Using Rumen Microbiome Profiles to Predict Enteric Methane Production

The rumen, the first chamber of the cow stomach, contains large numbers of symbiotic micro-organisms (the rumen microbiome) that could potentially influence the host’s phenotype.  There have been numerous exploratory studies of symbiotic micro-organisms in many species including cattle, but techniques for utilising this information to predict phenotypes are scant, particularly outside of human research.  Here, we describe an efficient methodology for predicting complex traits from quantitative microbiome profiles, that are produced using massively parallel sequencing, that is, the sequencing of millions of DNA fragments simultaneously.  This method was applied to over sixty rumen microbiome profiles to predict enteric methane production with an accuracy of r=0.404.  Methane, a potent greenhouse gas (approximately 21 times stronger than carbon dioxide), is produced as a result of digestion in the rumen.  Although our data set is small, so results must be regarded as preliminary, the ability to predict enteric methane production from cattle using this method would allow rumen microbiome profiles to be used as low cost proxies for methane emissions in individual cattle. Until now phenotyping such large numbers of animals was not feasible as direct measures are low throughput, requiring significant labour and conditioning of the animals. This work is an important step towards lowering the greenhouse gas footprint from cattle.