University of California, San Francisco

This multi-institutional team led by Michael Fischbach at UCSF has observed that antibiotic production is widespread among human gut bacteria. They propose to identify antibiotics produced by gut bacteria and characterize their role in modulating the composition of the gut microbiome. Antibiotic-mediated interactions could explain two intriguing observations from early data from the Human Microbiome Project: that the composition of the gut microbial community differs dramatically between people, and that even within individuals, the gut community consists of a stable ‘core community’ and a dynamic ‘auxiliary community’. This project will focus on 1) Functionally characterizing antibiotic production by gut microbes, 2) Using a new mass spec technology to create a molecular map of the gut community, and 3) Integrating these data into a quantitative network model of interspecies interactions in the gut community. These results may enable the team to begin modeling the dynamics of synthetic gut communities, and they will form a basis for studying how changes in host genetics (e.g., polymorphisms in innate immunity genes) and the environment (e.g., changes in diet) perturb the composition of the gut community.