Spatiotemporal and Host Variations in Faecal Microbiomes of Hairy‐Nosed Wombats ( Lasiorhinus spp.)

ABSTRACT

The gut microbiome can play a critical role in humans and wildlife, assisting with digestion, immunity and detoxification. This community is often adapted to the animal's ecosystem and fluctuates with seasonal shifts in diet. The gut microbiome can also be altered by anthropogenic effects such as invasive species creating increasingly homogenous landscapes. This in turn could reduce the overall diversity of the microbiome, which has been hypothesized to hinder adaptive potential. However, despite its probable importance, many species are still data deficient with regards to their specific gut microbiome. One data deficient species is the critically endangered northern hairy‐nosed wombat ( Lasiorhinus krefftii ). Northern hairy‐nosed wombats have undergone and slowly recovered from an extreme bottleneck over the last century, and the remaining populations live in increasingly homogeneous habitats dominated by invasive buffel grass ( Cenchrus ciliaris ). To fill in this gap we characterised the faecal microbiome of the northern‐hairy‐nosed wombat using 16S rRNA gene amplicon sequencing. To accomplish this, we collected fresh faecal samples from two populations across two seasons to generate a baseline profile of the microbiome as well as examine the effects of seasonality and geography. Additionally, we compared the faecal microbiome of the northern hairy‐nosed wombat to the closest related species, the southern‐hairy‐nosed wombat ( Lasiorhinus latifrons ). From our results we determined that the microbiome of the northern hairy‐nosed wombat changes from winter to spring and corresponding taxonomic shifts may be assisting the wombats with digestion during the dry months. Between the two wombat species we identified core taxa that are consistent with hindgut fermenting herbivores; however, differentially abundant taxa between the two species may indicate adaptations to the specific ecosystems they each inhabit.