Postdoctoral Fellowship: PRFB: Leveraging metagenomics, metatranscriptomics, and gnotobiotic models to facilitate protective microbiomes sourced from natural communities

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2024, 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. Deadly fungal skin infections are causing worldwide amphibian declines.

There are currently no treatments for these infections when they occur in natural settings. However, some amphibian skin microbes limit growth of fungal pathogens. This research will explore the mechanisms that skin microbes use to limit fungal growth and will pilot the use of skin probiotics for amphibians at risk of fungal disease.

This project will result in new resources and tools to combat amphibian declines. Also, the fellow will develop a fun and educational booklet about frog skin that she will use to teach all ages about this research and frog health.

Inoculating amphibians and their habitats with antifungal skin microbes is a promising avenue for prevention and treatment of diseases caused by pathogenic chytrid fungi. This project will address gaps in knowledge about the functional response of natural skin microbiomes to chytrid fungi and test methods of “antifungal probiotic” application in a captive setting.

Skin microbiomes will be sampled from Eastern newts (Notophthalmus viridescens), two-lined salamanders (Eurycea bislineata), and Eastern spadefoot toads (Scaphiopus holbrookii) in Massachusetts and then cultured in vitro to test for inhibition of the chytrid fungal pathogens Batrachochytrium dendrobatidis (“Bd”) and Batrachochytrium salamandrivorans (“Bsal”). Microbial community structure will be characterized by 16S rRNA (for bacteria) and ITS (for fungi) metabarcoding before and after chytrid exposure to understand the community compositional responses to pathogen exposure.

The fellow will then use metatranscriptomics and metabolomics to define the functional response of microbiomes that inhibit Bd and Bsal growth. Finally, the fellow will pilot the use of antifungal skin microbiomes as antifungal probiotics on gnotobiotic African clawed frogs. The depauperate skin microbial community of these animals will provide a favorable environment for probiotics to establish, persist, and subsequently protect the host from chytrid fungi.

The fellow will disseminate this work through academic research presentations as well as at local community educational events.

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.