NSF Postdoctoral Fellowship in Biology FY 2021: Bacterial spatial organization as a microscale mechanism of ecosystem resilience

Nguyen, Jen, Vancouver

Investigators

Abstract

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Ecosystems — from plant roots to animal guts to oceans — are sustained by their microbial communities: collections of microorganisms that can protect or promote disease, depending on the environmental conditions. These communities routinely experience and endure environmental change. Some environmental changes destabilize communities, leading to pronounced changes in the microbial species composing a community. How these changes persist, even long after normal environmental conditions return, is not yet understood. This project seeks to learn how the spatial organization of single bacterial cells can determine how the bacterial community within the mammalian gut responds to environmental perturbation. By combining sequence-based observation with biophysical insights, the Fellow seeks to provide the first causal mechanism to explain and visualize how some gut ecosystems recover from disturbance while others suffer lasting change. Students recruited from underrepresented groups in STEM disciplines will engage in these activities with the Fellow. This project will investigate how organization of intestinal communities maintains the homeostasis of their host’s gut ecosystem by changing the bacterial species residing in microscopic folds of the gut epithelium (crypts). Both crypt- and whole-gut species composition can be altered after diarrhea, a perturbation that increases the abundance of some bacterial species and causes the extinction of others. Diarrhea also alters mucus and fluid flow in the gut that might enable changes in bacterial spatial organization that favor or destabilize the presence of specific species in the gut. To test this, the Fellow will develop a microfluidic system to track bacterial movement in a structural mimic of the mucus and fluid flow in the gut. The Fellow will generate a spatio-temporal map of bacteria in pre- and post-diarrhea guts to link in situ spatial organization with whole community composition. These multiscale data will unveil bacterial behaviors currently masked by prevailing sequencing techniques. This dataset, and all tools developed to generate it, will be made available through public repositories to promote multiscale research across diverse ecosystems. The training objectives include developing new skills in bioinformatics and histology, enabling the Fellow to complement findings from these methods with existing expertise in microfluidics and bacterial growth. 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.