Scott Mitchell, PhD Student

The effect of microbiome composition on antibiotic resistance gene prevalence and horizontal gene transmission in the equine hindgut

Supervisors: Belinda Chapman (QB), Michelle Bull (QB), Nick Coleman (USyd)

Synopsis: The equine hindgut is a complex ecosystem (Dicks et al. 2014) where the effects of exogenous factors on the microbiome have not yet been fully characterized, but where there is evidence for both a core microbiome (e.g. Dougal et al. 2013) ) and dysbiosis (e.g. Costa et al. 2015) that mirrors concepts established for the human gastrointestinal tract. Like the human gut microbiome (Broaders et al. 2013; Ravi et al. 2015), the rich equine hindgut environment also appears to present ample opportunity for horizontal gene transfer (HGT), including acquisition and accumulation of antibiotic resistance (AR) determinants (Gronvøld et al. 2010). Acquisition of AR is a key area for HGT research, with much focus on the effect of anthropogenic activities (e.g. antibiotic overuse in humans and livestock, antibiotic contamination of grazing sites, etc.) (Davies & Davies, 2010). However, HGT is a much older response to competition and stress within complex microbial ecosystems that may also confer host advantages beyond the obvious AR (Davies & Davies, 2010). The equine hindgut, with its prokaryotic and eukaryotic diversity is a unique environment in which to study the evolutionary and ecological drivers and benefits of HGT. This study will contribute to an improved understanding of the broader problems of AR. The close interactions of horses and humans, including the use of horses in a variety of sporting pursuits, and the use of horse manures and bedding as fertilisers in large scale horticulture industries such as the mushroom industry, provide further reason for the study of AR gene transfer in horses, since these animals may be links in the chain of AR gene transfer in the environment.


Broaders, E., Gahan, C.G.M., Marchesi, J.R. 2013. Mobile genetic elements of the human gastrointestinal tract, potential for spread of antibiotic resistance genes. Gut Microbes, 4(4):271-280.

Costa, M.C, Stämpfli, H.R., Arroyo, L.G. Allen-Vercoe, E., Gomes, R.G., Weese, J.S. 2015. Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs. BMC Veterinary Research, 11:19. doi:10.1186/s12917-015-0335-7.

Davies, J., Davies, D. 2010. Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews, 74(3):417-433.

Dicks, L.M.T., Botha, M., Dicks, E., Botes, M. 2014. The equine gastro-intestinal tract: An overview of the microbiota, disease and treatment. Livestock Science, 160:69-81.

Dougal, K., de la Fuente, G., Harris, P.A., Girdwood, S.E., Pinloche, E., Newbold, C.J. 2013. Identification of a core bacterial community within the large intestine of the horse. PloS ONE, 8(10): e77660. doi:10.1371/journal.pone.0077660.

Gronvøld, A-M.R., Abée-Lund, T.M., Strand, E., Sørum, H., Yannarell, A.C., Mackie, R.I. 2010. Fecal microbiota in the clinical setting: potential effects of penicillin and general anesthesia. Veterinary Microbiology, 145:366-372.

Ravi, A., Avershina, E., Foley, S.L., Ludvigsen, J., Storrø, O., Øbien, T., Johnsen, R., McCartney, A.L., Abée-Lund, L., Rudi, K. 2015. The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Scientific Reports, 5:15317. doi:10.1038/srep15317.