Zachary Beller

Program: Computational and Systems Biology

Current advisor: Jeffrey I. Gordon, MD

Undergraduate university: Washington University

Research summary
The gut microbiota has been widely recognized as an important determinant of human health. However, our understanding of gut ecology and our ability to affect meaningful, long-lasting change on gut communities is lacking. I am interested in developing fiber-based prebiotics in order to affect targeted changes in microbiota state. An unavoidable challenge in this effort are the dynamics of gut bacterial interactions, which govern the change and community states possible. Using CRISPR-based knockdown of targeted gut bacteria in a model human gut microbiota, I will characterize the mechanisms and kinetics of these interactions to further our understanding. By performing combinatorial ‘leave-out’ experiments I will further resolve the web of interactions between gut bacteria. Finally, I will assay carbohydrate degradation using a newly developed bead-based technology to delineate the nutrient utilization patterns found within these community variants and knockdown states. Altogether these efforts will be used to inform the creation of more precise, efficacious prebiotic therapies.

Graduate publications
Wesener DA, Beller ZW, Peters SL, Rajabi A, Dimartino G, Giannone RJ, Hettich RL, Gordon JI. 2021 Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo. Elife, 10():e64478.

Patnode ML, Beller ZW, Han ND, Cheng J, Peters SL, Terrapon N, Henrissat B, Le Gall S, Saulnier L, Hayashi DK, Meynier A, Vinoy S, Giannone RJ, Hettich RL, Gordon JI. 2019 Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans. Cell, 179(1):59-73.e13.

Wolf AR, Wesener DA, Cheng J, Houston-Ludlam AN, Beller ZW, Hibberd MC, Giannone RJ, Peters SL, Hettich RL, Leyn SA, Rodionov DA, Osterman AL, Gordon JI. 2019 Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium. Cell Host Microbe, 26(4):463-477.e8.