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RoL: FELS: RAISE: Does everyone's microbiome follow the same rules?


Gut microbiomes are diverse microbial communities that play important roles in mammal physiology and health. However, scientists do not yet understand the rules that govern gut microbiome changes (such as how gut microbiomes change over time), or whether these rules are the same or different in different individuals. The goal of this project is to discover if gut microbiome dynamics are "universal" - that is, the same across hosts - or if these microbial changes are host-specific, such that each host's microbiome follows its own rules. Discovering whether each host's microbiome follows its own rules is relevant to human and animal health. If microbiome dynamics are universal, scientists can use these rules to design microbiome therapies that work the same way in different individuals. On the other hand, if these microbes are unique to each individual, then interventions to improve human or animal health must be designed separately for each individual. The work has benefits to broadening participation in STEM education through training in the investigators' labs and an educational outreach project with a public high school in Indiana. In addition, the researchers will make all statistical methods and code available online for use by other microbiome researchers and microbial ecologists.<br/><br/>Scientists are currently unable to test if gut microbiome dynamics are universal because they lack both the data and the statistical methods to analyze the data. This project overcomes these problems in two ways. First, it will develop new statistical theory and methods to jointly model multiple, highly multidimensional data sets such as those for microbiomes. Second, it will leverage an exceptional, longitudinal microbiome dataset, consisting of over 20,000 16S rRNA gene sequencing profiles on gut microbiome composition, generated for more than 500 wild baboons over a 15-year span. To these microbial composition data, this project will add data on the longitudinal, functional genetic dynamics of the gut microbiome via metagenomic sequencing. The baboons have been the subject of continuous, individual-based studies of baboon behavior and ecology for 47 years. As a result, this project has information on all of the covariates necessary to understand gut microbial dynamics, including the baboons' diets, abiotic environments, social interactions, and composition of the microbial communities themselves. The results of this project will be directly applicable to applied research on mammalian gut microbiomes aimed at improving gut microbiome function to improve host health.<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.

Elizabeth Archie; Jack Gilbert, Sayan Mukherjee
University of Notre Dame
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