Interactions between microbes are diverse, ranging from cross-feeding to killing with deadly microbial weapons. Our goal is to study these interactions to design strategies to edit the composition of microbiomes.
Microbes must compete for resources such as nutrients and space to survive and thrive. They have evolved diverse mechanisms for competition such as metabolic pathways to access rare nutrients, flagella to swim towards resources, or bacterial weapons used to directly kill competitors. How do these forms of competition tip the balance of success for a given species, and how does this depend on microbiome context. Our goal is to study these interactions in order to design new strategies to edit the composition of the microbiome for our own benefit.
Selected relevant publications:
Bakkeren E, Piskovsky V, Lee MNY, Jahn MT, Foster KR. Strain displacement in microbiomes via ecological competition. 2025 Nat. Microbiol.
We also wrote a Behind the Paper blog post about this work.
Bakkeren E, Piskovsky V, Foster KR. Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering. 2025. Cell Host Microbe.
The Bakkeren Lab 