Journal of Animal Science and Veterinary Medicine

There is an increasing need to boost livestock efficiency and sustainability as well as the ability to cope while meeting global protein demands. Genomic selection has made significant genetic gains but has been able to explain only a portion of the phenotype in complex characters such as feed efficiency, growth rates, methane emissions, and resistance to diseases. Recent studies have shown that the microbiome plays a crucial role in modulating the host metabolism and other processes including immune regulation. The microbiome is involved in nutrient breakdown, the production of short-chain fatty acids, vitamin formation, and immune regulation, making the host use it like an "organ." This resulted in the introduction of the holobiont idea, which regards the host organism and its associated microbiota as a single biological entity (hologenome). The selection strategy was thereby transformed from one focused solely on the host to a more holistic approach centered around the entire system. Incorporating information from the microbiome into host genomics via multi-omics, metagenomics, and artificial intelligence improves the precision of predicting complex traits and discovers new biomarkers for productivity and efficiency in the environment. However, obstacles persist, including high levels of microbiome diversity, non-standardization, insufficient causal knowledge, and technical difficulties. Nevertheless, combining the study of host genomics and gut microbiomes presents an innovative avenue for improving livestock.