Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

Somasundhari Shanmuganandam; Yiheng Hu; Tanja Strive; Benjamin Schwessinger; Robyn N Hall

doi:10.7717/peerj.9564

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

PeerJ. 2020 Aug 18:8:e9564. doi: 10.7717/peerj.9564. eCollection 2020.

Authors

Somasundhari Shanmuganandam^{1

2}, Yiheng Hu¹, Tanja Strive^{2

3}, Benjamin Schwessinger¹, Robyn N Hall^{2

3}

Affiliations

¹ Research School of Biology, Australian National University, Acton, ACT, Australia.
² Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.
³ Centre for Invasive Species Solutions, Bruce, ACT, Australia.

Abstract

Background: European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors.

Methods: We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms.

Results: We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.

Keywords: 16S rRNA; Illumina; Invasive species; Lagomorphs; Microbiome; Nanopore.

Grants and funding

Funding was provided by a Centre for Biodiversity Analysis ‘Ignition’ Grant, a collaborative initiative of the Australian National University, CSIRO and the University of Canberra. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.