Biodiversity indices and Random Forests reveal the potential for striped skunk (Mephitis mephitis) fecal microbial communities to function as a biomarker for oral rabies vaccination

Authors

Matthew W. Hopken, United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Fort Collins, COFollow
Darby Gilfillan, Colorado State University
Amy Gilbert, USDA APHIS Wildlife ServicesFollow
Antoinette J. Piaggio, USDA APHIS Wildlife ServicesFollow
Mikaela Samsel Hilton, USDA APHIS, Ft. Collins
James Pierce, Colorado State University
Bruce Kimball, Monell Chemical Senses Center, Philadelphia, Pennsylvania
Zaid Abdo, Colorado State University

ORCID IDs

Matthew W. Hopken https://orcid.org/0000-0003-3861-6153

Date of this Version

2023

Citation

Hopken MW, Gilfillan D, Gilbert AT, Piaggio AJ, Hilton MS, Pierce J, et al. (2023) Biodiversity indices and Random Forests reveal the potential for striped skunk (Mephitis mephitis) fecal microbial communities to function as a biomarker for oral rabies vaccination. PLoS ONE 18(8): e0285852. https://doi.org/10.1371/journal. pone.0285852

Comments

U.S. government work

Abstract

Wildlife disease surveillance and monitoring poses unique challenges when assessing rates of population vaccination, immunity, or infection prevalence. Non-invasively detected biomarkers can help reduce risk to both animal and field personnel during wildlife disease management activities. In this study, we investigated the utility of fecal microbiome data collected from captive striped skunks (Mephitis mephitis) in predicting rabies virus vaccination and infection status. We sequenced the hypervariable region 4 (V4) of the bacterial 16S gene and estimated alpha and beta diversity across timepoints in three groups of skunks: vaccination then rabies virus infection, sham vaccination then rabies virus infection, and rabies virus infected without vaccination. Alpha diversity did not differ among treatment groups but beta diversity between treatments was statistically significant. The phyla Firmicutes and Proteobacteria were dominant among all samples. Using Random Forests, we identified operational taxonomic units (OTUs) that greatly influenced classification of fecal samples into treatment groups. Each of these OTUs was correlated with fecal volatile organic compounds detected from the samples for companion treatment groups in another study. This research is the first to highlight striped skunk microbiome biodiversity as a vaccination biomarker which pushes the frontier on alternative methods for surveillance and monitoring of vaccination and disease in wildlife populations.