceedings of the National Academy of Sciences of the United States of America, 108(27), pp. 10940–5. Available at: https://doi.org/10.1073/pnas.1019079108.

Solari, Cristian A. et al. (2011) ‘Flagellar phenotypic plasticity in volvocalean algae correlates with Péclet number’, Journal of the Royal Society, Interface, 8(63), pp. 1409–17. Available at: https://doi.org/10.1098/rsif.2011.0023.

Solari, Cristian A., Drescher, Knut and Goldstein, Raymond E. (2011) ‘The flagellar photoresponse in Volvox species’, Journal of Phycology, 47(3), pp. 580–583. Available at: https://doi.org/10.1111/j.1529-8817.2011.00983.x.

Drescher, Knut et al. (2010) ‘Direct measurement of the flow field around swimming microorganisms’, Physical Review Letters, 105(16), p. 168101. Available at: https://doi.org/10.1103/physrevlett.105.168101.

Drescher, Knut, Goldstein, Raymond E. and Tuval, Idan (2010) ‘Fidelity of adaptive phototaxis’, Proceedings of the National Academy of Sciences of the United States of America, 107(25), pp. 11171–11176. Available at: https://doi.org/10.1073/pnas.1000901107.

Bulte, Daniel P., Drescher, Knut and Jezzard, Peter (2009) ‘Comparison of hypercapnia-based calibration techniques for measurement of cerebral oxygen metabolism with MRI’, Magnetic Resonance in Medicine, 61(2), pp. 391–8. Available at: https://doi.org/10.1002/mrm.21862.

Drescher, Knut, Leptos, Kyriacos C. and Goldstein, Raymond E. (2009) ‘How to track protists in three dimensions’, Review of Scientific Instruments, 80(1), p. 014301. Available at: https://doi.org/10.1063/1.3053242.

Drescher, Knut et al. (2009) ‘Dancing volvox: hydrodynamic bound states of swimming algae’, Physical Review Letters, 102(16), p. 168101. Available at: https://doi.org/10.1103/physrevlett.102.168101.

Polin, Marco et al. (2009) ‘Chlamydomonas swims with two ‘gears’ in a eukaryotic version of run-and-tumble locomotion’, Science, 325(5939), pp. 487–90. Available at: https://doi.org/10.1126/science.1172667.