Microbes commonly live in communities, microbiomes, that can be diverse and variable. We are interested in what drives the success of an incoming species, whether a pathogen or a beneficial microbe.
Microbial communities provide resistance to incoming strains and species. This is important when we think about protecting us against harmful strains and species like pathogens. Decades of research have taught us that. But, what exactly is the reason for this? Many mechanisms for how individual species can contribute to colonization resistance have been proposed, but the context in which these species exist is constantly changing.
Selected relevant publications:
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.
We also wrote a summary in a Conversation article 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 