Research Output

Latest Publications

Selected publications from the Microbiology theme research groups, showcasing our contributions to microbiology, systems biology, and related fields.

Recent Publications

• A mathematical kinetic model of memory in Bacillus subtilis spore germination. iScience.
  de Koster CG, Lin X, Li YQ, Brul S, de Koning LJ, Setlow P.
  iScience (2026) · Microbial Stress & Food Safety Group · Link
• Environmentally mediated interactions predict community assembly and invasion success in a gut microbiota synthetic community.
  van Leeuwen PT, Gadaleta P, Brul S, Seppen J, Wortel MT.
  mSystems (2026) · Microbial Stress & Food Safety Group · Link
• Relationship between fecal short-chain fatty acids (SCFAs) and microbial SCFA pathways with depressive symptoms in Dutch adults
  Vera Korenblik, Thomaz F. S. Bastiaanssen, Irina M. de Haas, Henrike Galenkamp, Max Nieuwdorp, Claudi L. H. Bockting, Aniko Korosi, Stanley Brul & Anja Lok
  Translational Psychiatry (2026) · Microbial Stress & Food Safety Group · Link
• Genetic adaptation to amoxicillin in Escherichia coli
  Teichmann L, Wenne M, Luitwieler S, Dugar G, et al.
  PLOS One (2025) · DNA & RNA Interaction Lab
• Ribosome pausing in amylase-producing Bacillus subtilis during long fermentation
  Han Y, Wang B, Agnolin A, Dugar G, Hamoen LW
  Microbial Cell Factories (2025) · DNA & RNA Interaction Lab
• Gut microbiota-mediated conversion of mangiferin to norathyriol alters short chain fatty acid and urate metabolism
  Bunt, D., Swalbe, M., Hayeeawaema, F., El Aidy, S.
  Gut Microbes (2025) · Microbiome Engineering Lab · Link
• Hydrogel-based experimental models of the gastrointestinal tract
  Sieders, M., Jones, L., Candry, P., El Aidy, S.
  Microbiome (2025) · Microbiome Engineering Lab · Link
• Enteroendocrine cells: The gatekeepers of microbiome-gut-brain communication
  Grundeken, E., El Aidy, S.
  npj Biofilms and Microbiomes (2025) · Microbiome Engineering Lab · Link
• Increasing enzyme production via LonA inactivation in Bacillus subtilis
  Wang B, Kes MBMJ, van den Berg van Saparoea ACH, Dugar G, Hamoen LW
  Microbial Cell Factories (2024) · DNA & RNA Interaction Lab
• Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community
  Jansma, J., Chatziioannou, A. C., Castricum, K., van Hemert, S., & El Aidy, S.
  mSystems (2023) · Microbiome Engineering Lab · Link
• A chromosomal loop anchor mediating bacterial genome organisation
  Dugar G, Hofmann A, Heermann DW, Hamoen LW
  Nature Genetics (2022) · DNA & RNA Interaction Lab · Link
• Gut microbiota transplantation drives the adoptive transfer of colonic genotype-phenotype characteristics between mice lacking catestatin and their wild type counterparts
  González-Dávila, P., Schwalbe, M., Danewalia, A., Wardenaar, R., Dalile, B., Verbeke, K., Mahata, S. K., & El Aidy, S.
  Gut Microbes (2022) · Microbiome Engineering Lab · Link
• Noncanonical crRNAs enabling multiplexable RNA detection by Cas9
  Jiao C, Sharma S, Dugar G, et al.
  Science (2021) · DNA & RNA Interaction Lab
• Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels
  Waclawiková, B., Bullock, A., Schwalbe, M., Aranzamendi, C., Nelemans, S. A., van Dijk, G., & El Aidy, S.
  PLoS Biology (2021) · Microbiome Engineering Lab · Link
• Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson's disease
  van Kessel, S. P., Frye, A. K., El-Gendy, A. O., Castejon, M., Keshavarzian, A., van Dijk, G., & El Aidy, S.
  Nature Communications (2019) · Microbiome Engineering Lab · Link