NSF PRFB FY23: Does bacterial endospore formation affect host-microbe codiversification?

Swanson, Mark T, Baton Rouge LA

Investigators

Abstract

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2023, 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. Animals need microbes in their guts to digest food, but it is unclear whether the same microbes live with the same animal species over long time periods. It is also unknown what characteristics allow some microbial lineages to live with the same animal species for a long time. This study will use live microbes and microbial DNA from rodent feces to see if certain microbial lineages stay with the same animal host species for many generations. The project will also determine if this process occurs primarily in microbes that lack structures that help them live outside the gut. Results of this fellowship will enable predictions of which microbes live with the same animal species for long time periods. The fellow will also make an online tutorial for other scientists to learn how to use this method with other animal-microbe systems. This project will test for codiversification of mammals and microbes in two rodent systems using high-throughput culturing and computational approaches. DNA will be extracted from museum fecal samples of Southeast Asian and North American rodent species and sequenced to assemble bacterial metagenome-assembled genomes (MAGs). Bacterial phylogenies inferred from the MAGs will be used to test for congruence with rodent host phylogenies, indicating a long-term association between these organisms. Additionally, bacteria will be cultured and isolated from the feces using a suite of diverse growth media under anaerobic conditions. Bacterial isolates will be assayed for endospore formation, and phylogenetic multilevel modeling will be used to test for an association between endospore formation and codiversification with the host. Identification of codiversifying microorganisms and mechanisms that affect this pattern will provide insight into how vertebrate microbiomes are assembled. The fellow will be trained in culturing, computational, and statistical techniques while extending the use of museum specimens to mechanistic studies of host-microbe ecology. Participation of underrepresented groups in STEM will be broadened through working with the University of Chicago’s SACNAS chapter to recruit 3 undergraduates to form a peer research community that will test their own codiversification hypotheses. 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.