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Intramuscular fat content (IMF) is a key meat quality trait determined by a complex host-microbiota co-metabolism. In this study, two rabbit lines divergently selected for IMF (high-IMF (H) and low-IMF (L) lines) were used to perform a metabolomic analysis of their caecal content, with the aim to unveil the genetically-determined microbial metabolism related to IMF. A large, correlated response to selection was found in their caecal metabolome composition. The discriminant multivariate analysis performed showed 99% classification accuracy, while linear multivariate analyses performed within each line showed prediction abilities of approximately 60%. The most relevant pathways differentiating the lines were those related to amino acids (aromatic, branched-chain and gamma-glutamyl), secondary bile acids, and purines. The greater content of secondary bile acids in the L-line was related to greater lipids absorption, while the differences found in purines suggested different fermentation activities, which could be related to greater nitrogen utilization and energy efficiencies in the L-line. The linear analyses showed that lipids metabolism had greater relative importance in IMF deposition in the L-line, while a more complex microbial metabolism was involved in the H-line. The lysophospholipids and gamma-glutamyl amino acids were associated with IMF in both lines; the nucleotide and secondary bile acid metabolisms were mostly associated in the H-line; and the long-chain and branched-chain fatty acids mostly in the L-line. A metabolic signature composed of two secondary bile acids and two proteins metabolites was found with 88% classification …