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Collaborative Research: Chemical and genetic mechanisms driving microbial interactions in a model microbiome


Microbes live in complex communities throughout the environment, but it remains unclear how specific microbes become members or maintain their role in these communities. This project will explore how bacteria and fungi use chemicals they produce to interact with one another and their environment. The bacteria and fungi in this project are all derived from the remarkably stable communities of microbes that inhabit cheese rinds that are consumed around the world. Currently, there is a poor understanding of how the chemicals bacteria and fungi produce on fermented foods stabilize or destabilize the roles of the members of their communities. In the short term, this project will identify key chemicals and processes that bacteria and fungi use to interact with one another on cheese rinds. In the long term, studying these microbes will give insight into the key processes bacteria and fungi use to operate within a community. The key processes used in this relatively simple system will be extended to other complex systems to explore how microbes use their own chemistry to affect other members in their communities. <br/><br/>Multispecies microbial communities (microbiomes) are important drivers of global ecosystems, human and animal health, and food production, but our understanding of the molecular mechanisms that drive the formation of these communities remains a significant gap in knowledge. A contributing factor to this gap is the fact that few biological systems are available where in situ microbial communities can be deconstructed and experimentally recreated in the lab. Because of the challenges in manipulating microbiomes, very little is known about the genetic and chemical basis of species interactions. Bacteria and fungi are known to produce and dedicate a large part of their genetic material to the production of specialized metabolites. However, many of the pathways remain cryptic or have yet to be discovered because they have not been implicated in bioactivity screening. In this project innovative mass spectrometry techniques will be combined with microbial genetic and genomic techniques and a novel model community system to determine the molecular mechanisms of species interactions and how these interactions shape the formation and stability of microbial communities. This research will uncover conserved genetic pathways that underlie microbial interactions and their accompanying metabolites.<br/><br/>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.

Rachel Dutton
University of California - San Diego
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