Predicting Complex Traits from the Rumen Microbiome: Applications for Greenhouse Gas Mitigation

The rumen microbiome (the population of microbes in the rumen) plays a key role in nutrient acquisition for the host animal, as well as being the major source of methane production from grazing ruminants. Despite a reasonable understanding of the basic biology and pathways involved in methanogenesis and bacterial fermentation, convincing links between microbiome variation and host phenotype variation are scant. With the advent of massively parallel sequencing it is now possible to profile large numbers of species from the rumen of production animals by sequencing the rumen metagenome (the DNA extracted from the microbiome). We have generated "metagenome profiles" in two independent experiments (N=32 and N=8x2 crossover) and identifed repeatable changes in the rumen microbiota when cattle were fed methane mitigating diets.  We have also used metagenome profiles to predict natural host phenotype variation in methane production (independent validation populations N=16 and N=13).  Accuracy of phenotype prediction using metagenomic predictions was 0.4, and this increased as the reference population numbers are increased, or more extreme phenotypes were added. Increasing the number of animals available of the reference population is an area of ongoing research, as is the impact of reference database source, breed of host, sex and genotype by metagenome interactions.