Understanding and engineering complex microbial communities

Our bodies all contain communities of microbes that protect us from harmful bacteria. However, taking antibiotics or having an upset stomach can remove this protection, leaving us vulnerable to infection. Moreover, many bacteria are now resistant to antibiotics making infections difficult to treat. Rather than relying solely on antibiotics, we need to learn to engineer our protective microbes to prevent, and perhaps even cure, disease. The challenge is that we carry many different species of microbes, which evolve and affect one another in complex ways.

We will develop theoretical tools that cut through the complexity of microbial communities. We will apply our theory and experimentally test our ability to design gut communities that prevent infection or are able to bounce back from antibiotic treatment. We will also ask whether probiotic communities can flexibly evolve to provide protection in response to disease bacteria, something that antibiotics cannot do.

Our findings may help find more effective ways to fight infection which avoids over-reliance on antimicrobials.