PUBLICATIONS

Research
Publications
People
Engagement
Join us

Read our publications here. If you can’t access an article, email me for a PDF.

Google scholar profile

  1. Bakkeren E, Piskovsky V, Lee MNY, Jahn MT, Foster KR. Strain displacement in microbiomes via ecological competition. 2025 Nat. Microbiol.
  2. Newson JPM, McHugh SC, Steiger Y, Gürtler F, Bakkeren E, Hardt WD. Antibiotic-recalcitrant Salmonella exploits post-antibiotic microbiota disruption to achieve virulence-dependent transmission. 2025. Cell Rep.
  3. Bakkeren E, Piskovsky V, Foster KR. Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering. 2025. Cell Host Microbe.
  4. Santamaria de Souza N, Cherrak Y, Andersen TB, Vetsch M, Barthel M, Kroon S, Bakkeren E, Schubert C, Christen P, Kiefer P, Vorholt JA, Nguyen BD, Hardt WD. Context-dependent change in the fitness effect of (in)organic phosphate antiporter glpT during Salmonella Typhimurium infection. 2025. Nat. Commun.
  5. Wenger A, Bakkeren E, Granato E, Tecon R, Mitri S, Möbius W. MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability. 2025. FEMS Microbiol. Lett.
  6. Hu G, Qu X, Bhalla K, Xue P, Bakkeren E, Lee CW, Kronstad JW. Loss of the putative Rab GTPase, Ypt7, impairs the virulence of Cryptococcus neoformans. 2024. Front. Microbiol.
  7. Gül E, Huuskonen J, Younes AA, Maurer L, Enz U, Zimmermann J, Sellin ME, Bakkeren E, Hardt WD. Salmonella T3SS-2 virulence enhances gut-luminal colonization by enabling chemotaxis-dependent exploitation of intestinal inflammation. 2024. Cell Rep.
  8. Spragge F*, Bakkeren E*, Jahn MT, Araujo EBN, Pearson CF, Wang X, Pankhurst L, Cunrath O, Foster KR. Microbiome diversity protects against pathogens by nutrient blocking. 2023. Science.
  9. Gül E, Bakkeren E, Salazar G, Steiger Y, Younes AA, Clerc M, Christen P, Fattinger SA, Nguyen BD, Kiefer P, Slack E, Ackermann M, Vorholt JA, Sunagawa S, Diard M, Hardt WD. The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence. 2023. PLoS Biol.
  10. Gül E, Younes AA, Huuskonen J, Diawara C, Nguyen BD, Maurer L, Bakkeren E, Hardt WD. Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut. 2023. Cell Host Microbe.
  11. Bakkeren E, Gül E, Huisman JS, Steiger Y, Rocker A, Hardt WD, Diard M. Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium. 2022. Nat. Commun.
  12. Gaissmaier MS, Laganenka L, Herzog MK, Bakkeren E, Hardt WD. The mobilizable plasmid P3 of Salmonella enterica serovar Typhimurium SL1344 depends on the P2 plasmid for conjugative transfer into a broad range of bacteria in vitro and in vivo. 2022. J. Bacteriol.
  13. Bakkeren E, Herter JA, Huisman JS, Steiger Y, Gül E, Newson JPM, Brachmann AO, Piel J, Regoes RR, Bonhoeffer S, Diard M, Hardt WD. Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut. 2021. eLife.
  14. Hu G*, Bakkeren E*, Caza M, Horianopoulos L, Sanchez-Leon E, Sorensen M, Jung W, Kronstad JW. Vam6/Vps39/TRAP1‐domain proteins influence vacuolar morphology, iron acquisition and virulence in Cryptococcus neoformans. 2021. Cell. Microbiol.
  15. Bakkeren E*, Newson JPM*, Hardt WD. Analysis of Salmonella Persister Population Sizes, Dynamics of Gut Luminal Seeding, and Plasmid Transfer Plasmid transfer in Mouse Models Mouse models of Salmonellosis. 2021. Book chapter in Bacterial Persistence: Methods and Protocols.
  16. Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Boehi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wuethrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. 2021. Nat. Microbiol.
  17. Fattinger S, Geiser P, Ventayol PS, Di Martino ML, Furter M, Felmy B, Bakkeren E, Hausmann A, Barthel-Scherrer M, Gul E, Hardt WD, Sellin M. Epithelium-autonomous NAIP/NLRC4 prevents TNF-driven inflammatory destruction of the gut epithelial barrier in Salmonella-infected mice. 2021. Mucosal Immunol.
  18. Bakkeren E, Diard M, Hardt WD. Evolutionary causes and consequences of bacterial antibiotic persistence. 2020. Nat. Rev. Microbiol.
  19. Benz F*, Huisman JS*, Bakkeren E*, Herter JA, Stadler T, Ackermann M, Diard M, Egli A, Hall AR, Hardt WD, Bonhoeffer S. Plasmid-and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo. 2020. ISME J.
  20. Hausmann A, Böck D, Geiser P, Berthold DL, Fattinger SA, Furter M, Bouman JA, Barthel-Scherrer M, Lang CM, Bakkeren E, Kolinko I, Diard M, Bumann D, Slack E, Regoes RR, Pilhofer M, Sellin ME, Hardt WD. Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression. 2020. Mucosal Immunol.
  21. Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M, Egli A, Slack E, Sellin ME, Bonhoeffer S, Regoes RR, Diard M, Hardt WD. Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut. 2019. Nature.
  22. Wotzka SY, Kreuzer M, Maier L, Arnoldini M, Nguyen BD, Brachmann AO, Berthold DL, Zünd M, Hausmann A, Bakkeren E, Hoces D, Gül E, Beutler M, Dolowschiak T, Zimmermann M, Fuhrer T, Moor K, Sauer U, Typas A, Piel J, Diard M, Macpherson AJ, Stecher B, Sunagawa S, Slack E, Hardt WD. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. 2019. Nat. Microbiol.
  23. Bakkeren E, Dolowschiak T, Diard MRJ. Detection of mutations affecting heterogeneously expressed phenotypes by colony immunoblot and dedicated semi-automated image analysis pipeline. 2017. Front. Microbiol.
  24. Moor K, Diard M, Sellin M, Felmy B, Wotzka S, Toska A, Bakkeren E, Arnoldini M, Bansept F, Dal Co A, Völler T, Minola A, Fernandez-Rodriguez B, Agatic G, Barbieri S, Piccoli L, Casiraghi C, Corti D, Lanzavecchia A, Regoes RR, Loverdo C, Stocker R, Brumley DR, Hardt WD, Slack E. High-avidity IgA protects the intestine by enchaining growing bacteria. 2017. Nature.
  25. Diard M, Bakkeren E, Cornuault JK, Moor K, Hausmann A, Sellin ME, Loverdo C, Aertsen A, Ackermann M, De Paepe M, Slack E, Hardt WD. Inflammation boosts bacteriophage transfer between Salmonella spp. 2017. Science.
  26. Hu G, Caza M, Bakkeren E, Kretschmer M, Bairwa G, Reiner E, Kronstad J. A P4‐ATPase subunit of the Cdc50 family plays a role in iron acquisition and virulence in Cryptococcus neoformans. 2017. Cell. Microbiol.
  27. Hu G, Caza M, Cadieux B, Bakkeren E, Do E, Jung WH, Kronstad JW. The endosomal sorting complex required for transport machinery influences haem uptake and capsule elaboration in Cryptococcus neoformans. 2015. Mol. Microbiol.

* = co-first authors