Abstract
With the universal adoption of genomic selection as a breeding standard, livestock farming is about to enter a new chapter in which deep phenotyping and multi-omics technologies will enhance the use of molecular data in the selection process. Microbiome composition represents a promising tool in this arena, serving simultaneously as a benchmark of environmental challenge, a predictor of animal physiological status, and a direct target for host selection. Our group has been researching the application of the gut microbiome in swine production, with a particular focus on growth and feed efficiency. We investigated how the microbiome is shaped in different production systems by comparing the microbiome composition of growing/finishing pigs raised in bio-secure nucleus farms and commercial facilities. Results suggested a strong impact of gut microbiome composition on pork production efficiency and a consistent effect of several microbial features across different systems. We found that microbial features associated with animal growth are heritable and identified host genomic markers contributing to their relative abundance. We have found that the microbiota composition is different across breeds but stable within breeds (Duroc, Large White, Landrace). Taxa differently represented among the breeds are also associated with feed efficiency and behavior. We estimated the ‘microbiability’ of meat and carcass quality traits. We found that the gut microbiome composition leaves an identifiable ‘footprint’ on the animal tissue deposition. Following these findings, we elucidated the complex relationship between genomic and microbial variation using structural equation modeling to test a causal path between the host genotype, the gut microbiome composition, and fat deposition. We identified direct and mediated (through microbiome) genomic variants affecting host trait expression, highlighting the potential for the ‘second genome’ to contribute to the recovery of genetic variance.