Pyrosequencing study of caecal bacterial community of rabbit does and kits from a farm affected by epizootic rabbit enteropathy

Epizootic Rabbit Enteropathy (ERE) is a disease of unknown aetiology that mainly affects post-weaning animals. Caecotrophs from animals in a farm affected by ERE were analysed to identify changes in the microbiological profile of growing rabbits. Does and kits at weaning (28 d) and the same rabbits ten days later (38 d) were used for a comparison using Roche 454 pyrosequencing of hypervariable V3-V5 regions of the 16S rRNA genes. The caecal bacterial community was dominated by the Firmicutes phylum (about 80%), followed by Bacteroidetes (15%), although relative abundances changed according to animal age (among does and kits at 28 and 38 d) and health status (affected or not by ERE). Two dominant families were classified within the Firmicutes phylum: Ruminococcaceae and Lachnospiraceae (50 and 20% of the sequences, respectively). In kits affected by ERE, relative abundance of Ruminococcus and Bacteroides genera decreased and increased, respectively, compared to healthy kits at the same age (28 and 38 d). The principal coordinate analysis plot revealed that kits at 28 d of age cluster together and apart from the does and the healthy 38-d rabbit groups. When only growing rabbits are considered, kits that showed symptoms of ERE clustered separately. Results suggest a different caecal bacterial community of rabbits affected by ERE. These findings highlight the need to identify different stages of the disease.