Species-specific maturation of the gut microbiome and its integration with host lipid metabolism in intensively reared broiler chickens and ducks
This study investigated phase-dependent changes in gut microbiome composition, predicted functional potential, and lipid metabolism in intensively reared poultry spe-cies using 16S rRNA sequencing and lipid profiling. Microbial diversity remained sta-ble across growth phases within each species, whereas clear interspecies differences were observed (p < 0.01). Microbiome maturation involved a shift from early faculta-tive and environmentally associated taxa toward a more stable, host-adapted commu-nity. Consistent with the maturation pattern, distinct phase-specific microbial signa-tures were identified between growth phases. At the functional pathway level, shifts between growth phases were more pronounced in ducks. Gene-level profiles showed phase-specific differentiation in chickens, with starter-associated genes linked to core carbon and nitrogen metabolism and finisher-associated with structural and transport functions. Ducks exhibited a more balanced reorganization, involving carbohydrate, energy, and nitrogen metabolism. Host lipid profiles between adjacent growth phases showed dynamic shifts in ducks (p < 0.05), followed by a similar pattern between the starter and finisher phases (p < 0.05). These species-specific lipid patterns were mir-rored by microbiome-lipid associations, with more coordinated correlations in chick-ens and more heterogeneous patterns in ducks. Overall, these findings demonstrate species-specific organization of gut microbiome maturation and its integration with host lipid metabolism under intensive production conditions.