A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes are controlled by the host animal, and to identify characteristics of the host-rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes therefore present primary targets for rumen manipulation towards sustainable and environmentally friendly agriculture.