Host Genetics, the Rumen Microbiome, and Holobiont Effects Jointly Contribute to Feed Efficiency in Beef Cattle

Improving efficiency of feed utilization in beef cattle increases profitability and sustainability of beef cattle operations. Many production-relevant traits are governed by complex interactions between physiological mechanisms and biological processes. While some feed efficiency measurements are moderately heritable, little genetic progress has been made towards improving animal energy utilization due to available technology and costliness related to measuring feed efficiency traits. Primary fermentation of feedstuffs occurs in the rumen, which is first compartment of the four-chambered gastrointestinal stomach. The rumen contains a diverse composition of bacteria, archaea, protozoa, fungi, and viruses that constitute the rumen microbiome and serve multifaceted roles in nutrient breakdown and utilization. Ruminal microorganisms contribute approximately 70% of required energy to the ruminant host via metabolic byproducts and have now been well-accepted to be under low-to-moderate host genetic control. The rumen microbiome and metabolome has been associated with many production-relevant traits, such as average daily gain, dry matter intake, and residual feed intake. Therefore, there is a complex relationship among host genetics, the rumen microbiome, and metabolome that drives variation in complex, polygenic traits. Including the effects of the microbiome and metabolome should improve phenotypic predictions, particularly for complex traits. Improving accuracy of phenotypic predictions will aid current strategies for genomic selection. These findings aim to identify the underlying biological mechanisms driving phenotypic variation in complex traits to improve sustainability of beef cattle operations.