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
• 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