In the egg industry, feed cost represents the majority of total production costs and breeding efforts are ongoing to improve feed efficiency of laying hens. The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we analysed the composition of the caecal microbiota of 31 week old hens by 16S metabarcoding sequencing to characterise its composition, interactions with the host and influence on phenotypes of interest. As an animal model, we used hens of the R+ and R- lines divergently selected for high (low feed efficiency) and low (high feed efficiency) residual feed intake values respectively, that were fed either a commercial wheat-soybean diet (CTR) or a low-energy corn-sunflower diet (LE). Our results show a line effect on the microbiota composition with the CTR diet, whereas in the LE diet, the microbiota was primarily affected by the diet change. A line x diet interaction was observed: the high efficient R- line presented a greater microbial richness and a reduced impact of the diet change compared to the low efficient R+ line. Interestingly, common taxonomies and/or predicted functions were highlighted between R+ and CTR diet, and between R- and LE diet, which could suggest that common microbiota mechanisms between feed efficiency and adaptation to nontraditional feedstuffs exist. These results provide insight into the role of the microbiota in laying hen feed efficiency and the impact of diet composition on microbiota.