• Garriga-Canut M, Cannon N, Benton M, Zanon A, Horsfield ST, Scheurich J, Remans K, Lees J, Paix A, van Gestel J. Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species. Mol Syst Biol. In press.

• Garriga-Canut M, Cannon N, Benton M, Zanon A, Horsfield ST, Scheurich J, Remans K, Lees J, Paix A, van Gestel J. 2025. Selection-free CRISPR-Cas9 editing protocol for distant Dictyostelid species. bioRxiv. 10.1101/2025.03.23.644600

• Koo BM, Todor H, Sun J, van Gestel J, Hawkins JS, Hearne CC, Banta AB, Huang KC, Peters JM, Gross CA. 2025.
  Comprehensive genetic interaction analysis of the Bacillus subtilis envelope using double-CRISPRi. Cell Syst. 16(11):101406.

• van Gestel J, Koo BM, Stürmer VS, Garriga-Canut M, Wagner J, Zanon A, Gross CA. 2025. Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation. Proc Natl Acad Sci U S A. 122(39):e2518989122.

• Sanchis Pla L, van Gestel J. 2024. Exploring the microbial savanna: predator-prey interactions in the soil. Molecular Systems Biology. 20(5): 477-480.

Soils host complex multi-trophic communities with diverse, mostly microbial, predator and prey species, including numerous bacterivorous protists and bacterial prey. The molecular mechanisms underlying microbial predator-prey interactions have thus far mainly been explored using reductionist methods, outside the soil environment and independent from the broader life history strategies that microbes display in soils. In this Comment, we advocate for an integrative research approach, combining molecular systems biology and microbial ecology, to investigate how predator-prey interactions shape microbial life history strategies and thereby population dynamics in natural soil communities.

• van Gestel J, Wagner A & Ackermann M. 2023. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol, 21:e3002338

• Gerhardt LMS, Koppitch K, van Gestel J, Guo J, Cho S, Wu H, Kirita Y, Humphreys BD, McMahon AP. 2023. Lineage tracing and single-nucleus multiomics reveal novel features of adaptive and maladaptive repair after acute kidney injury. JASN, 10.1681.

• Hölscher, T, van Gestel J, Kovács AT. 2022. Complex extracellular biology drives surface competition in Bacillus subtilis. ISME J, 16(10):2320-2328

• Staps M, van Gestel J, Tarnita CE. 2021 Life cycles as a central organizing theme for studying multicellularity. Book chapter in “The evolution of multicellularity” of CRC Press.

• van Gestel J, Wagner A. 2021. Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation. PLoS Biol, 19:e3001250

• van Gestel J, Hawkins JS, Todor H, Gross CA. 2021. Computational pipeline for designing guide RNAs for mismatch-CRISPRi. STAR protocols, 2: 100521

• van Gestel J, Bareia T, Tenennbaum B, Dal Co A, Guler P, Aframian N, Puyesky S, Grinberg I, D'Souza GG, Erez Z, Ackermann M, Eldar A. 2021. Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities. Nature Commun, 12: 2324

• Hernandez-Valdes JA, van Gestel J, Kuipers OP. 2020. A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium. Nature Commun, 11(1):1203

• van Gestel J. 2020 Slow lane to collectivity. Nature Ecology & Evolution, 4: 292-293

• van Gestel J, Ackermann M, Wagner A. 2019. Microbial life cycles link global modularity in regulation to mosaic evolution. Nature Ecology & Evolution, 3: 1184–1196

• Staps M, van Gestel J, Tarnita CE. 2019. Emergence of diverse life cycles and life histories at the origin of multicellularity. Nature Ecology & Evolution, 3: 1197–1205.

• van Gestel J, Kolter R 2019. When we stop thinking about microbes as cells. Journal of molecular biology, 431:2487-2492

• Ramos Y, Rocha J, Hael AL, van Gestel J, Vlamakis H, Cywes-Bentley C, Cubillos-Ruiz JR, Pier GB, Gilmore MS, Kolter R, Morales DK. 2019 PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis. PLoS Pathog, 15:e1007571

• van Gestel J, Weissing FJ. 2018. Is plasticity caused by single genes? Nature, 555: E19-E20

• van Gestel J, Tarnita CE. 2017. On the origin of biological construction, with a focus on multicellularity. PNAS 114: 11018–11026

• van Gestel J, Nowak MA. 2016. Phenotypic heterogeneity and the evolution of bacterial life cycles. PLoS Comput Biol 12: e1004764

• van Gestel J, Weissing FJ. 2016. Regulatory mechanisms link phenotypic plasticity to evolvability. Scientific reports, 6: 24524

• van Gestel J, Vlamakis H, Kolter R. 2015 From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate. PLoS Biol 13: e1002141

• van Gestel J, Vlamakis H, Kolter R. 2015. New tools for comparing microscopy images: a quantitative analysis of cell types in Bacillus subtilis. Journal of Bacteriology 197: 699-709

• van Gestel J, Vlamakis HC, Kolter R. 2015. Division of labor in biofilms: the ecology of cell differentiation. Microbiology Spectrum 3: MB-0002-2014. Book chapter in ‘Microbial Biofilms’ (2nd ed.), eds. Ghannoum M., Parsek M., Whiteley M., Mukherjee P.K., ASM Press, Washington DC, USA

• Solopova A, van Gestel J, Weissing FJ, Bachmann H, Teusink B, Kok J, Kuipers OP. 2014. Bet-hedging during bacterial diauxic shift. PNAS, 111: 7427-7432

• van Gestel J, Weissing FJ, Kuipers OP, Kovács AT. 2014. Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms. ISME J 8: 2069-2079

• van Gestel J, Nowak MA, Tarnita CE. 2012. The evolution of cell-to-cell communication in a sporulating bacterium. PLoS Comput Biol 8: e1002818

• Kovács AT, van Gestel J, Kuipers OP. 2012. The protective layer of biofilm: a repellent function for a new class of amphiphilic proteins. Molecular Microbiology 85: 8-11.

• Schroeder J, Roodbergen M, van Gestel J, van den Brink V, Groen NM, Gerritsen GJ 2010 Associations in male plumage ornamentation and reproductive parameters in the Icelandic Black-tailed Godwit Limosa limosa islandica. Wader Study Group Bull. 117: 85-90