Microbiomes in animal systems

Relationships of animals with gut bacteria are ancient and impact animal health. Yet, little is known about how these relationships have emerged and are maintained over the course of evolution, and we are far from able to engineer microbiomes in a rational manner to the benefit of human or animal health.

The objectives of WP2 are to:

  • Probe the functions of microbiomes in animal health and disease
  • Analyse and manipulate pathogen–microbiome–host interactions
  • Understand host adaptation of microbes using experimental evolution
  • Develop targeted intervention strategies for pathogen control based on microbiome manipulation

Model systems with microbial communities of reduced complexity are powerful means to probe general principles of animal–microbiome relationships and to test the roles of microbes implicated in promoting human health. WP2 relies on three well-established animal models for microbiome research: the mouse, fruit fly and honeybee.

WP2 studies the mechanisms facilitating pathogen establishment, or promoting their elimination from the host ecosystem. In a later stage, the identification of niche competitors of major human pathogens could enable new intervention strategies, and insights from the bee model may guide biological applications that promote bee health and counter worldwide bee declines.

Work Package Leaders
Prof. Philip Engel
University of Lausanne
Prof. Wolf-Dietrich Hardt
ETH Zurich

Latest publications

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Daniel, B. B. J., Steiger, Y., Sintsova, A., Field, C. M., Nguyen, B. D., Schubert, C., Cherrak, Y., Sunagawa, S., Hardt, W.-D., Vorholt, J. A. (2024).
An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment
Chhun, A., Moriano-Gutierrez, S., Zoppi, F., Cabirol, A., Engel, P., Schaerli, Y. (2024).
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
Sintsova, A., Ruscheweyh, H.-J., Field, C. M., Feer, L., Nguyen, B., Daniel, B., Hardt, W.-D., Vorholt, J. A., Sunagawa, S. (2024).