This study was carried out on two lines, each selected for a feed efficiency criterion (growth on restricted feed for the AlimR line or residual consumption on ad libitum diet for the ConsR line), introduced in a building by adoption of newborn rabbits by SPF females. Following this break in symbiotic transmission, females feces samples was used to study the composition of the microbiota of the two lines over 7 generations (17 females per line and per generation). The proportion of Firmicutes was significantly higher in the AlimR line than in the ConsR line (82.22% vs 78.21% respectively, p<0.0001). Conversely, the proportion of Bacteroidota was significantly higher in the ConsR line than in the AlimR line (20.38% vs 16.50% respectively, p < 0.0001). The effect of generation was also significant for Firmicutes and Bacteroidota abundance (p=0.0009 and p < 0.0001, respectively). The Shannon diversity index was significantly higher in the AlimR line than in the ConsR line, (5.23 vs. 5.14 respectively, p=0.02). The effect of generation was also significant for the Shannon index (p=0.003). Finally, a discriminant principal component analysis of the composition of the microbiota allowed to distinguish between the two lines and between generations, in particular the 11th generation of selection corresponding to animals adopted by EOPS females and the 18th generation.