Skip to main content

Research Repository

Advanced Search

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing.

Crowley, Edward J.; King, Jonathan M.; Wilkinson, Toby; Worgan, Hilary J.; Huson, Kathryn M.; Rose, Michael T.; McEwan, Neil R.


Edward J. Crowley

Jonathan M. King

Toby Wilkinson

Hilary J. Worgan

Kathryn M. Huson

Michael T. Rose

Neil R. McEwan


This study aimed to determine the microbial composition of faeces from two groups of caecotrophagic animals; rabbits and guinea pigs. In addition the study aimed to determine the community present in the different organs in the rabbit. DNA was extracted from seven of the organs in wild rabbits (n = 5) and from faecal samples from domesticated rabbits (n = 6) and guinea pigs (n = 6). Partial regions of the small ribosomal sub-unit were amplified by PCR and then the sequences present in each sample were determined by next generation sequencing. Differences were detected between samples from rabbit and guinea pig faeces, suggesting that there is not a microbial community common to caecotrophagic animals. Differences were also detected in the different regions of the rabbits' digestive tracts. As with previous work, many of the organisms detected were Firmicutes or unclassified species and there was a lack of Fibrobacteres, but for the first time we observed a high number of Bacteroidetes in rabbit samples. This work re-iterates high levels of Firmicutes and unclassified species are present in the rabbit gut, together with low number of Fibrobacteres. This suggests that in the rabbit gut, organisms other than the Fibrobacteres must be responsible for fibre digestion. However observation of high numbers of Bacteroidetes suggests that this phylum may indeed have a role to play in digestion in the rabbit gut.


CROWLEY, E.J., KING, J.M., WILKINSON, T., WORGAN, H.J., HUSON, K.M., ROSE, M.T. and MCEWAN, N.R. 2017. Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing. PLOS one [online], 12(2), e0165779. Available from:

Journal Article Type Article
Acceptance Date Oct 18, 2016
Online Publication Date Feb 9, 2017
Publication Date Feb 9, 2017
Deposit Date Feb 15, 2017
Publicly Available Date Feb 15, 2017
Journal PLoS ONE
Print ISSN 1932-6203
Electronic ISSN 1932-6203
Publisher Public Library of Science
Peer Reviewed Peer Reviewed
Volume 12
Issue 2
Article Number e0165779
Keywords Rabbits; Guinea pigs; Faeces; Microbial composition
Public URL


Downloadable Citations