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

The microbial communities of seven organs in the digestive tract of the wild rabbit were studied using next generation sequencing. The sequences were compared with sequences derived from fresh faeces collected from domesticated rabbits and guinea pigs. This is the first report of sequences from throughout the rabbit’s digestive tract, and also from guinea pigs. Significant differences were detected between samples from rabbit and guinea pig faeces, suggesting that there is not a microbial community common to caecotrophs. This work re-iterates the high levels of Firmicutes and unclassified species present in the rabbit gut, and also the lack of Fibrobacteres. However it is the first report of high levels of Bacteroidetes, which were previously considered to be a minority group in the rabbit, suggesting that this phylum may indeed have a role to play in digestion in the rabbit gut.