Microbial communities on and inside of animals play profound roles in biology, affecting the behavior, nutritional status, and resilience of the host. Much of the behavior of microbial communities is driven by interactions between proteins of microbes and the host. These interactions are used by microbes to adhere to, attack, or communicate with other cells in their surroundings. Because microbial communities are tremendously complex, it has proven difficult to determine the set of protein-protein interactions that define and stabilize a community or affect other community members. Understanding the mechanics of those interactions is essential to engineer or manipulate microbial communities, e.g., by encouraging the presence of beneficial microbes or driving out those that are problematic. This project will unravel the rules governing how protein-protein interactions establish and maintain microbial communities using a combination of bioinformatics and biochemical approaches. The project will target the interaction of two well-known probiotic (‘good’) bacteria with models of the human intestine. The developed methods will also be applicable to a wide range of other microbial communities, both those involving mammals (with applications to agriculture and medicine) and those involving non-living surfaces (with applications to food processing and infrastructure maintenance). Other broader impacts include outreach activities at a museum and training of the next generation scientists in microbiome research.
This project will develop a combination of computational and experimental approaches to determine the identities and functional implications of host-microbe protein-protein interactions (PPIs), in the context of synthetic microbial communities grown on epithelial cell cultures and in human organoids. The studies will focus on colonization by the well-known probiotic strains E. coli Nissle and Lactobacillus rhamnosus GG. The use of a highly controllable, reductionist system to study the roles of PPIs in the broader behavior of microbial communities will permit the investigators to develop, test, and benchmark experimental and computational tools to identify important PPIs and examine their functional implications. The project will be anchored by the development of advanced computational pipelines to enable large-scale high-quality prediction of the structure and function of PPI networks. In parallel, for the target organoid-microbe communities, the researchers will make use of recently developed crosslinking mass spectrometry methods to experimentally examine the landscape of PPIs in vivo, and transposon library profiling experiments to identify the microbial genes that contribute substantially to host colonization or microbe-microbe competition. This will be followed by the identification of PPIs in multi-species communities using mouse fecal extracts and/or anaerobes that play an important role in the gut microbiome. The research proposed here will contribute to our knowledge base and technical capabilities both through the enumeration of key trans-kingdom protein-protein interactions driving bacterial host colonization (including identification of the interactions that are functionally important), and through the development and refinement of a computational framework for high throughput prediction of inter-organism protein-protein interactions and their functional importance. The methods developed here will be generalizable to permit rapid enumeration of key host-microbe and microbe-microbe PPIs in complex microbial communities.
This project is funded by the Understanding the Rules of Life: Microbiome Theory and Mechanisms Program, administered as part of NSF's Ten Big Ideas and the Division of Emerging Frontiers in the Directorate for Biological Sciences.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
