Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans)

The microbiome is significant for conservation biology and should be considered in threatened species management programs. Commensal microbes contribute important functions for host health, while pathogenic microbes can negatively impact the host, leading to morbidity, mortality, and population declines. Shotgun metagenomics, involving the agnostic sequencing of all DNA within a sample, has utility for simultaneous microbial community profiling and pathogen detection. Herein, we used shotgun metagenomics to profile the faecal bacteriome and mycobiome of the southern greater glider (Petauroides volans), an endangered Australian marsupial, and identify putative pathogens that could represent threats to population health. We analysed faecal samples collected from wild southern greater gliders (n = 48) across southeastern New South Wales, Australia. Geographic location had significant effects on both bacterial and fungal community composition. The bacteriome was dominated by Firmicutes, Proteobacteria and Bacteroidetes, with 58 core bacterial species shared among all locations. The mycobiome was dominated by the Ascomycetes, with 261 core fungal species shared among all locations. Geographic location was associated with significant differences in bacterial and fungal microbiota abundance but not host sex or weight. We identified 18 bacterial pathogens and 41 fungal pathogens of veterinary interest, ranging from low prevalence to ubiquitous. Bacteroides fragilis was associated with shifts in the Firmicutes:Bacteroidetes ratio, and therefore, potential dysbiosis. Geographic location is a key determinant of faecal microbial community structure and abundance in southern greater gliders. Core communities of faecal bacteria and fungi are conserved within and among populations. Southern greater gliders carry genetic material from a variety of putative bacterial and fungal pathogens. These microbes may present threats to the health of greater gliders, their possum relatives, or other animals in Australian forest ecosystems. Scientists and natural resource managers should consider the holobiont, rather than just the individual, when planning for conservation management actions such as translocation.