Study of holobiont resilience following a break in symbiotic transmission in two rabbit lines selected for feed efficiency

This study was carried out on two rabbit lines, each selected for a feed-efficiency criterion (growth on restricted feed for the AlimR line or residual consumption on an ad libitum diet for the ConsR line), introduced into a facility by adoption of newborn kits by SPF (specific-pathogen-free) females. Following this break in symbiotic transmission, fecal samples from females were used to study the microbiota composition of the two lines over seven 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 %, 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 %, p < 0.0001). The effect of generation was also significant for the abundance of Firmicutes and Bacteroidota (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, 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 microbiota composition allowed us to distinguish both the two lines and the generations, in particular the 11th selected generation (animals adopted by SPF females) and the 18th generation.