Department Environmental Microbiology

NCCR Microbiomes


Life as we know it is intimately tied to microorganisms. Often, these microorganisms live in communities called microbiomes. Microbiomes behave as more than the sum of their parts, displaying functions and roles not easily predicted. Importantly, they are a major force shaping human health, biogeochemical cycles, agricultural productivity, and nutrition, touching nearly every aspect of everyday life.

In collaboration with research groups across Switzerland, our Microbial Systems Ecology group is combining computational, experimental, and clinical approaches to develop a clearer view of microbiomes. By understanding how microbiomes develop and function we can harness these discoveries for the improvement of human and environmental health.

Our major contribution to this consortium is to measure and mathematically model physiologically relevant chemical and spatial interactions between microbial species. The hope is to put these interactions into context to address two main goals: how microbial ecosystems influence infectious disease and how interactions between microbes can enhance food production.

Reference: Microbiota-derived metabolites inhibit Salmonella virulent subpopulation development by acting on single-cell behaviors


Bakkeren, E.; Diard, M.; Lentsch, V.; Rocker, A.; Bekele, N. A.; Hoces, D.; Aslani, S.; Arnoldini, M.; Böhi, F.; Schumann-Moor, K.; Adamcik, J.; Piccoli, L.; Lanzavecchia, A.; Stadtmueller, B. M.; Donohue, N.; van der Woude, M. W.; Hockenberry, A.; Viollier, P. H.; Falquet, L.; Wüthrich, D.; Bonfiglio, F.; Loverdo, C.; Egli, A.; Zandomeneghi, G.; Mezzenga, R.; Holst, O.; Meier, B. H.; Hardt, W. D.; Slack, E. (2021) A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants, Nature Microbiology, 6, 830-841, doi:10.1038/s41564-021-00911-1, Institutional Repository


Swiss National Science Foundation

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