Leveraging the microbiome of the rumen
Genomic enhanced EPDs allow us to make even more accurate predictions.
By Andrew D. Lakamp and Matthew L. Spangler
Humans have been attempting to predict future animal performance for a long time. Initially, and unfortunately still, this was based on visual appraisal of an animal. Science has advanced such that expected progeny differences (EPDs) enable science-based predictions of how an animal’s offspring will perform, on average, compared to the offspring of other prospective parents. More recently, genomic enhanced EPDs (GE-EPDs) allow us to leverage genomic markers to make even more accurate predictions. However, the cattle themselves aren’t the only organism with DNA that can be useful in predicting an animal’s phenotype.
Anyone who has taken an animal nutrition class knows the rumen of a cow is full of microbial organisms. It’s these microbes which digest the feedstuffs inedible to humans and turn it into nutritious beef. Collectively, these organisms are called the rumen microbiome.
We know from years of research that the rumen microbiome is associated with several economically important traits like feed intake, average daily gain, milk production and even health outcomes. Of course, being living things, all these microorganisms have DNA of their own. The same way all of an animal’s DNA is its genome, all of the DNA of the rumen microbiome is known as the rumen metagenome. Interest in the rumen metagenome is growing because altering the rumen metagenome has the potential to improve animal performance.
By coupling knowledge of the animal’s genome and information from the rumen metagenome, we can make more accurate predictions about how an animal is going to perform. In a recent study completed at the University of Nebraska-Lincoln (UNL) we collected genomic and metagenomic information, along with data on feed intake and average daily gain, from approximately 700 animals housed at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. The heifers were fed one of two forage-based diets and the steers were fed one of two concentrate-based diets. The goal of this project was to quantify the accuracy of predicting either average daily gain or average daily feed intake using genomic, metagenomic, or the combination of the two.
Similar to the way genomic markers are used to determine the relationship among animals, metagenomic “relationships” were formed to quantify the similarity among animals based on their rumen metagenome. The best predictions of animal performance were those which use both genomic and metagenomic information.
In short, if the goal is to predict the performance of an animal, knowing its genomics is helpful, but knowing its genomics and metagenomics is even better.
Lakamp is a post-doctoral research associate and Spangler is a professor, both in the Department of Animal Science at University of Nebraska-Lincoln.