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Rules of Resilience: Modeling impacts of host-microbe interactions during perturbations

The gut microbiota has emerged as an integral component of organism well-being, influencing the most basic of functions such as metabolism, to more specialized systems e.g., immunological function. While work has been done to understand the interactions of host, microbiota, and environment in one dimension, few have attempted to integrate all three of these aspects. This gap is largely due to a lack of computational tools that have the capability to integrate and build models from the large multi-omic datasets that arise from each component. Viewing the combined data as high dimensional tensors allows us to use techniques such as factor analysis and latent feature representations to find multi-way correlations across the three components. The increased dimensionality also necessitates the need for being able to perform such analyses in a scalable fashion using modern supercomputers, (e.g., NSF-funded Frontera). We propose a new collaboration among the research teams of microbiome experimentalists and computer scientists to build a highly inter-disciplinary group with the goal of advancing knowledge (U goal 1) of how host microbe interactions respond and recover from perturbations. This work will also provide deeply engaged learning opportunities for students (U goal 2). We will collect preliminary microbiome data, and begin to design new computing approaches. This effort will be translated into a proposal to the NSF solicitation “URoL: Microbiome Theory and Mechanisms.


College of Science
School of Biological Sciences
Project Owner

College of Engineering
School of Computing

June Round
School of Medicine

William Stephens
School of Medicine

Hari Sundar
College of Engineering
School of Computing

Project Info

Funded Project Amount

microbiome, supercomputing, big data, environmental perturbations, metagenomics, 16S, diet, germ-free mice

Project Status
Funded 2020
Last Updated: 1/23/20