Uncovering the hare microbiome

Image: inaturalist.org

Ignition Grant Round 7, July 2017

Two invasive lagomorph species are currently present in Australia, the European rabbit (Oryctolagus cuniculus) and the European brown hare (Lepus europeaus). Hares are not usually considered in wild rabbit control programs, however, the recent detection of Rabbit haemorrhagic disease virus 2 in European brown hares in Australia highlights the need for a better understanding of the role of hares in lagomorph microbial diversity and epidemiology. For example, which microbes are shared between rabbits and hares? What role do hares have in transmission of these microbes to rabbits and spread in the environment? Do hares help or hinder the spread of pathogens in wild rabbits? Do hares in Australia act as a reservoir for zoonotic pathogens, for example the organisms causing tularaemia or brucellosis?

This project aims to investigate the diversity of the hare microbiome using emerging long-read (Nanopore) sequencing technology.


  • Improved understanding into the microbial diversity present in Australian hares, with insights into the role of hares in the epidemiology of lagomorph pathogens, which may help to inform future rabbit and hare biocontrol strategies.
  • Knowledge of the role of hares as a reservoir for zoonotic pathogens.
  • At least one peer-reviewed journal publication in preparation by November 2018.

Project representatives

Project status and outcomes

Somasundhari Shanmuganandam was engaged on this Ignition project as part of her Masters of Biotechnology (Advanced) degree.  Soma submitted her thesis in May 2019, and was subsequently awarded First Class Honours. A paper titled “Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia” has been published.

This Ignition Grant has been extremely valuable in fostering connections between ANU Research School of Biology (RSB) and CSIRO, as well as delivering excellent science that has improved our understanding of the microbial diversity in Australian introduced rabbits and hares and how these species differ. Though these species inhabit the same habitat, their behaviour and dietary preferences clearly influence differences in faecal bacterial diversity. The more diverse and variable gastrointestinal microbiota of rabbits compared to hares could be a contributing factor in their ability to spread very successfully and establish in new environments.

This study also provides additional evidence that the environmental impacts of rabbits are more severe than that of hares, as demonstrated by their less discriminate dietary preferences.

Future studies correlating different bacterial species in lagomorph microbiomes with specific plant species may provide further insights into the environmental impacts of wild rabbits and hares in Australia.

The linkages formed during this Ignition grant have generated additional connections between RSB and CSIRO, that may potentially lead to co-supervision of a PhD student by Dr Schwessinger and Dr Tom Walsh at CSIRO. Although the project is not related to this Ignition grant, the grant was instrumental in generating networks between these institutions and scientists.