Genome-wide association study of the cecal microbiota revealing novel genetic insights into lipid deposition

Abstract Background Lipid deposition is a critical indicator of the economic and nutritional value of animal products. Among various regulatory factors, the cecal microbiota has been recognized as an important effect influencing lipid deposition capacity in tissues such as skin fat and breast muscle in ducks. Elucidating how the host regulates the abundance of the cecal microbiota is crucial for a deeper understanding of the mechanisms driving variation in lipid deposition. Results To elucidate the associations between the cecal microbiota and host genetics, we perform metagenomic sequencing on cecal content samples obtained from two duck populations: a Pekin × Liancheng white duck gradient consanguinity segregating population and a Pekin × Call duck F 2 population. The level lipid deposition in the host and the community structure of cecal microbiota exhibits gradual variation along with differences in genetic structure. Regression analyses reveal significant associations between 921 microbial species and two key lipid deposition traits, skin fat ratio and intramuscular fat content. Genome-wide association analysis identifies 18 candidate genes implicated in modulating microbial relative abundance. 15 of these genes are functionally enriched in membrane-related signal transduction processes. We pinpoint two microbial species— Acinetobacter baumannii and Akkermansia muciniphila —that are associated with host lipid deposition and genetically linked to two genes LIMS2 and ST3GAL1 respectively. Conclusion Our findings reveal the significant role of membrane signal transduction-related genes in regulating the relative abundance of cecal microbiota linked to lipid deposition, offering deeper insight into how the host genetically modulates the cecal microbiota and its potential impact on lipid metabolism.