Deciphering multi-scale interaction networks driving microbial community dynamics and functions

Envision a world where the trillions of bacteria inhabiting our bodies become the frontier of personalized medicine, having the ability to shape our health, performance and even influence behavior. When in harmony, this teeming world of bacteria offers numerous health benefits. However, a shift in this delicate balance can lead to substantial negative health effects due to contrasting evolutionary objectives. Precision engineering of the gut microbiome that can add, remove or modify functional capabilities of the system holds tremendous therapeutic potential for personalized and precision medicine. However, the complexity of this system that encompasses hundreds of species, unknown interaction networks and mechanisms driving these interactions have precluded our ability to effectively manipulate this system to our benefit. A detailed and quantitative understanding of this system would enable the discovery of molecular and ecological design principles of the system as well as novel control knobs for steering the gut microbiome to desired states. By integrating bottom-up construction of microbial communities with computational models, we reveal the networks of interactions driving microbial community assembly, health-relevant metabolite production and human gut pathogens. Our work provides a foundation for exploring and exploiting the interaction networks driving microbial communities for a wide range of potential applications in precision medicine, agriculture and bioprocessing.