Comparison of the archaeal community in the fermentative compartment and faeces of the cow and the rabbit

The archaeal community in the fermentative compartment and faeces of the cow and the rabbit were compared by analysis capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. Ruminal and faecal contents were sampled in five cows for three weeks. Hard and soft faeces were collected in 14 rabbits for three consecutive weeks and cæcal contents were sampled in the third week. The archaeal community differed according to the host species (ANOSIM-R = 0.53 and 0.72 respectively for the comparison of the fermentative compartments and faeces; P < 0.001) and to the location within the digestive tract of both species (ANOSIM-R = 0.37, 0.52 respectively for the cow and the rabbit; P < 0.001). In both species, the archaeal community of the digestive tract was stable over weeks and varied very little between individual animals. The structure (NS) and the richness index (9.9 ± 2.7, 10.1 ± 3.1 respectively, NS) of the archaeal community were similar for the cæcal content and the soft faeces which permitted to use the latter as a representative indicator.