Molecular analysis of the bacterial community in digestive tract of rabbit

This work aimed to study the stability over time of the bacterial community in caecum and faeces of the rabbit (diversity index and structure) without experimental disturbance and to evaluate its relationships with environmental parameters. Soft and hard faeces of 14 rabbits were sampled for 5 weeks while caecal content was sampled on the 3rd week (by surgery) and the 5th week (at slaughter). Bacterial communities were assessed by studying CE-SSCP profiles of 16S rRNA genes fragments. Redox potential, pH, NH3-N concentration and volatile fatty acid concentrations were measured in the caecum. Data showed that bacterial communities of soft and hard faeces barely differed from that of the caecum (ANOSIM-R<0.25; p<0.05). Without disturbance, the bacterial communities of faeces were stable over time (ANOSIM-R<0.25; p<0.001). However, the bacterial communities of caecum and faeces were affected by the surgery (ANOSIM-R=0.22-0.33; p<0.001). The caecal content was an acidic (pH=6.03+/-0.33) and an anaerobic environment (redox potential=-160+/-43 mV). Only the redox potential was correlated with the diversity index of the bacterial community of the caecum (R(2)=0.35; p<0.05) and no environmental parameters were correlated to its structure.