Microbial community control: from theory to practice

Microbial communities are complex systems of interacting species. Engineering complex systems to reach desired outcomes is notoriously difficult, as proven by failed attempts to manipulate ecosystems. Recent work suggests that microbial communities in the human gut contain so-called driver species that can trigger the shift towards a different community composition when targeted. Theoretical methods are available to identify such driver species and to predict how to manipulate them. However, these methods have not yet been proven to work in practice. The core idea of this project is to test these methods in a proof-of-concept experiment on a community of human gut bacteria grown in vitro. For this, we will first predict in silico how to shift a test community with a low abundance of health-associated species towards a configuration with a higher abundance of these species and then carry out the predicted perturbation in vitro. Triggering a community change in this manner requires a good knowledge of the microbial species and their interactions, but has the potential to be more accurate than broad-range treatments for instance with prebiotics. Thus, this proof-of-concept study is a step towards the personalized modulation of gut microbiota.