NSF Postdoctoral Fellowship in Biology: Microbial Interactions across Trophic Scales and their Contributions to Host Phenotype in a Carnivore Model

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2022, 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. The trillions of microbes that inhabit animals’ bodies, collectively known as microbiomes, are vital to animal ecology and health.

This research explores whether microbes from the environment (soil, water, or dietary items) can contribute to the formation of animal-associated microbiomes in an endangered carnivore: the black-footed ferret. Studying these dynamics in ferrets undergoing reintroduction to natural habitats will also test whether microbial relationships impact the ferret’s health, reproduction, and overall survival in the wild.

In addition to providing valuable ecological data on the role of microbes in animal-environment interactions, this research will have applied value in informing conservation strategies for other endangered animals. The Fellow will be working with the Smithsonian National Zoological Park and Conservation Biology Institute (NZP-SCBI) to conduct this research as well as to disseminate the results to the public and conservation groups; this will bring awareness of the importance of microbiomes in animal ecology and conservation to a broad and diverse audience.

Outreach will include K-12 students in the Washington DC Metropolitan Area who are underrepresented in STEM disciplines.

This research tests the hypothesis that microbes from external sources become ‘souvenir microbes’ by being incorporated into and persisting within host-associated microbiomes and that these microbes ultimately affect host phenotype. Using amplicon and shotgun metagenomic sequencing (with microbial source tracking software) the Fellow will (1) characterize external microbiomes in soil, water, and prey gut and skin consortia; (2) quantify the contributions of these communities to the composition and function of ferret gut microbiomes (thereby identifying souvenir microbes); and (3) use experimental approaches (including fecal microbiota transplants) to test whether souvenir microbes persist in ferret microbiomes and influence phenotypes (e.g., immune markers, digestive function, and pathogen load).

The research focuses on three black-footed ferret populations (captive, semi-wild, and wild) to assess how souvenir microbes are influenced by different environmental conditions among populations and over time. The Fellow will be jointly mentored at NZP-SCBI’s Center for Conservation Genomics and Department of Nutrition Science, providing an interdisciplinary training approach that will expand the Fellow’s knowledge, provide novel skills that integrate microbial ecology and animal physiology, and promote science communication and outreach.

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.